PyMOL Wiki - User contributions [en]

Category:Script Library

2009-04-27T16:24:27Z

Jcorn: /* Descriptions */

= Overview =
Here we provide a trove of scripts. The descriptions immediately follow. For the entire category, please see the bottom of this page.

'''Warning the following list is incomplete. For the complete list, see the category table beneath it.'''

= Descriptions =
* [[ObjectByArrows]] -- Navigate between objects by using the arrow keys

* [[ConnectedCloud]] -- Find connected clouds of objects in PyMOL

* [[FilterByMol]] -- Filter a directory of files, and save their ligands to disk (by molecule).

* [[LoadDir]] -- loads all the files of a type you specify from the path you specify and puts them into the group you specify (or none).

* [[LigAlign]] -- Ligand-based active site alignment and comparison.

* [[ImmersiveViz]] -- A script used in conjunction with head tracking software to provide an immersive virtual experience.

* [[Rasmolify]] -- A work in progress - a script to map Rasmol commands onto the equivalent PyMOL commands.

* [[Zero_residues]] -- Renumber residues such that the first residue is 0. Useful for alignments.

* [[Cealign]] -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.

* [[WriteSS]] -- Writes secondary structural elements, for each residues, to a file.

* [[Process_All_Files_In_Directory]] -- Do something to all files in a directory. The examples show how to print the disulfide bond lengths, then in general all sulfur distances (not necessarily bound).

* [[Kabsch]] -- Kabsch alignment of two sets of vectors. (Part 2 of a protein alignment.)

* [[Transform_odb]] -- Transform a selection of an existing object and output as a new object. The transformation matrix is read from an "O"-style tranformation matrix file (.odb) written by "O" or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.

* [[Stereo_Ray]] -- This script will create two resolution specific ray traced images rotated appropriately for inclusion into a single file to represent a stereo view of the desired macromolecule.

* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X

* [[Show aromatics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for aromatic residues displayed as green "sticks". Usage: Save this as "show_aromatics.pml", load your protein in PyMOL, and run the script (select "Run" from the "File" menu). (PyMOL script; TStout)

* [[Show hydrophobics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophobic residues displayed as orange "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show charged]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for charged residues displayed as red (negative) or blue (posititve) "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show hydrophilic]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophilic residues displayed as green "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show NMR constrains]] -- This script will display the NMR constrains used for a structure calculation atop a structure. Usage: Save this as "NMRcnstr.py" load your protein in PyMOL, and run the script. type upl('fname') or cns('fname') where fname is the filename with the NMR constrains you want to display.

* [[Perp Maker]] -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/[[User:Tree|Tree]])

* [[PythonTerminal]] -- Allows execution of python commands from the PyMOL command line.

* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.

* [[Symmetry Axis]] -- Draw a 3D-CGO line given a point and a direction.

* [[CGO Text]] -- Creates a 3D-CGO text object.

* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).

* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).

* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').

* [[Split Movement]] -- Moves two parts of one object into different directions.

* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.

* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.

* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).

* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''

* [[apropos]] -- List all commands matching a given keyword or whose docs contain the keyword. - ''by EHP''

* [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''

* [[Measure Distance]] -- Measures the distance between two atoms (Python script).

* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.

* [[Color Objects]] -- Colors all objects differently (Python script).

* [[Key Wait]] -- Process key events in a Python script.

* [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)

* [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)

* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)

* [[resicolor]] -- Colors proteins according to residue type.

* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.

* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!

* [[grepsel]] -- Make named selections using regular expressions (protein sequence).

* [[PowerMate Dial OS X]] -- Script and instructions to use the PowerMate dial on Mac OS X.

* [[Plane Wizard]] -- Wizard to draw planes between three picked points.

* [[Slerpy]] -- Pymol command extensions for key frame animation movie making.

* [[Helicity_check]] -- helicity_check show the evolution of O - N distances over an amino acid sequence

* [[Center Of Mass]] -- Given a selection of atoms (of equal weight) - Calculates the center of mass and represents it with a CGO sphere

* [[ss]] -- Simple command to summarise the Secondary Structure as a list of "start-end type" like sses.

* [[iterate_sses]] -- Slightly more complex version of "ss" that allows the user to pass in a function to act on the sse list.

