PyMOL Wiki - User contributions [en]

PowerMate Dial OS X

2013-09-04T00:11:05Z

Wgscott: fixed link

[http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Using_powermate_dials_with_PyMOL Link to W. G. Scott's web page] (off site). Use of the script below is explained in that link. Briefly, the PowerMate driver must be installed and configured as explained in detail in that link before this script will work.

Pymol lets you define some keys (the function keys, ALT-[A-Z,0-9], left, right, up, down, etc) as pythonic pymol commands, like those below. I chose 2 degree increments for rotation and 0.5 for translations because these values give a visually smooth response, but change this to suit your own taste. Type

help set_key

in pymol for more information.

The code below dynamically assigns functions to the four programmed keys by running python scripts in pymol to reset the key bindings. Clicking the Powermate dial to activate the toggle function (assigned to F5) allows you to toggle cyclically through dial functionality options, thus giving you three sets of rotations and translations.

In other words, turn the dial right or left to rotate in the plus y or minus y directions. Push down while turning right or left to get the plus and minus y translations. Click the dial (press down and release rapidly) to toggle to an analogous dial set for z, and then click again for x, and then again for y.

<source lang="python">
from pymol import cmd

# Define aliases for mapping in [x,y,z] rotations and translations into a single Powermate
# dial. Toggling between the three is possible if you then assign these to special keys.

# Functions for x,y,z rotations and translations using Powermate dial
# Program F1 and F2 for Rotate Right and Rotate Left
# Program F3 and F4 for Click & Rotate Right and Click & Rotate Left
# Program F5 for Click (to toggle between dialsets)

# dialset = 2

def dialx(): \
global dialset \
dialset = 1 \
cmd.set_key ('F1', cmd.turn,('x',-2.0)) \
cmd.set_key ('F2', cmd.turn,('x',2.0)) \
cmd.set_key ('F3', cmd.move,('x',-0.5)) \
cmd.set_key ('F4', cmd.move,('x',0.5)) \
print "dialset ", dialset, " [ X ]\n" \
return dialset

def dialy(): \
global dialset \
dialset = 2 \
cmd.set_key ('F1', cmd.turn,('y',-2.0)) \
cmd.set_key ('F2', cmd.turn,('y',2.0)) \
cmd.set_key ('F3', cmd.move,('y',-0.5)) \
cmd.set_key ('F4', cmd.move,('y',0.5)) \
print "dialset ", dialset, " [ Y ]\n" \
return dialset

def dialz(): \
global dialset \
dialset = 3 \
cmd.set_key ('F1', cmd.turn,('z',-2.0)) \
cmd.set_key ('F2', cmd.turn,('z',2.0)) \
cmd.set_key ('F3', cmd.move,('z',-0.5)) \
cmd.set_key ('F4', cmd.move,('z',0.5)) \
print "dialset ", dialset, " [ Z ]\n" \
return dialset

def toggle_dial(): \
if dialset == 1 : \
print "Changing to y" \
dialy() \
elif dialset == 2 : \
print "Changing to z" \
dialz() \
elif dialset == 3 : \
print "Changing to x" \
dialx() \
else: print "Dial assignment isn't working"

cmd.set_key ('F5', toggle_dial)

# Start default dial state for rotate y (arbitrary choice)

dialy()

</source>
[[Category:Script_Library|Powermate Dial OS X]]
[[Category:UI_Scripts]]

File:Ribbon hh1.png

2008-09-13T03:37:11Z

Wgscott:

Ribbon pymol image of full-length hammerhead ribozyme with Mn2+ bound, April 2008 Chemistry and Biology cover.

'''Reference:''' Monika Martick, Tai-Sung Lee, Darrin M. York and William G. Scott, Solvent Structure and Hammerhead Ribozyme Catalysis, ''[http://sage.ucsc.edu/scottlab/reprints/2008_Scott_ChemBio.pdf Chemistry and Biology]'' '''15''': 332-342 (2008).

File:Ribbon hh1.png

2008-09-13T03:36:51Z

Wgscott: Added link to reference.

Ribbon pymol image of full-length hammerhead ribozyme with Mn2+ bound, April 2008 Chemistry and Biology cover.

Reference: Monika Martick, Tai-Sung Lee, Darrin M. York and William G. Scott, Solvent Structure and Hammerhead Ribozyme Catalysis, ''[http://sage.ucsc.edu/scottlab/reprints/2008_Scott_ChemBio.pdf Chemistry and Biology]'' '''15''': 332-342 (2008).

Covers

2008-09-13T03:32:33Z

Wgscott: Added our RNA cover

= PyMOL-created Journal Covers =
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.

Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.

<gallery perrow="5">
Image:080602cnen.pdf.jpg
Image:071213nature.pdf.jpg
Image:071123science.pdf.jpg
Image:071009science.pdf.jpg
Image:070920nature.pdf.jpg
Image:070816nature.pdf.jpg
Image:070405nature.pdf.jpg
Image:070219cnen.pdf.jpg
Image:070215nature.pdf.jpg
Image:060904cnen.pdf.jpg
Image:060817nature.pdf.jpg
Image:060522cnen.pdf.jpg
Image:051020nature.pdf.jpg
Image:050908nature.pdf.jpg
Image:050722science.pdf.jpg
Image:050609nature.pdf.jpg
Image:050429science.pdf.jpg
Image:040910science.pdf.jpg
Image:040123science.pdf.jpg
Image:Ribbon_hh1.png
</gallery>

File:Ribbon hh1.png

2008-09-13T03:31:08Z

Wgscott: Ribbon pymol image of full-length hammerhead ribozyme with Mn2+ bound, April 2008 Chemistry and Biology cover.

Ribbon pymol image of full-length hammerhead ribozyme with Mn2+ bound, April 2008 Chemistry and Biology cover.

PowerMate Dial OS X

2008-04-16T01:21:40Z

Wgscott: fixed busted link

[http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Using_powermate_dials_with_PyMOL Link to W. G. Scott's web page] (off site). Use of the script below is explained in that link. Briefly, the PowerMate driver must be installed and configured as explained in detail in that link before this script will work.

Pymol lets you define some keys (the function keys, ALT-[A-Z,0-9], left, right, up, down, etc) as pythonic pymol commands, like those below. I chose 2 degree increments for rotation and 0.5 for translations because these values give a visually smooth response, but change this to suit your own taste. Type

help set_key

in pymol for more information.

The code below dynamically assigns functions to the four programmed keys by running python scripts in pymol to reset the key bindings. Clicking the Powermate dial to activate the toggle function (assigned to F5) allows you to toggle cyclically through dial functionality options, thus giving you three sets of rotations and translations.

In other words, turn the dial right or left to rotate in the plus y or minus y directions. Push down while turning right or left to get the plus and minus y translations. Click the dial (press down and release rapidly) to toggle to an analogous dial set for z, and then click again for x, and then again for y.

<source lang="python">
from pymol import cmd

# Define aliases for mapping in [x,y,z] rotations and translations into a single Powermate
# dial. Toggling between the three is possible if you then assign these to special keys.

# Functions for x,y,z rotations and translations using Powermate dial
# Program F1 and F2 for Rotate Right and Rotate Left
# Program F3 and F4 for Click & Rotate Right and Click & Rotate Left
# Program F5 for Click (to toggle between dialsets)

# dialset = 2

def dialx(): \
global dialset \
dialset = 1 \
cmd.set_key ('F1', cmd.turn,('x',-2.0)) \
cmd.set_key ('F2', cmd.turn,('x',2.0)) \
cmd.set_key ('F3', cmd.move,('x',-0.5)) \
cmd.set_key ('F4', cmd.move,('x',0.5)) \
print "dialset ", dialset, " [ X ]\n" \
return dialset

def dialy(): \
global dialset \
dialset = 2 \
cmd.set_key ('F1', cmd.turn,('y',-2.0)) \
cmd.set_key ('F2', cmd.turn,('y',2.0)) \
cmd.set_key ('F3', cmd.move,('y',-0.5)) \
cmd.set_key ('F4', cmd.move,('y',0.5)) \
print "dialset ", dialset, " [ Y ]\n" \
return dialset

def dialz(): \
global dialset \
dialset = 3 \
cmd.set_key ('F1', cmd.turn,('z',-2.0)) \
cmd.set_key ('F2', cmd.turn,('z',2.0)) \
cmd.set_key ('F3', cmd.move,('z',-0.5)) \
cmd.set_key ('F4', cmd.move,('z',0.5)) \
print "dialset ", dialset, " [ Z ]\n" \
return dialset

def toggle_dial(): \
if dialset == 1 : \
print "Changing to y" \
dialy() \
elif dialset == 2 : \
print "Changing to z" \
dialz() \
elif dialset == 3 : \
print "Changing to x" \
dialx() \
else: print "Dial assignment isn't working"

cmd.set_key ('F5', toggle_dial)

# Start default dial state for rotate y (arbitrary choice)

dialy()

</source>
[[Category:Script_Library|Powermate Dial OS X]]

MAC Install

2007-11-22T03:46:37Z

Wgscott: /* PyMOLX11Hybrid */

[[Category:Installation|Mac]]
http://images.apple.com/powermac/images/solutionsscience20050427.jpg

__TOC__

=Installing MacPyMOL=
http://delsci.com/macpymol/macpymol350.jpg

===Essentials===

The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.