* [[motif]] -- Designed for easy display of backbone motifs (nests, catgrips, etc).

* [[createAtom]] -- Make an atom at a distance along the line of a bond.

* [[pucker]] -- Calculates the sugar pucker information for a given selection

* [[modevectors]] -- A wonderful script that allows you to draw highly customizable vectors between two states (NMA, TMD, etc)

[[Category:Scripting|Script Library]]

Category:Script Library

2009-04-27T16:21:01Z

Jcorn: /* Descriptions */

= Overview =
Here we provide a trove of scripts. The descriptions immediately follow. For the entire category, please see the bottom of this page.

'''Warning the following list is incomplete. For the complete list, see the category table beneath it.'''

= Descriptions =
* [[ObjArrows]] -- Navigate between objects by using the arrow keys

* [[ConnectedCloud]] -- Find connected clouds of objects in PyMOL

* [[FilterByMol]] -- Filter a directory of files, and save their ligands to disk (by molecule).

* [[LoadDir]] -- loads all the files of a type you specify from the path you specify and puts them into the group you specify (or none).

* [[LigAlign]] -- Ligand-based active site alignment and comparison.

* [[ImmersiveViz]] -- A script used in conjunction with head tracking software to provide an immersive virtual experience.

* [[Rasmolify]] -- A work in progress - a script to map Rasmol commands onto the equivalent PyMOL commands.

* [[Zero_residues]] -- Renumber residues such that the first residue is 0. Useful for alignments.

* [[Cealign]] -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.

* [[WriteSS]] -- Writes secondary structural elements, for each residues, to a file.

* [[Process_All_Files_In_Directory]] -- Do something to all files in a directory. The examples show how to print the disulfide bond lengths, then in general all sulfur distances (not necessarily bound).

* [[Kabsch]] -- Kabsch alignment of two sets of vectors. (Part 2 of a protein alignment.)

* [[Transform_odb]] -- Transform a selection of an existing object and output as a new object. The transformation matrix is read from an "O"-style tranformation matrix file (.odb) written by "O" or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.

* [[Stereo_Ray]] -- This script will create two resolution specific ray traced images rotated appropriately for inclusion into a single file to represent a stereo view of the desired macromolecule.

* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X

* [[Show aromatics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for aromatic residues displayed as green "sticks". Usage: Save this as "show_aromatics.pml", load your protein in PyMOL, and run the script (select "Run" from the "File" menu). (PyMOL script; TStout)

* [[Show hydrophobics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophobic residues displayed as orange "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show charged]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for charged residues displayed as red (negative) or blue (posititve) "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show hydrophilic]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophilic residues displayed as green "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show NMR constrains]] -- This script will display the NMR constrains used for a structure calculation atop a structure. Usage: Save this as "NMRcnstr.py" load your protein in PyMOL, and run the script. type upl('fname') or cns('fname') where fname is the filename with the NMR constrains you want to display.

* [[Perp Maker]] -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/[[User:Tree|Tree]])

* [[PythonTerminal]] -- Allows execution of python commands from the PyMOL command line.

* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.

* [[Symmetry Axis]] -- Draw a 3D-CGO line given a point and a direction.

* [[CGO Text]] -- Creates a 3D-CGO text object.

* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).

* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).

* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').

* [[Split Movement]] -- Moves two parts of one object into different directions.

* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.

* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.

* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).

* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''

* [[apropos]] -- List all commands matching a given keyword or whose docs contain the keyword. - ''by EHP''

* [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''

* [[Measure Distance]] -- Measures the distance between two atoms (Python script).

* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.

* [[Color Objects]] -- Colors all objects differently (Python script).

* [[Key Wait]] -- Process key events in a Python script.

* [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)

* [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)

* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)

* [[resicolor]] -- Colors proteins according to residue type.

* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.

* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!

* [[grepsel]] -- Make named selections using regular expressions (protein sequence).

* [[PowerMate Dial OS X]] -- Script and instructions to use the PowerMate dial on Mac OS X.

* [[Plane Wizard]] -- Wizard to draw planes between three picked points.

* [[Slerpy]] -- Pymol command extensions for key frame animation movie making.

* [[Helicity_check]] -- helicity_check show the evolution of O - N distances over an amino acid sequence

* [[Center Of Mass]] -- Given a selection of atoms (of equal weight) - Calculates the center of mass and represents it with a CGO sphere

* [[ss]] -- Simple command to summarise the Secondary Structure as a list of "start-end type" like sses.

* [[iterate_sses]] -- Slightly more complex version of "ss" that allows the user to pass in a function to act on the sse list.

* [[motif]] -- Designed for easy display of backbone motifs (nests, catgrips, etc).

* [[createAtom]] -- Make an atom at a distance along the line of a bond.

* [[pucker]] -- Calculates the sugar pucker information for a given selection

* [[modevectors]] -- A wonderful script that allows you to draw highly customizable vectors between two states (NMA, TMD, etc)

[[Category:Scripting|Script Library]]

Main Page

2007-04-03T20:10:13Z

Jcorn: added info on installing APBS from source

* [[TOPTOC|'''Table of Contents''']]

* [[Special:Allpages|Alphabetized Index of all pages]]

* [[Improvements|Discussion of PyMolWiki Improvements]]
 

== 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 ==
Welcome! New users who wish to contribute appropriate content are welcome to join. Feel free to add any appropriate content; make an account and get started!

==News==
===PyMol===
* [[Cealign|CE Align v0.6]] released. Better than before. See test case comparisons.
* Important bug fixed in [[Cealign|CE Align v0.5]] and [[Kabsch]]. Both updated.
* [[Cealign|CE Align v0.4]], code now available. See the [[Cealign]] page for changes.
* [[Cealign|CE Align v0.1]], code now available. Windows installer coming soon.
* [[Slerpy]], a set of pymol command extensions to simplify complex movie making is now available.
* Updated the [[Kabsch#The_New_Code|Kabsch]] code with a more elegant solution; fixed a small rotation bug.
* 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.
* New cool [[ray]] tracing features added!

===Wiki===
* Added useful mini-script for re-assigning the B Factor column to something new and coloring it.
* captcha system installed.
* If you notice something out of the ordinary, please contact the admin. I updated some software.
* [[Settings]] now contains documentation on:
- helix roundness
- ribbon sampling
- cartoon sampling
- cartoon highlight coloring
- cartoon color blending vs discrete colors
- and more! now 48 documented (with examples); just 470 to go....

* [[SURFNET]] information on reading surfaces from other programs added.
* Two new [[:Category:Plugins|Plugins]] have been added, [[NsSNP Loader]] and [[Proxy Config]].
* Added a page that lists all [[Settings|PyMol settings]]. We need to start documenting these.
* [[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.
** Added info on installing APBS from source

===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!)
* [[Settings|PyMol Settings]] (6 newly documented; only 470 to go...)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

APBS

2007-03-27T21:15:02Z

Jcorn: /* Packaged */

== 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-py24

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.==

APBS

2007-03-27T21:14:42Z

Jcorn: Added instructions for installing APBS from source

== 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-py24

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>

====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.==

Named Atom Selections

2005-02-21T00:48:56Z

Jcorn:

Atom selections can be named for repeated use by using the select command:

<pre>
SYNTAX

select selection-name, selection-expression
# The selection-name and
# the selection-expression
# are both arguments to select
# so they are separated by a comma.

EXAMPLE

PyMOL> select bb, name c+o+n+ca # Create an atom selection named "bb"
# including all atoms named
# "C","O","N", or "CA";
PyMOL> color red, bb # color the selection red,
PyMOL> hide lines, bb # hide the line representation,
PyMOL> show sticks, bb # show it using the stick representation,
PyMOL> zoom bb # and zoom in on it.
</pre>
In this case, the selection-expression is the property selector name, which takes the list of identifiers ca+c+n+o to complete the specification. Property selectors and their identifiers are discussed below.

Named atom selections appear in the PyMOL names list in the control panel. They are distinguished from objects by a surrounding set of parentheses. The control panel options available under the diamond menu differ between objects and atom-selections, because objects and named selections play slightly different roles in PyMOL. Named selections are pointers to subsets of data that are found under an object name. After an object is deleted, the data are no longer available, unless you reload the object. Any named selections that refer to atoms in that object will no longer work. But when named selections are deleted, the data are still available under the object name. Disabling objects eliminates them from the viewer, but disabling named-selections just turns off the pink dots that highlight them in the viewer.