===Warning on Mouse Drivers===

One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.

===Invoking pymol from the unix command line===

The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL

I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.

Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]

===Extras===

You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.

====Mighty Mouse====

http://images.apple.com/mightymouse/images/index360scroll220050802.gif

A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.

====PowerMate Dial====

http://www.griffintechnology.com/assets/images/products/powermate/prod_powermate_sub01b.jpg

The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].

====Stereo====

http://images.apple.com/powermac/images/graphicspymol20051018.jpg

The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.

====Second Monitor====
The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate "-X #" (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support.
<source lang="python">
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100
</source>

'''Source:''' ''Warren DeLano; PyMOL Users Archive''

=Installing X-windows based pymol on Mac OS X=

===Why would you want to do this?===

#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.

----

===Simplest Installation===

====Install pymol with Fink====
http://pdb.finkproject.org/img/mlogo.png

By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system]. To compile it, all you need to do is issue the command

fink install pymol-py25

(This will install python2.5 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.4 and even python2.3. Fink uses its own unix-type python installation.)

The [http://pdb.finkproject.org/pdb/package.php/pymol-py25 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:

sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.

You might need to create the latter directory if it doesn't already exist, i.e., issue the command

sudo mkdir -p /sw/fink/dists/local/main/finkinfo

10.4 ONLY: Be sure to set your display environment in your start up shell script to use pymol. For example in your home directory, the .bashrc (or .bash_profile) file should contain:

export DISPLAY=":0.0"

Do NOT set the DISPLAY variable for 10.5, as God does this for you automatically.

I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].

The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.

====Install APBS and friends with fink====

[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]

To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi mpi version of apbs].

Issuing the command

fink install apbs

will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://xanana.ucsc.edu/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].

'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.

----

===PyMOLX11Hybrid===

MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.

[[Category:Nucleic_Acids|MAC Install]]
[[Category:Technical Issues|MAC Install]]

MAC Install

2007-11-22T03:45:47Z

Wgscott: /* Gratuitous Eye-Candy Tweaks */ This no longer works for reasons obscure to me.

[[Category:Installation|Mac]]
http://images.apple.com/powermac/images/solutionsscience20050427.jpg

__TOC__

=Installing MacPyMOL=
http://delsci.com/macpymol/macpymol350.jpg

===Essentials===

The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.

===Warning on Mouse Drivers===

One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.

===Invoking pymol from the unix command line===

The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL

I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.

Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]

===Extras===

You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.

====Mighty Mouse====

http://images.apple.com/mightymouse/images/index360scroll220050802.gif

A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.

====PowerMate Dial====

http://www.griffintechnology.com/assets/images/products/powermate/prod_powermate_sub01b.jpg

The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].

====Stereo====

http://images.apple.com/powermac/images/graphicspymol20051018.jpg

The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.

====Second Monitor====
The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate "-X #" (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support.
<source lang="python">
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100
</source>

'''Source:''' ''Warren DeLano; PyMOL Users Archive''

=Installing X-windows based pymol on Mac OS X=

===Why would you want to do this?===

#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.

----

===Simplest Installation===

====Install pymol with Fink====
http://pdb.finkproject.org/img/mlogo.png

By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system]. To compile it, all you need to do is issue the command

fink install pymol-py25

(This will install python2.5 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.4 and even python2.3. Fink uses its own unix-type python installation.)

The [http://pdb.finkproject.org/pdb/package.php/pymol-py25 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:

sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.

You might need to create the latter directory if it doesn't already exist, i.e., issue the command

sudo mkdir -p /sw/fink/dists/local/main/finkinfo

10.4 ONLY: Be sure to set your display environment in your start up shell script to use pymol. For example in your home directory, the .bashrc (or .bash_profile) file should contain:

export DISPLAY=":0.0"

Do NOT set the DISPLAY variable for 10.5, as God does this for you automatically.

I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].

The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.

====Install APBS and friends with fink====

[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]

To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi mpi version of apbs].

Issuing the command

fink install apbs

will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://xanana.ucsc.edu/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].

'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.

----

===PyMOLX11Hybrid===

MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.

Doing this creates the inverse situation of the previous tweak; the molecular viewer window is aqua-based and the tkinter GUI is X11 based. (Naturally, I had to try the trick of making an aqua-tkinter GUI. It sort of works, but the GUI is dead, thanks to a threading bug in the aqua Tcl/Tk framework that comes with Apple. Bummer.)

[[Category:Nucleic_Acids|MAC Install]]
[[Category:Technical Issues|MAC Install]]

MAC Install

2007-11-22T03:44:26Z

Wgscott: /* Install pymol with Fink */

[[Category:Installation|Mac]]
http://images.apple.com/powermac/images/solutionsscience20050427.jpg

__TOC__

=Installing MacPyMOL=
http://delsci.com/macpymol/macpymol350.jpg

===Essentials===

The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.

===Warning on Mouse Drivers===

One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.

===Invoking pymol from the unix command line===

The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL

I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.

Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]

===Extras===

You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.

====Mighty Mouse====

http://images.apple.com/mightymouse/images/index360scroll220050802.gif

A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.

====PowerMate Dial====

http://www.griffintechnology.com/assets/images/products/powermate/prod_powermate_sub01b.jpg

The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].

====Stereo====

http://images.apple.com/powermac/images/graphicspymol20051018.jpg

The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.

====Second Monitor====
The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate "-X #" (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support.
<source lang="python">
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100
</source>

'''Source:''' ''Warren DeLano; PyMOL Users Archive''

=Installing X-windows based pymol on Mac OS X=

===Why would you want to do this?===

#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.

----

===Simplest Installation===

====Install pymol with Fink====
http://pdb.finkproject.org/img/mlogo.png

By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system]. To compile it, all you need to do is issue the command

fink install pymol-py25

(This will install python2.5 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.4 and even python2.3. Fink uses its own unix-type python installation.)

The [http://pdb.finkproject.org/pdb/package.php/pymol-py25 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:

sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.

You might need to create the latter directory if it doesn't already exist, i.e., issue the command

sudo mkdir -p /sw/fink/dists/local/main/finkinfo

10.4 ONLY: Be sure to set your display environment in your start up shell script to use pymol. For example in your home directory, the .bashrc (or .bash_profile) file should contain:

export DISPLAY=":0.0"

Do NOT set the DISPLAY variable for 10.5, as God does this for you automatically.

I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].

The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.

====Install APBS and friends with fink====

[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]

To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi mpi version of apbs].

Issuing the command

fink install apbs

will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://xanana.ucsc.edu/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].

'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.

----

===Gratuitous Eye-Candy Tweaks===
[[Image:snap_mac.png|thumb|aqua-tkinter]]

You can get the fink installed X-windows based pymol-py24 to use an aqua-based tkinter menu as follows:

====Install a Framework build of Python2.4====
as follows:

mkdir src
cd src
curl -O http://www.python.org/ftp/python/2.4.2/Python-2.4.2.tgz
tar xvfz Python-2.4.2.tgz
cd Python-2.4.2
export PATH=/usr/bin:$PATH
./configure --enable-framework
make
sudo make frameworkinstall

====Getting Fink's PyMOL to use a Framework build of Python====

1. Remove the following empty directory by issuing the command

sudo rmdir /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages

2. Make a symbolic link to your fink site-packages directory:

sudo ln -s /sw/lib/python2.4/site-packages /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages

This enables your new framework python to use all of the extras, like pmw, that you installed as dependencies for pymol.

3. Edit the file /sw/bin/python, and change the line

/sw/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

to

/Library/Frameworks/Python.framework/Versions/Current/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

4. Now issue

/sw/bin/pymol

and you should see something that looks like this full-size [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png screenshot of pymol with an aqua-tkinter pmw GUI] and X-windows based molecular display window. Also shown in this screenshot is the APBS plugin in action.

----

===PyMOLX11Hybrid===

MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.

Doing this creates the inverse situation of the previous tweak; the molecular viewer window is aqua-based and the tkinter GUI is X11 based. (Naturally, I had to try the trick of making an aqua-tkinter GUI. It sort of works, but the GUI is dead, thanks to a threading bug in the aqua Tcl/Tk framework that comes with Apple. Bummer.)

[[Category:Nucleic_Acids|MAC Install]]
[[Category:Technical Issues|MAC Install]]

MAC Install

2007-11-22T03:43:46Z

Wgscott: /* Install pymol with Fink */ update for python-2.5 and 10.5

[[Category:Installation|Mac]]
http://images.apple.com/powermac/images/solutionsscience20050427.jpg

__TOC__

=Installing MacPyMOL=
http://delsci.com/macpymol/macpymol350.jpg

===Essentials===

The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.

===Warning on Mouse Drivers===

One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.

===Invoking pymol from the unix command line===

The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL

I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.

Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]

===Extras===

You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.

====Mighty Mouse====

http://images.apple.com/mightymouse/images/index360scroll220050802.gif

A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.

====PowerMate Dial====

http://www.griffintechnology.com/assets/images/products/powermate/prod_powermate_sub01b.jpg

The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].

====Stereo====

http://images.apple.com/powermac/images/graphicspymol20051018.jpg

The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.

====Second Monitor====
The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate "-X #" (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support.
<source lang="python">
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100
</source>

'''Source:''' ''Warren DeLano; PyMOL Users Archive''

=Installing X-windows based pymol on Mac OS X=

===Why would you want to do this?===

#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.

----

===Simplest Installation===

====Install pymol with Fink====
http://pdb.finkproject.org/img/mlogo.png

By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system]. To compile it, all you need to do is issue the command

fink install pymol-py25

(This will install python2.5 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.4 and even python2.3. Fink uses its own unix-type python installation, but you can trick pymol into using the aqua framework to get a prettier GUI after the fact.)

The [http://pdb.finkproject.org/pdb/package.php/pymol-py25 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:

sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.

You might need to create the latter directory if it doesn't already exist, i.e., issue the command

sudo mkdir -p /sw/fink/dists/local/main/finkinfo

10.4 ONLY: Be sure to set your display environment in your start up shell script to use pymol. For example in your home directory, the .bashrc (or .bash_profile) file should contain:

export DISPLAY=":0.0"

Do NOT set the DISPLAY variable for 10.5, as God does this for you automatically.

I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].

The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.

====Install APBS and friends with fink====

[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]

To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi mpi version of apbs].

Issuing the command

fink install apbs

will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://xanana.ucsc.edu/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].

'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.

----

===Gratuitous Eye-Candy Tweaks===
[[Image:snap_mac.png|thumb|aqua-tkinter]]

You can get the fink installed X-windows based pymol-py24 to use an aqua-based tkinter menu as follows:

====Install a Framework build of Python2.4====
as follows:

mkdir src
cd src
curl -O http://www.python.org/ftp/python/2.4.2/Python-2.4.2.tgz
tar xvfz Python-2.4.2.tgz
cd Python-2.4.2
export PATH=/usr/bin:$PATH
./configure --enable-framework
make
sudo make frameworkinstall

====Getting Fink's PyMOL to use a Framework build of Python====

1. Remove the following empty directory by issuing the command

sudo rmdir /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages

2. Make a symbolic link to your fink site-packages directory:

sudo ln -s /sw/lib/python2.4/site-packages /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages

This enables your new framework python to use all of the extras, like pmw, that you installed as dependencies for pymol.

3. Edit the file /sw/bin/python, and change the line

/sw/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

to

/Library/Frameworks/Python.framework/Versions/Current/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

4. Now issue

/sw/bin/pymol

and you should see something that looks like this full-size [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png screenshot of pymol with an aqua-tkinter pmw GUI] and X-windows based molecular display window. Also shown in this screenshot is the APBS plugin in action.

----

===PyMOLX11Hybrid===

MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.

Doing this creates the inverse situation of the previous tweak; the molecular viewer window is aqua-based and the tkinter GUI is X11 based. (Naturally, I had to try the trick of making an aqua-tkinter GUI. It sort of works, but the GUI is dead, thanks to a threading bug in the aqua Tcl/Tk framework that comes with Apple. Bummer.)

[[Category:Nucleic_Acids|MAC Install]]
[[Category:Technical Issues|MAC Install]]

APBS

2007-04-15T16:22:38Z

Wgscott: /* Installing the Dependencies on OS X */

== Introduction ==
[[Image:Rna_surface_apbs.png|thumb|APBS-generated electrostatic surface displayed in PyMOL]]
[http://apbs.sourceforge.net APBS], the Adaptive Poisson-Boltzmann Solver, is a [http://www.oreilly.com/openbook/freedom/ freely] available macromolecular electrostatics calculation program released under the [http://www.gnu.org/copyleft/gpl.html GPL]. It is a cost-effective but uncompromised alternative to [http://trantor.bioc.columbia.edu/grasp/ GRASP], and it can be used within pymol. Pymol can display the results of the calculations as an electrostatic potential molecular surface.

PyMol currently supports the '''APBS plugin''' written by Michael Lerner. This plugin makes it possible to run APBS from within PyMOL, and then display the results as a color-coded electrostatic surface (units kbT/ec) in the molecular display window (as with the image to the right). See [http://www-personal.umich.edu/~mlerner/PyMOL/ Michael Lerner's Page] for more details, including instructions on how to download, install and use the plugin.

'''Nucleic acids may prove problematic for the apbs plugin.''' If so, use the [http://pdb2pqr.sourceforge.net/ pdb2pqr] command-line tool to create a pqr file manually, instead of using the plugin to generate it. Then direct the APBS GUI on the [http://www-personal.umich.edu/~mlerner/PyMOL/images/main.png main menu] to read the pqr file you '''externally generated.'''

==Required Dependencies==
[http://apbs.sourceforge.net APBS] and its dependencies like [http://pdb2pqr.sourceforge.net pdb2pqr] and [http://scicomp.ucsd.edu/~mholst/codes/maloc/ maloc] are [http://www.oreilly.com/openbook/freedom/ freely] available under the [http://www.gnu.org/copyleft/gpl.html GPL]. The author of the software however [http://agave.wustl.edu/apbs/download/ asks that users register] with him to aid him in obtaining grant funding.

----
===Installing the Dependencies on OS X===
#First, [http://agave.wustl.edu/apbs/download/ register] your use of the software. This will keep everyone happy.
#Second, if you don't already have the [http://fink.sourceforge.net fink package management system], now is a good time to get it. Here is a [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start quick-start set of instructions] for getting X-windows, compilers, and fink all installed.
#Once you are up and going, [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch in fink], and then issue the commands

fink self-update
fink install apbs

or if you want to use the multi-processor version, issue

fink self-update
fink install apbs

Then install the X-windows based version of pymol using the command

fink install pymol-py25

Note that the fink version of pymol '''already has''' the latest version of the APBS plugin. You are set to go!

Further details, as well as screen shots, are given [http://www.pymolwiki.org/index.php/MAC_Install#Install_APBS_and_friends_with_fink elsewhere in this wiki].

----

===Installing the Dependencies on Linux===

====From Scratch====
Note that this tutorial assumes you're using the bash shell and have root privileges
<OL><LI>
Obtain APBS and MALOC from... 
APBS = http://apbs.sourceforge.net (currently 0.4) 
MALOC = http://www.fetk.org/codes/maloc/index.html#download (currently 0.1-2) 
<LI>Set up some environment variables & directories (temporary for building)
<pre>
$ export FETK_SRC=/<building directory>/temp_apbs
$ export FETK_PREFIX=/usr/local/apbs-0.4.0 (or wherever you want it to live)
$ export FETK_INCLUDE=${FETK_PREFIX}/include
$ export FETK_LIBRARY=${FETK_PREFIX}/lib
$ mkdir -p ${FETK_SRC} ${FETK_INCLUDE} ${FETK_LIBRARY}
</pre></LI>
<LI>Unpack the source packages
<pre>
$ cd ${FETK_SRC}
$ gzip -dc maloc-0.1-2.tar.gz | tar xvf -
$ gzip -dc apbs-0.4.0.tar.gz | tar xvf -</pre>
</LI>
<LI>Compile MALOC
<pre>
$ cd ${FETK_SRC}/maloc
$ ./configure --prefix=${FETK_PREFIX}</pre>
If everything went well, then
<pre>$ make; make install</pre></LI>
<LI>Go get a coffee. Compilation/installation takes about 15 minutes on a 3GHz computer with 1GB of RAM.</LI>
<LI>Now on to compiling APBS itself
<pre>
$ cd ${FETK_SRC}/apbs-0.4.0
$ ./configure --prefix=${FETK_PREFIX}</pre>
If all goes well:
<pre>$ make all; make install</pre></LI>
<LI>No time for coffee. Takes about 5 minutes on that fast computer.</LI>
<LI> There will now be an APBS binary at
<pre>/usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs</pre></LI>
<LI> Make appropriate links
<pre>
$ ln -s /usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs /usr/local/bin/apbs
</pre></LI>
<LI> Get rid of /<building directory dir>/temp_apbs
<LI> Open PyMOL and make sure that the APBS plugin points to /usr/local/bin/apbs
<LI> Rock and or Roll.
</OL>

====Pre-Packaged====
=====RPMs=====

A variety of RPMs are available from the [http://sourceforge.net/project/showfiles.php?group_id=148472&package_id=163734&release_id=378273 APBS downloads website]. Again, please [http://agave.wustl.edu/apbs/download/ register] your use of the software if you have not yet done so.