Atom-selections, named or not, can span multiple objects:

<pre>
EXAMPLE

PyMOL> load $PYMOL_PATH/test/dat/fc.pdb
PyMOL> load $PYMOL_PATH/test/dat/pept.pdb

PyMOL> select alpha_c, name ca # The named selection "alpha_c"
# is created -- it includes atoms
# in both "fc" and "pept" objects.
PyMOL> color red, name ca # "CA" atoms in both objects
# are colored red.
</pre>

Named selections will continue working after you have made changes to a molecular structure:

<pre>
EXAMPLE

PyMOL> load $PYMOL_PATH/test/dat/pept.pdb
PyMOL> select bb, name c+o+n+ca # The named selection "bb"
# is created.

PyMOL> count_atoms bb # PyMOL counts 52 atoms in "bb."

PyMOL> remove resi 5 # All atoms in residue 5 are removed
# from the object "pept."

PyMOL> count_atoms bb # Now PyMOL counts
# the remaining 48 atoms in "bb."
</pre>

Named selections are static. Only atoms that exist at the time the selection is defined are included in the selection, even if atoms which are loaded subsequently fall within the selection criterion:

<pre>
EXAMPLE

PyMOL> load $PYMOL_PATH/test/dat/pept.pdb

PyMOL> select static_demo, pept # The named selection "static_demo"
# is created to reference all atoms.

PyMOL> count_atoms static_demo # PyMOL counts 107 atoms
# in "static_demo."

PyMOL> h_add # PyMol adds hydrogens in
# the appropriate places

PyMOL> count_atoms static_demo # PyMOL still counts 107 atoms
# in "static_demo,"
PyMOL> count_atoms # even though it counts 200 atoms
# in "pept."
</pre>

Named selections can also be used in subsequent atom selections:

<pre>
EXAMPLE

PyMOL> select bb, name c+o+n+ca # An atom selection named "bb"
# is made, consisting of all
# atoms named "C","O","N", or "CA."

PyMOL> select c_beta_bb, bb or name cb
# An atom selection named "c_beta_bb"
# is made, consisting of
# all atoms named "C", "O", "N", "CA" or "CB."
</pre>

Note that the word "or" is used to select all atoms in the two groups, "bb" and "cb." The word "and" would have selected no atoms because it is interpreted in its boolean logical sense, not its natural language sense. See the subsection on "Selection Algebra" below.

[[Category:Making Selections]]

Named Atom Selections

2005-02-21T00:48:46Z

Jcorn:

Named Atom Selections

Atom selections can be named for repeated use by using the select command:

<pre>
SYNTAX

select selection-name, selection-expression
# The selection-name and
# the selection-expression
# are both arguments to select
# so they are separated by a comma.

EXAMPLE

PyMOL> select bb, name c+o+n+ca # Create an atom selection named "bb"
# including all atoms named
# "C","O","N", or "CA";
PyMOL> color red, bb # color the selection red,
PyMOL> hide lines, bb # hide the line representation,
PyMOL> show sticks, bb # show it using the stick representation,
PyMOL> zoom bb # and zoom in on it.
</pre>
In this case, the selection-expression is the property selector name, which takes the list of identifiers ca+c+n+o to complete the specification. Property selectors and their identifiers are discussed below.

Named atom selections appear in the PyMOL names list in the control panel. They are distinguished from objects by a surrounding set of parentheses. The control panel options available under the diamond menu differ between objects and atom-selections, because objects and named selections play slightly different roles in PyMOL. Named selections are pointers to subsets of data that are found under an object name. After an object is deleted, the data are no longer available, unless you reload the object. Any named selections that refer to atoms in that object will no longer work. But when named selections are deleted, the data are still available under the object name. Disabling objects eliminates them from the viewer, but disabling named-selections just turns off the pink dots that highlight them in the viewer.

Atom-selections, named or not, can span multiple objects:

<pre>
EXAMPLE

PyMOL> load $PYMOL_PATH/test/dat/fc.pdb
PyMOL> load $PYMOL_PATH/test/dat/pept.pdb

PyMOL> select alpha_c, name ca # The named selection "alpha_c"
# is created -- it includes atoms
# in both "fc" and "pept" objects.
PyMOL> color red, name ca # "CA" atoms in both objects
# are colored red.
</pre>

Named selections will continue working after you have made changes to a molecular structure:

<pre>
EXAMPLE

PyMOL> load $PYMOL_PATH/test/dat/pept.pdb
PyMOL> select bb, name c+o+n+ca # The named selection "bb"
# is created.

PyMOL> count_atoms bb # PyMOL counts 52 atoms in "bb."

PyMOL> remove resi 5 # All atoms in residue 5 are removed
# from the object "pept."

PyMOL> count_atoms bb # Now PyMOL counts
# the remaining 48 atoms in "bb."
</pre>

Named selections are static. Only atoms that exist at the time the selection is defined are included in the selection, even if atoms which are loaded subsequently fall within the selection criterion:

<pre>
EXAMPLE

PyMOL> load $PYMOL_PATH/test/dat/pept.pdb

PyMOL> select static_demo, pept # The named selection "static_demo"
# is created to reference all atoms.

PyMOL> count_atoms static_demo # PyMOL counts 107 atoms
# in "static_demo."

PyMOL> h_add # PyMol adds hydrogens in
# the appropriate places

PyMOL> count_atoms static_demo # PyMOL still counts 107 atoms
# in "static_demo,"
PyMOL> count_atoms # even though it counts 200 atoms
# in "pept."
</pre>

Named selections can also be used in subsequent atom selections:

<pre>
EXAMPLE

PyMOL> select bb, name c+o+n+ca # An atom selection named "bb"
# is made, consisting of all
# atoms named "C","O","N", or "CA."

PyMOL> select c_beta_bb, bb or name cb
# An atom selection named "c_beta_bb"
# is made, consisting of
# all atoms named "C", "O", "N", "CA" or "CB."
</pre>

Note that the word "or" is used to select all atoms in the two groups, "bb" and "cb." The word "and" would have selected no atoms because it is interpreted in its boolean logical sense, not its natural language sense. See the subsection on "Selection Algebra" below.

[[Category:Making Selections]]

Selection-expressions

2005-02-21T00:46:53Z

Jcorn:

Selection-expressions

Selection-expressions stand for lists of atoms in arguments that are subject to PyMOL commands. You can name the selections to facilitate their re-use, or you can specify them anonymously (without names). Object and selection names may include the upper or lower case characters A/a to Z/z, numerals 0 to 9, and the underscore character (_). Characters to avoid include:

! @ # $ % ^ &* ( ) ' " [ ] { } \ | ~ ` <> . ? /

Selection-expressions describe the class of atoms you are referencing. Most of them require identifiers to complete the specification. For example, the selector resi references biopolymer residues by sequence number, and the identifier gives the number. The selector name references atoms according to the names described in the PDB, and the identifier gives the name (ca for alpha carbons, cb for beta carbons, etc). A handful of selection-expressions don't require identifiers, but most do.

PyMOL uses several logical operators to increase the generality or specificity of selection-expressions. Logical combinations of selectors can get complex, so PyMOL accepts short forms and macros that express them with a minimum of keystrokes. This section describes named-selections, and then gives the syntax for making selections in a progression from simple one-word selectors to complex combinations of selectors, using macros and short forms.

[[Category:Making Selections]]

Single-word Selectors

2005-02-21T00:45:09Z

Jcorn: /* Single-word Selectors */

== Single-word Selectors ==

The very simplest ''selection-expressions'' are single-word selectors. These selectors do not take identifiers; they are complete by themselves.