=====Debian packages=====

For ubuntu and other debian linux distributions, probably the simplest thing is to download a promising looking rpm, convert it with the program [http://kitenet.net/programs/alien/ alien], and then install the [http://xanana.ucsc.edu/linux newly generated debian package] with the command

sudo dpkg -i apbs*.deb

=====Gentoo=====

You have to install apbs and pdb2pqr. Both are masked via keywords atm. Type as root:

echo sci-chemistry/pdb2pqr >> /etc/portage/packages.keywords

echo sci-chemistry/apbs >> /etc/portage/packages.keywords

emerge -av sci-chemistry/apbs sci-chemistry/pdb2pqr

----

==Further contributions and edits are needed.==

MAC Install

2006-10-07T17:47:19Z

Wgscott: /* PowerMate Dial */

[[Category:Installation|Mac]]
http://images.apple.com/powermac/images/solutionsscience20050427.jpg

__TOC__

=Installing MacPyMOL=
http://delsci.com/macpymol/macpymol350.jpg

===Essentials===

The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.

===Warning on Mouse Drivers===

One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.

===Invoking pymol from the unix command line===

The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL

I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.

Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]

===Extras===

You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.

====Mighty Mouse====

http://images.apple.com/mightymouse/images/index360scroll220050802.gif

A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.

====PowerMate Dial====

http://www.griffintechnology.com/assets/images/products/powermate/prod_powermate_sub01b.jpg

The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].

====Stereo====

http://images.apple.com/powermac/images/graphicspymol20051018.jpg

The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.

=Installing X-windows based pymol on Mac OS X=

===Why would you want to do this?===

#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.

----

===Simplest Installation===

====Install pymol with Fink====
http://pdb.finkproject.org/img/mlogo.png

By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system]. To compile it, all you need to do is issue the command

fink install pymol-py24

(This will install python2.4 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.3 and even python2.2. Fink uses its own unix-type python installation, but you can trick pymol into using the aqua framework to get a prettier GUI after the fact.)

The [http://pdb.finkproject.org/pdb/package.php/pymol-py24 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:

sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.

You might need to create the latter directory if it doesn't already exist, i.e., issue the command

sudo mkdir -p /sw/fink/dists/local/main/finkinfo

I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].

The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.

====Install APBS and friends with fink====

[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]

To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi mpi version of apbs].

Issuing the command

fink install apbs

will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].

'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.

----

===Gratuitous Eye-Candy Tweaks===
[[Image:snap_mac.png|thumb|aqua-tkinter]]

You can get the fink installed X-windows based pymol-py24 to use an aqua-based tkinter menu as follows:

====Install a Framework build of Python2.4====
as follows:

mkdir src
cd src
curl -O http://www.python.org/ftp/python/2.4.2/Python-2.4.2.tgz
tar xvfz Python-2.4.2.tgz
cd Python-2.4.2
export PATH=/usr/bin:$PATH
./configure --enable-framework
make
sudo make frameworkinstall

====Getting Fink's PyMOL to use a Framework build of Python====

1. Remove the following empty directory by issuing the command

sudo rmdir /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages

2. Make a symbolic link to your fink site-packages directory:

sudo ln -s /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages /sw/lib/python2.4/site-packages

This enables your new framework python to use all of the extras, like pmw, that you installed as dependencies for pymol.

3. Edit the file /sw/bin/python, and change the line

/sw/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

to

/Library/Frameworks/Python.framework/Versions/Current/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

4. Now issue

/sw/bin/pymol

and you should see something that looks like this full-size [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png screenshot of pymol with an aqua-tkinter pmw GUI] and X-windows based molecular display window. Also shown in this screenshot is the APBS plugin in action.

----

===PyMOLX11Hybrid===

MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.

Doing this creates the inverse situation of the previous tweak; the molecular viewer window is aqua-based and the tkinter GUI is X11 based. (Naturally, I had to try the trick of making an aqua-tkinter GUI. It sort of works, but the GUI is dead, thanks to a threading bug in the aqua Tcl/Tk framework that comes with Apple. Bummer.)

Linux Install

2006-07-07T15:52:34Z

Wgscott: /* Ubuntu Linux (x86 32,64; mac ppc) */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])

== Generic Linux ==

=== 0.99rc1 note! ===
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.

Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.

=== From Source ===
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
or for the latest version,
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol.com".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform.

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray

you may also need to add the pgp key for the repository before yum will get packages from it by either saying:

rpm --import http://www.bioxray.dk/~mok/404825e7.asc

or with older versions of rpm:

wget http://www.bioxray.dk/~mok/404825e7.asc
rpm --import 404825e7.asc

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==

http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then try changing the permissons on libnvidia-tls.so.1. i.e,

<pre> sudo chmod 777 /usr/lib/ibnvidia-tls.so.1 </pre>

Linux Install

2006-07-07T01:15:32Z

Wgscott: /* libnvidia-tls.so.1: cannot handle TLS data */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])

== Generic Linux ==

=== 0.99rc1 note! ===
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.

Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.

=== From Source ===
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
or for the latest version,
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol.com".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform.

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray

you may also need to add the pgp key for the repository before yum will get packages from it by either saying:

rpm --import http://www.bioxray.dk/~mok/404825e7.asc

or with older versions of rpm:

wget http://www.bioxray.dk/~mok/404825e7.asc
rpm --import 404825e7.asc

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==
http://ubuntuforum s.org/images/ubuntu-small.gif

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then try changing the permissons on libnvidia-tls.so.1. i.e,

<pre> sudo chmod 777 /usr/lib/ibnvidia-tls.so.1 </pre>

Linux Install

2006-07-07T00:40:50Z

Wgscott: /* libnvidia-tls.so.1: cannot handle TLS data */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])

== Generic Linux ==

=== 0.99rc1 note! ===
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.

Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.

=== From Source ===
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
or for the latest version,
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol.com".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform.

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray

you may also need to add the pgp key for the repository before yum will get packages from it by either saying:

rpm --import http://www.bioxray.dk/~mok/404825e7.asc

or with older versions of rpm:

wget http://www.bioxray.dk/~mok/404825e7.asc
rpm --import 404825e7.asc

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==
http://ubuntuforum s.org/images/ubuntu-small.gif

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then [http://imgseek.sourceforge.net/faq.html#faq3 move the file] <tt> mv /usr/lib/tls/ibnvidia-tls.so.1</tt>, e.g:

sudo mv /usr/lib/tls /usr/lib/ibnvidia-tls.so.1 /usr/lib/tls /usr/lib/ibnvidia-tls.so.1.bak

This temporarily cures the problem for me (Ubuntu 5.10; nvidia driver), but creates display problems upon rebooting.

Linux Install

2006-07-07T00:39:34Z

Wgscott: /* Ubuntu Linux (x86 32,64; mac ppc) */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])

== Generic Linux ==

=== 0.99rc1 note! ===
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.

Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.

=== From Source ===
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
or for the latest version,
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol.com".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform.

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray

you may also need to add the pgp key for the repository before yum will get packages from it by either saying:

rpm --import http://www.bioxray.dk/~mok/404825e7.asc

or with older versions of rpm:

wget http://www.bioxray.dk/~mok/404825e7.asc
rpm --import 404825e7.asc

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==
http://ubuntuforum s.org/images/ubuntu-small.gif

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then [http://imgseek.sourceforge.net/faq.html#faq3 move the directory] <tt> mv /usr/lib/tls</tt>, e.g:

sudo mv /usr/lib/tls /usr/lib/tls-feb15-2006

This temporarily cures the problem for me (Ubuntu 5.10; nvidia driver), but creates display problems upon rebooting.

Linux Install

2006-04-07T18:38:22Z

Wgscott: /* libnvidia-tls.so.1: cannot handle TLS data */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])

== Generic Linux ==

=== 0.99rc1 note! ===
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.

Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.

=== From Source ===
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
or for the latest version,
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol.com".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform.

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/$releasever/$basearch/xray

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [[http://www.sf.net/projects/pmw Pmw]] from [[http://www.sf.net/ SourceForge]].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<code>
sudo cp ./pymol.com /usr/local/bin
</code>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==
http://ubuntuforums.org/images/ubuntu-small.gif

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then [http://imgseek.sourceforge.net/faq.html#faq3 move the directory] <tt> mv /usr/lib/tls</tt>, e.g:

sudo mv /usr/lib/tls /usr/lib/tls-feb15-2006

This temporarily cures the problem for me (Ubuntu 5.10; nvidia driver), but creates display problems upon rebooting.

MAC Install

2006-02-18T19:13:49Z

Wgscott: /* Invoking pymol from the unix command line */

[[Category:Installation|Mac]]
http://images.apple.com/powermac/images/solutionsscience20050427.jpg

__TOC__

=Installing MacPyMOL=
http://delsci.com/macpymol/macpymol350.jpg

===Essentials===

The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.

===Warning on Mouse Drivers===

One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.

===Invoking pymol from the unix command line===

The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL

I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.

Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]

===Extras===

You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.

====Mighty Mouse====

http://images.apple.com/mightymouse/images/index360scroll220050802.gif

A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.

====PowerMate Dial====

http://www.griffintechnology.com/images/products/prod_powermate_a.jpg

The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].

====Stereo====

http://images.apple.com/powermac/images/graphicspymol20051018.jpg

The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.