<TABLE BORDER="1">
<TR><TH ALIGN="CENTER">Single Word Selector</TH>
<TH ALIGN="CENTER">Short Form Selector</TH>
<TH ALIGN="CENTER">Description</TH></TR>
<TR><TD ALIGN="CENTER">all</TD><TD ALIGN="CENTER">*</TD><TD>All atoms currently loaded into PyMOL</TD></TR>
<TR><TD ALIGN="CENTER">none</TD><TD ALIGN="CENTER">none</TD>
<TD>No atoms (empty selection)</TD></TR>
<TR><TD ALIGN="CENTER">hydro</TD><TD ALIGN="CENTER">h.</TD>
<TD>All hydrogen atoms currently loaded into PyMOL</TD></TR>
<TR><TD ALIGN="CENTER">hetatm</TD><TD ALIGN="CENTER">het</TD>
<TD>All atoms loaded from Protein Data Bank HETATM records</TD></TR>
<TR><TD ALIGN="CENTER">visible</TD><TD ALIGN="CENTER">v.</TD>
<TD>All atoms in enabled objects with at least one visible representation</TD></TR>
<TR><TD ALIGN="CENTER">present</TD><TD ALIGN="CENTER">pr.</TD><TD>All atoms with defined coordinates in the current state (used in creating movies)</TD></TR>
</TABLE>

The selector '''none''' won't come up much when you are typing commands directly into PyMOL, but it is useful in programming scripts.

As the table shows, many single-word selectors have short forms to save on typing. Some short forms must be followed by a period and a space, in order to delimit the word. Short forms and long forms have the same effect, so choose the form that suits you.

<pre>
PyMOL> color blue, all # It all turns blue.
PyMOL> color blue, *

PyMOL> hide hydro # Representations of all
PyMOL> hide h. # hydrogen atoms are hidden.

PyMOL> show spheres, hetatom # All the atoms defined as HETATOMS
PyMOL> show spheres, het # in the PDB input file
# are represented as spheres.
</pre>

[[Category:Selector Quick Reference]]

[[Making Selections]]

Selection Macros

2005-02-21T00:44:56Z

Jcorn: /* Selection Macros */

==Selection Macros==
===General===
Macros make it possible to represent a long atom selection phrase such as

<pre>PyMOL> select pept and segi lig and chain b and resi 142 and name ca</pre>

in a more compact form:

<pre>PyMOL> select /pept/lig/b/142/ca</pre>

An atom selection macro uses slashes to define fields corresponding to identifiers. The macro is used to select atoms using the boolean "and," that is, the selected atoms must have all the matching identifiers:

<pre> /object-name/segi-identifier/chain-identifier/resi-identifier/name-identifier</pre>

These identifiers form a hierarchy from the object-name at the top, down to the name-identifier at the bottom. PyMOL has to be able to recognize the macro as one word, so no spaces are allowed within it.

Macros come in two flavors: those that begin with a slash and those that don't. The presence or absence of a slash at the beginning of the macro determines how it is interpreted. If the macro begins with a slash, PyMOL expects to find the fields starting from the top of the hierarchy: the first field to the right of the slash is interpreted as an object-name; the second field as an identifier to segi; the third as an identifier to chain, and so on. It may take any of the following forms:

===Macros Beginning With a Slash===
<pre>
/object-name/segi-identifier/chain-identifier/resi-identifier/name-identifier
/object-name/segi-identifier/chain-identifier/resi-identifier
/object-name/segi-identifier/chain-identifier
/object-name/segi-identifier
/object-name

EXAMPLES
PyMOL> zoom /pept
PyMOL> show spheres, /pept/lig/
PyMOL> show cartoon, /pept/lig/a
PyMOL> color pink, /pept/lig/a/10
PyMOL> color yellow, /pept/lig/a/10/ca
</pre>

===Macros Not Beginning With a Slash===
If the macro does not begin with a slash, it is interpreted differently. In this case, PyMOL expects to find the fields ending with the bottom of the hierarchy. Macros that don't start with a slash may take the following forms:
<pre>
resi-identifier/name-identifier
chain-identifier/resi-identifier/name-identifier
segi-identifier/chain-identifier/resi-identifier/name-identifier
object-name/segi-identifier/chain-identifier/resi-identifier/name-identifier

EXAMPLES
PyMOL> zoom 10/cb
PyMOL> show spheres, a/10-12/ca
PyMOL> show cartoon, lig/b/6+8/c+o
PyMOL> color pink, pept/enz/c/3/n
</pre>

===Omitting Fields in a Macro===
You can also omit fields between slashes. Omitted fields will be interpreted as wildcards, as in the following forms:

<pre>
resi-identifier/
resi-identifier/name-identifier
chain-identifier//
object-name//chain-identifier

EXAMPLES
PyMOL> zoom 142/ # Residue 142 fills the viewer.

PyMOL> show spheres, 156/ca # The alpha carbon of residue 156
# is shown as a sphere

PyMOL> show cartoon, a// # Chain "A" is shown as a cartoon.

PyMOL> color pink, pept//b # Chain "B" in object "pept"
# is colored pink.
</pre>

Selection macros must contain at least one forward slash in order to distinguish them from other words in the selection language. Being words, they must not contain any spaces. When using macros, it is also important to understand that they are converted into long form before being submitted to the selection engine. This can help in the interpretation of error messages.

[[Category:Selector Quick Reference]]

[[Category:Making Selections]]

Selection Algebra

2005-02-21T00:44:38Z

Jcorn: /* Selection Algebra */

==Selection Algebra==
===Intro===
Selections can be made more precise or inclusive by combining them with logical operators, including the boolean '''and''', '''or''', and '''not'''. The boolean '''and''' selects only those items that have both (or all) of the named properties, and the boolean '''or''' selects items that have either (or any) of them. Venn diagrams show that '''and ''' selects the areas of overlap, while '''or''' selects both areas.

http://pymol.sourceforge.net/newman/user/S0220venn.jpg

===Selection Operator/Modifier Table===
Selection operators and modifiers are listed below. The dummy variables ''s1'' and ''s2'' stand for selection-expressions such as "chain a" or "hydro."

<TABLE BORDER="1">
<TR><TH ALIGN="CENTER" WIDTH="100">Operator</TH><TH>Short form</TH>
<TH>Effect</TH>
</TR>
<TR><TD ALIGN="CENTER">nots1</TD>
<TD ALIGN="CENTER">!s1</TD>
<TD>Selects atoms that are not included in s1
<pre>PyMOL> select sidechains, ! bb</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> s1 and s2</TD>
<TD ALIGN="CENTER"> s1 & s2</TD>
<TD>Selects atoms included in both s1 and s2
<pre>PyMOL> select far_bb, bb &farfrm_ten</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> s1 or s2</TD>
<TD ALIGN="CENTER"> s1 | s2</TD><TD>Selects atoms included in either s1 or s2
<pre>PyMOL> select all_prot, bb | sidechain</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> s1 in s2</TD>
<TD ALIGN="CENTER"> s1 in s2</TD><TD>Selects atoms in s1 whose
identifiers name, resi, resn, chain and segi all match atoms in s2
<pre>PyMOL> select same_atms, pept in prot</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> s1 like s2</TD><TD ALIGN="CENTER"> s1 l. s2</TD><TD>Selects atoms in s1 whose identifiers name and resi match atoms in s2
<pre>PyMOL> select similar_atms, pept like prot</pre>

</TD></TR>
<TR><TD ALIGN="CENTER"> s1 gap X</TD>
<TD ALIGN="CENTER"> s1 gap X</TD><TD>Selects all atoms whose van der Waals radii are separated from the van der Waals radii of s1 by a minimum of X Angstroms.
<pre>PyMOL> select farfrm_ten, resi 10 gap 5</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> s1 around X</TD>
<TD ALIGN="CENTER"> s1 a. X</TD><TD>Selects atoms with centers within X Angstroms of the center of any atom in s1
<pre>PyMOL> select near_ten, resi 10 around 5</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> s1 expand X
</TD><TD ALIGN="CENTER"> s1 e. X</TD><TD>Expands s1 by all atoms within X Angstroms of the center of any atom in s1
<pre>PyMOL> select near_ten_x, near10 expand 3</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">  s1 within X of s2 </TD>
<TD ALIGN="CENTER"> s1 w. X of s2 </TD><TD>Selects atoms in s1 that are within X Angstroms of the s2
<pre>PyMOL> select bbnearten, bb w. 4 of resi 10</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">byres s1</TD>
<TD ALIGN="CENTER">br. s1</TD><TD>Expands selection to complete residues
<pre>PyMOL> select complete_res, br. bbnear10</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">byobject s1</TD>
<TD ALIGN="CENTER">bo. s1</TD><TD>Expands selection to complete objects>
<pre>PyMOL> select near_obj, bo. near_res</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">neighbor s1</TD>
<TD ALIGN="CENTER">nbr. s1</TD><TD>Selects atoms directly bonded to s1
<pre>PyMOL> select vicinos, neighbor resi 10</pre>
</TD></TR>
</TABLE>

===Examples===
Logical selections can be combined. For example, you might select atoms that are part of chain a, but not residue number 125:

<pre>
PyMOL> select chain a and (not resi 125) # selects atoms that are part of
# chain a, but not
# residue number 125.