=Installing X-windows based pymol on Mac OS X=

===Why would you want to do this?===

#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.

----

===Simplest Installation===

====Install pymol with Fink====
http://pdb.finkproject.org/img/mlogo.png

By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system]. To compile it, all you need to do is issue the command

fink install pymol-py24

(This will install python2.4 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.3 and even python2.2. Fink uses its own unix-type python installation, but you can trick pymol into using the aqua framework to get a prettier GUI after the fact.)

The [http://pdb.finkproject.org/pdb/package.php/pymol-py24 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:

sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.

You might need to create the latter directory if it doesn't already exist, i.e., issue the command

sudo mkdir -p /sw/fink/dists/local/main/finkinfo

I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].

The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.

====Install APBS and friends with fink====

[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]

To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi mpi version of apbs].

Issuing the command

fink install apbs

will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].

'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.

----

===Gratuitous Eye-Candy Tweaks===
[[Image:snap_mac.png|thumb|aqua-tkinter]]

You can get the fink installed X-windows based pymol-py24 to use an aqua-based tkinter menu as follows:

====Install a Framework build of Python2.4====
as follows:

mkdir src
cd src
curl -O http://www.python.org/ftp/python/2.4.2/Python-2.4.2.tgz
tar xvfz Python-2.4.2.tgz
cd Python-2.4.2
export PATH=/usr/bin:$PATH
./configure --enable-framework
make
sudo make frameworkinstall

====Getting Fink's PyMOL to use a Framework build of Python====

1. Remove the following empty directory by issuing the command

sudo rmdir /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages

2. Make a symbolic link to your fink site-packages directory:

sudo ln -s /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages /sw/lib/python2.4/site-packages

This enables your new framework python to use all of the extras, like pmw, that you installed as dependencies for pymol.

3. Edit the file /sw/bin/python, and change the line

/sw/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

to

/Library/Frameworks/Python.framework/Versions/Current/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

4. Now issue

/sw/bin/pymol

and you should see something that looks like this full-size [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png screenshot of pymol with an aqua-tkinter pmw GUI] and X-windows based molecular display window. Also shown in this screenshot is the APBS plugin in action.

----

===PyMOLX11Hybrid===

MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.

Doing this creates the inverse situation of the previous tweak; the molecular viewer window is aqua-based and the tkinter GUI is X11 based. (Naturally, I had to try the trick of making an aqua-tkinter GUI. It sort of works, but the GUI is dead, thanks to a threading bug in the aqua Tcl/Tk framework that comes with Apple. Bummer.)

MacOSX-specific .pymolrc file

2006-02-18T19:08:48Z

Wgscott:

Here is an example of a ~/.pymolrc file that [[User:Wgscott|I]] use on Mac OS X. There are two main things going on here:

* It defines a bunch of aliases, including one that ribbonizes protein/nucleic acid comples (this could benefit from updating)

* It runs a series of pythonized pymol commands to permit interaction with the [[MAC_Install#PowerMate_Dial | PowerMate Dial]]

<source lang="python">

_ feedback push
_ feedback disable,all,everything

alias clear, mstop; mclear; hide all
alias nogui, set internal_gui=0
alias gui, set internal_gui=1
alias shiny, set spec_power=250; set spec_refl=1.5; set antialias=1; ray
alias grab, os.system("open -a Grab")
alias stop, quit
alias exit, quit
alias white, bg_color white; set depth_cue=0; set ray_trace_fog=0

from pymol import cmd

# Define aliases for mapping in [x,y,z] rotations and translations into a single Powermate
# dial. Toggling between the three is possible if you then assign these to special keys.

# Functions for x,y,z rotations and translations using Powermate dial
# Program F1 and F2 for Rotate Right and Rotate Left
# Program F3 and F4 for Click & Rotate Right and Click & Rotate Left
# Program F5 for Click (to toggle between dialsets)

# dialset = 2

def dialx(): \
global dialset \
dialset = 1 \
cmd.set_key ('F1', cmd.turn,('x',-2.0)) \
cmd.set_key ('F2', cmd.turn,('x',2.0)) \
cmd.set_key ('F3', cmd.move,('x',-0.5)) \
cmd.set_key ('F4', cmd.move,('x',0.5)) \
print "dialset ", dialset, " [ X ]\n" \
return dialset

def dialy(): \
global dialset \
dialset = 2 \
cmd.set_key ('F1', cmd.turn,('y',-2.0)) \
cmd.set_key ('F2', cmd.turn,('y',2.0)) \
cmd.set_key ('F3', cmd.move,('y',-0.5)) \
cmd.set_key ('F4', cmd.move,('y',0.5)) \
print "dialset ", dialset, " [ Y ]\n" \
return dialset

def dialz(): \
global dialset \
dialset = 3 \
cmd.set_key ('F1', cmd.turn,('z',-2.0)) \
cmd.set_key ('F2', cmd.turn,('z',2.0)) \
cmd.set_key ('F3', cmd.move,('z',-0.5)) \
cmd.set_key ('F4', cmd.move,('z',0.5)) \
print "dialset ", dialset, " [ Z ]\n" \
return dialset

def toggle_dial(): \
if dialset == 1 : \
print "Changing to y" \
dialy() \
elif dialset == 2 : \
print "Changing to z" \
dialz() \
elif dialset == 3 : \
print "Changing to x" \
dialx() \
else: print "Dial assignment isn't working"

cmd.set_key ('F5', toggle_dial)

# Start default dial state for rotate y (arbitrary choice)

dialy()

alias ribbonize,\
hide; show cartoon; set cartoon_fancy_helices, 1; \
hide cartoon, ( resname A or resname G or resname C or resname U or resname T ); \
show sticks, ( resname A or resname G or resname C or resname U or resname T ); \
util.rainbow; color hotpink, ( resname A or resname G or resname C or resname U or resname T )

# END COMMANDS
_ feedback pop

print "PowerMate Dial interface has been enabled"

print "Finished reading ~/.pymolrc"

</source>

MacOSX-specific .pymolrc file

2006-02-18T19:01:31Z

Wgscott:

<source lang="python">

_ feedback push
_ feedback disable,all,everything

alias clear, mstop; mclear; hide all
alias nogui, set internal_gui=0
alias gui, set internal_gui=1
alias shiny, set spec_power=250; set spec_refl=1.5; set antialias=1; ray
alias grab, os.system("open -a Grab")
alias stop, quit
alias exit, quit
alias white, bg_color white; set depth_cue=0; set ray_trace_fog=0

from pymol import cmd

# Define aliases for mapping in [x,y,z] rotations and translations into a single Powermate
# dial. Toggling between the three is possible if you then assign these to special keys.

# Functions for x,y,z rotations and translations using Powermate dial
# Program F1 and F2 for Rotate Right and Rotate Left
# Program F3 and F4 for Click & Rotate Right and Click & Rotate Left
# Program F5 for Click (to toggle between dialsets)

# dialset = 2

def dialx(): \
global dialset \
dialset = 1 \
cmd.set_key ('F1', cmd.turn,('x',-2.0)) \
cmd.set_key ('F2', cmd.turn,('x',2.0)) \
cmd.set_key ('F3', cmd.move,('x',-0.5)) \
cmd.set_key ('F4', cmd.move,('x',0.5)) \
print "dialset ", dialset, " [ X ]\n" \
return dialset

def dialy(): \
global dialset \
dialset = 2 \
cmd.set_key ('F1', cmd.turn,('y',-2.0)) \
cmd.set_key ('F2', cmd.turn,('y',2.0)) \
cmd.set_key ('F3', cmd.move,('y',-0.5)) \
cmd.set_key ('F4', cmd.move,('y',0.5)) \
print "dialset ", dialset, " [ Y ]\n" \
return dialset

def dialz(): \
global dialset \
dialset = 3 \
cmd.set_key ('F1', cmd.turn,('z',-2.0)) \
cmd.set_key ('F2', cmd.turn,('z',2.0)) \
cmd.set_key ('F3', cmd.move,('z',-0.5)) \
cmd.set_key ('F4', cmd.move,('z',0.5)) \
print "dialset ", dialset, " [ Z ]\n" \
return dialset

def toggle_dial(): \
if dialset == 1 : \
print "Changing to y" \
dialy() \
elif dialset == 2 : \
print "Changing to z" \
dialz() \
elif dialset == 3 : \
print "Changing to x" \
dialx() \
else: print "Dial assignment isn't working"

cmd.set_key ('F5', toggle_dial)

# Start default dial state for rotate y (arbitrary choice)

dialy()

alias ribbonize,\
hide; show cartoon; set cartoon_fancy_helices, 1; \
hide cartoon, ( resname A or resname G or resname C or resname U or resname T ); \
show sticks, ( resname A or resname G or resname C or resname U or resname T ); \
util.rainbow; color hotpink, ( resname A or resname G or resname C or resname U or resname T )

# END COMMANDS
_ feedback pop

print "PowerMate Dial interface has been enabled"

print "Finished reading ~/.pymolrc"

</source>

Main Page

2006-02-18T18:31:23Z

Wgscott:

* [[TOPTOC|'''Table of Contents''']]
 
* [[Special:Allpages|Alphabetized Index of all pages]]
 

== PyMol Wiki Home ==
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.

We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use

== New Users ==
The PyMol Wiki actively seeks new users and contributors! However, due to massive amount of spamming, we've changed the registration process, until further notice. '''If you would like access,''' you will need to be verified by a system administrator/sysop. To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol). Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''. Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.

==News==
===PyMol===
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* A new version of APBS plugin is available on [http://www-personal.umich.edu/~mlerner/PyMOL/ Michael Lerner's Page].
* New [http://www.delsci.com/beta Beta Releases] available.

===Wiki===
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page has been established.
* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.
* New cool [[ray]] tracing features added!

===News Archive===
*See our [[Older_News]].

== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

MAC Install

2006-02-18T18:24:27Z

Wgscott: /* Invoking pymol from the unix command line */

[[Category:Installation|Mac]]
http://images.apple.com/powermac/images/solutionsscience20050427.jpg

__TOC__

=Installing MacPyMOL=
http://delsci.com/macpymol/macpymol350.jpg

===Essentials===

The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.

===Warning on Mouse Drivers===

One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.

===Invoking pymol from the unix command line===

The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL

I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable.

Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]

===Extras===

You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.

====Mighty Mouse====

http://images.apple.com/mightymouse/images/index360scroll220050802.gif

A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.

====PowerMate Dial====

http://www.griffintechnology.com/images/products/prod_powermate_a.jpg

The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].

====Stereo====

http://images.apple.com/powermac/images/graphicspymol20051018.jpg

The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.

=Installing X-windows based pymol on Mac OS X=

===Why would you want to do this?===

#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.

----

===Simplest Installation===

====Install pymol with Fink====
http://pdb.finkproject.org/img/mlogo.png

By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system]. To compile it, all you need to do is issue the command

fink install pymol-py24

(This will install python2.4 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.3 and even python2.2. Fink uses its own unix-type python installation, but you can trick pymol into using the aqua framework to get a prettier GUI after the fact.)

The [http://pdb.finkproject.org/pdb/package.php/pymol-py24 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:

sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.

You might need to create the latter directory if it doesn't already exist, i.e., issue the command

sudo mkdir -p /sw/fink/dists/local/main/finkinfo

I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].

The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.

====Install APBS and friends with fink====

[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]

To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi mpi version of apbs].

Issuing the command

fink install apbs

will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].

'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.

----

===Gratuitous Eye-Candy Tweaks===
[[Image:snap_mac.png|thumb|aqua-tkinter]]

You can get the fink installed X-windows based pymol-py24 to use an aqua-based tkinter menu as follows:

====Install a Framework build of Python2.4====
as follows:

mkdir src
cd src
curl -O http://www.python.org/ftp/python/2.4.2/Python-2.4.2.tgz
tar xvfz Python-2.4.2.tgz
cd Python-2.4.2
export PATH=/usr/bin:$PATH
./configure --enable-framework
make
sudo make frameworkinstall

====Getting Fink's PyMOL to use a Framework build of Python====

1. Remove the following empty directory by issuing the command

sudo rmdir /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages

2. Make a symbolic link to your fink site-packages directory:

sudo ln -s /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages /sw/lib/python2.4/site-packages

This enables your new framework python to use all of the extras, like pmw, that you installed as dependencies for pymol.

3. Edit the file /sw/bin/python, and change the line

/sw/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

to

/Library/Frameworks/Python.framework/Versions/Current/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

4. Now issue

/sw/bin/pymol

and you should see something that looks like this full-size [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png screenshot of pymol with an aqua-tkinter pmw GUI] and X-windows based molecular display window. Also shown in this screenshot is the APBS plugin in action.

----

===PyMOLX11Hybrid===

MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.

Doing this creates the inverse situation of the previous tweak; the molecular viewer window is aqua-based and the tkinter GUI is X11 based. (Naturally, I had to try the trick of making an aqua-tkinter GUI. It sort of works, but the GUI is dead, thanks to a threading bug in the aqua Tcl/Tk framework that comes with Apple. Bummer.)

MAC Install

2006-02-18T18:19:17Z

Wgscott: /* Invoking pymol from the unix command line */

[[Category:Installation|Mac]]
http://images.apple.com/powermac/images/solutionsscience20050427.jpg

__TOC__

=Installing MacPyMOL=
http://delsci.com/macpymol/macpymol350.jpg

===Essentials===

The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.

===Warning on Mouse Drivers===

One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.

===Invoking pymol from the unix command line===

The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL

I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable.

Additional options are discussed under

===Extras===

You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.

====Mighty Mouse====

http://images.apple.com/mightymouse/images/index360scroll220050802.gif

A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.

====PowerMate Dial====

http://www.griffintechnology.com/images/products/prod_powermate_a.jpg

The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].

====Stereo====

http://images.apple.com/powermac/images/graphicspymol20051018.jpg

The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.

=Installing X-windows based pymol on Mac OS X=

===Why would you want to do this?===

#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.

----

===Simplest Installation===

====Install pymol with Fink====
http://pdb.finkproject.org/img/mlogo.png

By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system]. To compile it, all you need to do is issue the command

fink install pymol-py24

(This will install python2.4 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.3 and even python2.2. Fink uses its own unix-type python installation, but you can trick pymol into using the aqua framework to get a prettier GUI after the fact.)

The [http://pdb.finkproject.org/pdb/package.php/pymol-py24 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:

sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.

You might need to create the latter directory if it doesn't already exist, i.e., issue the command

sudo mkdir -p /sw/fink/dists/local/main/finkinfo

I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].

The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.

====Install APBS and friends with fink====

[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]

To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi mpi version of apbs].

Issuing the command

fink install apbs

will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].

'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.

----

===Gratuitous Eye-Candy Tweaks===
[[Image:snap_mac.png|thumb|aqua-tkinter]]

You can get the fink installed X-windows based pymol-py24 to use an aqua-based tkinter menu as follows:

====Install a Framework build of Python2.4====
as follows:

mkdir src
cd src
curl -O http://www.python.org/ftp/python/2.4.2/Python-2.4.2.tgz
tar xvfz Python-2.4.2.tgz
cd Python-2.4.2
export PATH=/usr/bin:$PATH
./configure --enable-framework
make
sudo make frameworkinstall

====Getting Fink's PyMOL to use a Framework build of Python====

1. Remove the following empty directory by issuing the command

sudo rmdir /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages

2. Make a symbolic link to your fink site-packages directory:

sudo ln -s /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages /sw/lib/python2.4/site-packages

This enables your new framework python to use all of the extras, like pmw, that you installed as dependencies for pymol.

3. Edit the file /sw/bin/python, and change the line

/sw/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

to

/Library/Frameworks/Python.framework/Versions/Current/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

4. Now issue

/sw/bin/pymol

and you should see something that looks like this full-size [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png screenshot of pymol with an aqua-tkinter pmw GUI] and X-windows based molecular display window. Also shown in this screenshot is the APBS plugin in action.

----

===PyMOLX11Hybrid===

MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.

Doing this creates the inverse situation of the previous tweak; the molecular viewer window is aqua-based and the tkinter GUI is X11 based. (Naturally, I had to try the trick of making an aqua-tkinter GUI. It sort of works, but the GUI is dead, thanks to a threading bug in the aqua Tcl/Tk framework that comes with Apple. Bummer.)

APBS

2006-02-18T04:47:53Z

Wgscott: /* Introduction */

APBS

2006-02-18T04:44:40Z

Wgscott: /* Introduction */

APBS

2006-02-18T04:43:02Z

Wgscott: /* Introduction */

APBS

2006-02-18T04:34:50Z

Wgscott: /* Introduction */

APBS

2006-02-18T04:34:23Z

Wgscott: /* Introduction */

File:Rna surface apbs.png

2006-02-17T19:28:18Z

Wgscott:

An APBS calculation of the electrostatic surface of [http://www.chemistry.ucsc.edu/~wgscott/sars/ sars s2m RNA]. The baseline has been changed drastically to reveal variations within a highly polyanionic macromolecule. The surface was generated using the X-11 based PyMOL, but the pymol saved session is easily re-displayed in the OS X native application.

APBS

2006-02-16T21:48:08Z

Wgscott: /* Debian packages */

APBS

2006-02-16T21:46:06Z

Wgscott: /* Installing the Dependencies on OS X */

MAC Install

2006-02-16T21:44:42Z

Wgscott: /* Install pymol with Fink */

[[Category:Installation|Mac]]
http://images.apple.com/powermac/images/solutionsscience20050427.jpg

__TOC__

=Installing MacPyMOL=
http://delsci.com/macpymol/macpymol350.jpg

===Essentials===

The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.

===Warning on Mouse Drivers===

One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.

===Invoking pymol from the unix command line===

The unix executable resides at MacPyMOL.app/Contents/MacOS/PyMOL

I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable.

===Extras===

You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.

====Mighty Mouse====

http://images.apple.com/mightymouse/images/index360scroll220050802.gif

A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.