PyMOL> select (name cb or name cg1 or name cg2) and chain A # These two
# selections are
PyMOL> select name cb+cg1+cg2 and chain A # equivalent.
# select c-beta's,
# c-gamma-1's and
# c-gamma-2's
# that are
# in chain A.
</pre>

Like the results of groups of arithmetic operations, the results of groups of logical operations depend on which operation is performed first. They have an order of precedence. To ensure that the operations are performed in the order you have in mind, use parentheses:

<pre> byres ((chain a or (chain b and (not resi 125))) around 5) </pre>

PyMOL will expand its logical selection out from the innermost parentheses.

[[Category:Selector Quick Reference]]

[[Category:Making Selections]]

Property Selectors

2005-02-21T00:43:37Z

Jcorn: /* Layout Schema */

Main Page

2005-02-17T20:16:43Z

Jcorn: /* Layout Schema */

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

=== Helping ===
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* A wiki edit/user policy is needed.
* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]
== Section Layout ==
Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.

=== Layout Schema ===
# [[:Category:News|News]]
## [[:Category:Discussion|Discussion]]
## [[:Category:PyMOL Beta|The Bleeding Edge]]
# [[Technical Issues]] (installation, hardware)
## [[Installation]]
### [[OS Dependent]]
#### [[Linux]]
#### [[MAC]]
#### [[Windows]]
# [[Using the GUI]]
## [[Launching PyMOL (has been asked often)]]
## [[Mouse Controls]]
## [[Objects and Selections]]
### [[Working with Objects]]
### [[Working with Selections]]
### [[Selector Quick Reference]]
#### [[Single-word Selectors]]
#### [[Property Selectors]]
#### [[Selection Algebra]]
#### [[Selection Macros]]
### [[Representations]]
#### [[Lines]]
#### [[Sticks]]
#### [[Cartoon]]
#### [[Surface]]
#### [[Mesh]]
#### [[Spheres]]
#### [[Dots]]
### [[Color]]
### [[Displaying biochemical properties]]
## [[Display Settings]]
## [[Stereo 3D Display]]
### [[Hardware Options]]
### [[Linux XFree86 Configuration]]
## [[Scenes]]
## [[Mouse Settings]]
## [[Wizards]]
## [[Plugins]]
## [[Ray-tracing]]
## [[Settings Reference (all settings and what they do)]]
## [[Movies and Animations]]
## [[Structure Alignment]]
## [[Structure Alignment Editor]]
# [[:Category:Commands|Command Language]]
## [[PyMOL Command Script]]
## [[PyMOL Python API]]
# [[Advanced Issues]] (Ray tracing, settings)
## [[Launching PyMOL (has been asked often)]]
## [[Advanced Atom Selections]]
## [[Modeling and editing structures.]]
### [[Editing atoms]]
### [[Molecular sculpting]]
### [[Homology modeling]]
## [[Image Manipulation]]
### [[labels]]
### [[Photoshop/GIMP]]
### [[Stereo Figures]]
### [[Creating publication-quality images HOWTO]]
# [[Scripting]]
## [[Example Scripts]]
## [[Script Library]]
# [[Plugins]]
## [[List of Plugins]]
## [[How to do electrostatics and energy minimization.]]
### [[APBS Plugin]]
## [[rtools Plugin]]
## [[Tutorial on writing plugins]]
## [[Others]]
# [[High-level applications]] (Crystallography, NMR)
## [[Crystallography Applications]]
### [[Symmetry]]
### [[Electron Density]]
## [[NMR Applications]]
### [[Working with a Family of Structures]]
### [[Superimposition and RMSD]]
### [[NMR Restraints Analysis]]
# [[3rd Party Software]]
## [[3rd Party Applications]]
### [[Movies]]
### [[Codecs]]
# [[Python Integration]]
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)
## [[Arbitrary Graphics Objects]]
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----