====PowerMate Dial====

http://www.griffintechnology.com/images/products/prod_powermate_a.jpg

The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].

====Stereo====

http://images.apple.com/powermac/images/graphicspymol20051018.jpg

The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.

=Installing X-windows based pymol on Mac OS X=

===Why would you want to do this?===

#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.

----

===Simplest Installation===

====Install pymol with Fink====
http://pdb.finkproject.org/img/mlogo.png

By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system]. To compile it, all you need to do is issue the command

fink install pymol-py24

(This will install python2.4 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.3 and even python2.2. Fink uses its own unix-type python installation, but you can trick pymol into using the aqua framework to get a prettier GUI after the fact.)

The [http://pdb.finkproject.org/pdb/package.php/pymol-py24 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:

sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.

You might need to create the latter directory if it doesn't already exist, i.e., issue the command

sudo mkdir -p /sw/fink/dists/local/main/finkinfo

I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].

The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.

====Install APBS and friends with fink====

[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]

To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi mpi version of apbs].

Issuing the command

fink install apbs

will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].

'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.

----

===Gratuitous Eye-Candy Tweaks===
[[Image:snap_mac.png|thumb|aqua-tkinter]]

You can get the fink installed X-windows based pymol-py24 to use an aqua-based tkinter menu as follows:

====Install a Framework build of Python2.4====
as follows:

mkdir src
cd src
curl -O http://www.python.org/ftp/python/2.4.2/Python-2.4.2.tgz
tar xvfz Python-2.4.2.tgz
cd Python-2.4.2
export PATH=/usr/bin:$PATH
./configure --enable-framework
make
sudo make frameworkinstall

====Getting Fink's PyMOL to use a Framework build of Python====

1. Remove the following empty directory by issuing the command

sudo rmdir /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages

2. Make a symbolic link to your fink site-packages directory:

sudo ln -s /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages /sw/lib/python2.4/site-packages

This enables your new framework python to use all of the extras, like pmw, that you installed as dependencies for pymol.

3. Edit the file /sw/bin/python, and change the line

/sw/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

to

/Library/Frameworks/Python.framework/Versions/Current/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

4. Now issue

/sw/bin/pymol

and you should see something that looks like this full-size [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png screenshot of pymol with an aqua-tkinter pmw GUI] and X-windows based molecular display window. Also shown in this screenshot is the APBS plugin in action.

----

===PyMOLX11Hybrid===

MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.

Doing this creates the inverse situation of the previous tweak; the molecular viewer window is aqua-based and the tkinter GUI is X11 based. (Naturally, I had to try the trick of making an aqua-tkinter GUI. It sort of works, but the GUI is dead, thanks to a threading bug in the aqua Tcl/Tk framework that comes with Apple. Bummer.)

MAC Install

2006-02-16T21:43:59Z

Wgscott: /* Install pymol with Fink */

[[Category:Installation|Mac]]
http://images.apple.com/powermac/images/solutionsscience20050427.jpg

__TOC__

=Installing MacPyMOL=
http://delsci.com/macpymol/macpymol350.jpg

===Essentials===

The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.

===Warning on Mouse Drivers===

One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.

===Invoking pymol from the unix command line===

The unix executable resides at MacPyMOL.app/Contents/MacOS/PyMOL

I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable.

===Extras===

You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.

====Mighty Mouse====

http://images.apple.com/mightymouse/images/index360scroll220050802.gif

A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.

====PowerMate Dial====

http://www.griffintechnology.com/images/products/prod_powermate_a.jpg

The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].

====Stereo====

http://images.apple.com/powermac/images/graphicspymol20051018.jpg

The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.

=Installing X-windows based pymol on Mac OS X=

===Why would you want to do this?===

#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.

----

===Simplest Installation===

====Install pymol with Fink====
http://pdb.finkproject.org/img/mlogo.png

By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system]. To compile it, all you need to do is issue the command

fink install pymol-py24

(This will install python2.4 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.3 and even python2.2. Fink uses its own unix-type python installation, but you can trick pymol into using the aqua framework to get a prettier GUI after the fact.)

The [http://pdb.finkproject.org/pdb/package.php/pymol-py24 fink pymol package] currently exists in the [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:

sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.

You might need to create the latter directory if it doesn't already exist, i.e., issue the command

sudo mkdir -p /sw/fink/dists/local/main/finkinfo

I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].

The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.

====Install APBS and friends with fink====

[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]

To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi mpi version of apbs].

Issuing the command

fink install apbs

will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].

'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.

----

===Gratuitous Eye-Candy Tweaks===
[[Image:snap_mac.png|thumb|aqua-tkinter]]

You can get the fink installed X-windows based pymol-py24 to use an aqua-based tkinter menu as follows:

====Install a Framework build of Python2.4====
as follows:

mkdir src
cd src
curl -O http://www.python.org/ftp/python/2.4.2/Python-2.4.2.tgz
tar xvfz Python-2.4.2.tgz
cd Python-2.4.2
export PATH=/usr/bin:$PATH
./configure --enable-framework
make
sudo make frameworkinstall

====Getting Fink's PyMOL to use a Framework build of Python====

1. Remove the following empty directory by issuing the command

sudo rmdir /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages

2. Make a symbolic link to your fink site-packages directory:

sudo ln -s /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages /sw/lib/python2.4/site-packages

This enables your new framework python to use all of the extras, like pmw, that you installed as dependencies for pymol.

3. Edit the file /sw/bin/python, and change the line

/sw/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

to

/Library/Frameworks/Python.framework/Versions/Current/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"

4. Now issue

/sw/bin/pymol

and you should see something that looks like this full-size [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png screenshot of pymol with an aqua-tkinter pmw GUI] and X-windows based molecular display window. Also shown in this screenshot is the APBS plugin in action.

----

===PyMOLX11Hybrid===

MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.

Doing this creates the inverse situation of the previous tweak; the molecular viewer window is aqua-based and the tkinter GUI is X11 based. (Naturally, I had to try the trick of making an aqua-tkinter GUI. It sort of works, but the GUI is dead, thanks to a threading bug in the aqua Tcl/Tk framework that comes with Apple. Bummer.)

Linux Install

2006-02-16T07:26:49Z

Wgscott: /* Ubuntu Linux (x86 32,64; mac ppc) */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])

== Generic Linux ==

=== 0.99rc1 note! ===
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.

Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.

=== From Source ===
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
or for the latest version,
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol.com".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform.

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/$releasever/$basearch/xray

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [[http://www.sf.net/projects/pmw Pmw]] from [[http://www.sf.net/ SourceForge]].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<code>
sudo cp ./pymol.com /usr/local/bin
</code>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==
http://ubuntuforums.org/images/ubuntu-small.gif

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then [http://imgseek.sourceforge.net/faq.html#faq3 move the directory] <tt> mv /usr/lib/tls</tt>, e.g:

sudo mv /usr/lib/tls /usr/lib/tls-feb15-2006

This cured the problem for me (Ubuntu 5.10; nvidia driver).

Linux Install

2006-02-16T07:08:00Z

Wgscott: /* libnvidia-tls.so.1: cannot handle TLS data */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])

== Generic Linux ==

=== 0.99rc1 note! ===
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.

Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.

=== From Source ===
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
or for the latest version,
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol.com".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform.

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/$releasever/$basearch/xray

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [[http://www.sf.net/projects/pmw Pmw]] from [[http://www.sf.net/ SourceForge]].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<code>
sudo cp ./pymol.com /usr/local/bin
</code>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==
http://ubuntuforums.org/images/ubuntu-small.gif

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked.

PyMol also compiles from source on Ubuntu following the generic instructions given above.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then [http://imgseek.sourceforge.net/faq.html#faq3 move the directory] <tt> mv /usr/lib/tls</tt>, e.g:

sudo mv /usr/lib/tls /usr/lib/tls-feb15-2006

This cured the problem for me (Ubuntu 5.10; nvidia driver).

Linux Install

2006-02-16T07:06:10Z

Wgscott: /* Input */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])

== Generic Linux ==

=== 0.99rc1 note! ===
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.

Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.

=== From Source ===
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
or for the latest version,
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol.com".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform.

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/$releasever/$basearch/xray

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [[http://www.sf.net/projects/pmw Pmw]] from [[http://www.sf.net/ SourceForge]].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<code>
sudo cp ./pymol.com /usr/local/bin
</code>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==
http://ubuntuforums.org/images/ubuntu-small.gif

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked.

PyMol also compiles from source on Ubuntu following the generic instructions given above.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then [http://imgseek.sourceforge.net/faq.html#faq3 move the directory] <tt> mv /usr/lib/tls</tt>, e.g:

sudo mv /usr/lib/tls /usr/lib/tls-feb15-2006

and then it should work.

Linux Install

2006-02-16T07:00:08Z

Wgscott: /* Ubuntu Linux (x86 32,64; mac ppc) */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])

== Generic Linux ==

=== 0.99rc1 note! ===
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.

Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.

=== From Source ===
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
or for the latest version,
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol.com".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform.

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/$releasever/$basearch/xray

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [[http://www.sf.net/projects/pmw Pmw]] from [[http://www.sf.net/ SourceForge]].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<code>
sudo cp ./pymol.com /usr/local/bin
</code>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==
http://ubuntuforums.org/images/ubuntu-small.gif

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked.

PyMol also compiles from source on Ubuntu following the generic instructions given above.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

Linux Install

2006-02-16T06:57:44Z

Wgscott: /* From Source */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])

== Generic Linux ==

=== 0.99rc1 note! ===
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.

Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.

=== From Source ===
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
or for the latest version,
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol.com".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform.

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/$releasever/$basearch/xray

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [[http://www.sf.net/projects/pmw Pmw]] from [[http://www.sf.net/ SourceForge]].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<code>
sudo cp ./pymol.com /usr/local/bin
</code>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==
http://ubuntuforums.org/images/ubuntu-small.gif

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

Main Page

2006-02-15T23:34:43Z

Wgscott:

* [[TOPTOC|'''Table of Contents''']]
 

== PyMol Wiki Home ==
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.

We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use

== New Users ==
The PyMol Wiki actively seeks new users and contributors! However, due to massive amount of spamming, we've changed the registration process, until further notice. '''If you would like access,''' you will need to be verified by a system administrator/sysop. To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol). Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''. Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.

==News==
===PyMol===
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* A new version of APBS plugin is available on [http://www-personal.umich.edu/~mlerner/PyMOL/ Michael Lerner's Page].
* New [http://www.delsci.com/beta Beta Releases] available.

===Wiki===
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page has been established.
* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.
* New cool [[ray]] tracing features added!

===News Archive===
*See our [[Older_News]].

== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

Main Page

2006-02-15T23:34:17Z

Wgscott:

* [[TOPTOC|'''Table of Contents''']]
 

== PyMol Wiki Home ==
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.

We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use

== New Users ==
The PyMol Wiki actively seeks new users and contributors! However, due to massive amount of spamming, we've changed the registration process, until further notice. '''If you would like access,''' you will need to be verified by a system administrator/sysop. To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol). Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''. Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.

==News==
===PyMol===
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* A new version of APBS plugin is available on [http://www-personal.umich.edu/~mlerner/PyMOL/ Michael Lerner's Page].
* New [http://www.delsci.com/beta Beta Releases] available.

===Wiki===
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page has been established.
* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.
* New cool [[ray]] tracing features added!

===News Archive===
*See our [[Older_News]].

== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

APBS

2006-02-15T22:15:07Z

Wgscott: /* Introduction */

Main Page

2006-02-15T22:07:56Z

Wgscott:

* [[TOPTOC|'''Table of Contents''']]

----

== PyMol Wiki Home ==
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.

We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use

== New Users ==
The PyMol Wiki actively seeks new users and contributors! However, due to massive amount of spamming, we've changed the registration process, until further notice. '''If you would like access,''' you will need to be verified by a system administrator/sysop. To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol). Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''. Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.

==News==
===PyMol===
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* A new version of APBS plugin is available on [http://www-personal.umich.edu/~mlerner/PyMOL/ Michael Lerner's Page].
* New [http://www.delsci.com/beta Beta Releases] available.

===Wiki===
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page has been established.
* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.
* New cool [[ray]] tracing features added!

===News Archive===
*See our [[Older_News]].

== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

Main Page

2006-02-15T22:07:07Z

Wgscott: /* News Archive */

* [[TOPTOC|Table of Contents]]

----

== PyMol Wiki Home ==
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.

We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use

== New Users ==
The PyMol Wiki actively seeks new users and contributors! However, due to massive amount of spamming, we've changed the registration process, until further notice. '''If you would like access,''' you will need to be verified by a system administrator/sysop. To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol). Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''. Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.

==News==
===PyMol===
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* A new version of APBS plugin is available on [http://www-personal.umich.edu/~mlerner/PyMOL/ Michael Lerner's Page].
* New [http://www.delsci.com/beta Beta Releases] available.

===Wiki===
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page has been established.
* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.
* New cool [[ray]] tracing features added!

===News Archive===
*See our [[Older_News]].

== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

Main Page

2006-02-15T22:06:45Z

Wgscott: /* PyMol */

* [[TOPTOC|Table of Contents]]

----

== PyMol Wiki Home ==
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.

We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use

== New Users ==
The PyMol Wiki actively seeks new users and contributors! However, due to massive amount of spamming, we've changed the registration process, until further notice. '''If you would like access,''' you will need to be verified by a system administrator/sysop. To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol). Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''. Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.

==News==
===PyMol===
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* A new version of APBS plugin is available on [http://www-personal.umich.edu/~mlerner/PyMOL/ Michael Lerner's Page].
* New [http://www.delsci.com/beta Beta Releases] available.

===Wiki===
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page has been established.
* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.
* New cool [[ray]] tracing features added!

===News Archive===
See our [[Older_News]].

== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

Main Page

2006-02-15T22:04:39Z

Wgscott: /* Wiki */

* [[TOPTOC|Table of Contents]]

----

== PyMol Wiki Home ==
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.

We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use

== New Users ==
The PyMol Wiki actively seeks new users and contributors! However, due to massive amount of spamming, we've changed the registration process, until further notice. '''If you would like access,''' you will need to be verified by a system administrator/sysop. To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol). Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''. Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.

==News==
===PyMol===
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* New [http://www.delsci.com/beta Beta Releases] available.
===Wiki===
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page has been established.
* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.
* New cool [[ray]] tracing features added!

===News Archive===
See our [[Older_News]].

== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

Main Page

2006-02-15T22:03:55Z

Wgscott: /* Wiki */

* [[TOPTOC|Table of Contents]]

----

== PyMol Wiki Home ==
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.

We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use

== New Users ==
The PyMol Wiki actively seeks new users and contributors! However, due to massive amount of spamming, we've changed the registration process, until further notice. '''If you would like access,''' you will need to be verified by a system administrator/sysop. To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol). Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''. Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.

==News==
===PyMol===
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* New [http://www.delsci.com/beta Beta Releases] available.
===Wiki===
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page has been established. A new version of APBS plugin is provided.
* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.
* New cool [[ray]] tracing features added!

===News Archive===
See our [[Older_News]].

== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

Main Page

2006-02-15T20:15:40Z

Wgscott: /* PyMol Wiki Home */

* [[TOPTOC|Table of Contents]]

----

== PyMol Wiki Home ==
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.

We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use

== New Users ==
The PyMol Wiki actively seeks new users and contributors! However, due to massive amount of spamming, we've changed the registration process, until further notice. '''If you would like access,''' you will need to be verified by a system administrator/sysop. To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol). Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''. Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.

==News==
===PyMol===
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* New [http://www.delsci.com/beta Beta Releases] available.
===Wiki===
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page has been established. A new version of APBS plugin is provided.
* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.
* New cool [[ray]] tracing features added!

See our [[Older_News]].

== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

Main Page

2006-02-15T20:13:36Z

Wgscott: /* Wiki */

== PyMol Wiki Home ==
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.

We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use

== New Users ==
The PyMol Wiki actively seeks new users and contributors! However, due to massive amount of spamming, we've changed the registration process, until further notice. '''If you would like access,''' you will need to be verified by a system administrator/sysop. To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol). Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''. Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.

==News==
===PyMol===
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* New [http://www.delsci.com/beta Beta Releases] available.
===Wiki===
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page has been established. A new version of APBS plugin is provided.
* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.
* New cool [[ray]] tracing features added!

See our [[Older_News]].

== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

Main Page

2006-02-15T20:10:32Z

Wgscott: /* News */

== PyMol Wiki Home ==
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.

We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use

== New Users ==
The PyMol Wiki actively seeks new users and contributors! However, due to massive amount of spamming, we've changed the registration process, until further notice. '''If you would like access,''' you will need to be verified by a system administrator/sysop. To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol). Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''. Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.

==News==
===PyMol===
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* New [http://www.delsci.com/beta Beta Releases] available.
===Wiki===
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page established. A new version of APBS plugin is provided. An overview of how to set this up on OS X and on Linux has been started but needs contributions.
* New cool [[ray]] tracing features added!

See our [[Older_News]].

== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

PyMOLWiki:Community Portal

2006-02-15T20:02:58Z

Wgscott: /* How to Get Involved */

= How to Get Involved =
* First, go request and account (see [[Main_Page]]).

== What to Do ==
* Next, we need folks to clean up the commands.
* If you have a nifty script, feel free to upload it and add an index to your entry on the main page.
* We need examples included with the commands.

== Features ==
=== New! GeShi: Syntax Highlighting for Python & More ===
Use Geshi for syntax highlighting your Python code! '''Update''': I have added the option for numbered syntax highlighting and non-numbered.
<pre>
<source lang="python">Non line-numbered code here</source>
</pre>

<pre>
<npython>line-numbered code here</npython>
</pre>

Now with line numbers (or not)!

<npython>
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</npython>

See [http://qbnz.com/highlighter/index.php The Geshi Home Page]