Molecular Sculpting

2011-04-28T17:11:26Z

Orbeckst: /* What the heck is molecular sculpting? */ reformatted

==What the heck is molecular sculpting?==

Molecular sculpting works like a real-time energy minimizer, except that it isn't minimizing the energy. Instead, its just trying to return local atomic geometries (bonds, angles, chirality, planarity) to the configuration the molecules possess when they were first loaded into PyMOL.

To actually use this feature:

# Load a PDB file.
# Configure the mouse for editing (''Mouse'' menu) or click in the mouse/key matrix box.
# Select ''Sculpting'' from the ''Wizard'' menu. (or: Select ''auto-sculpting'' from the ''Sculpting'' menu.)
# ''Ctrl-middle-click'' on any atom in your protein to activate sculpting. The green part will be free to move. The cyan part will be a fixed cushion to provide context. The grey part will be excluded.
# Now perform any conformational editing operation in the green region such as:
#* ''ctrl-left-click-and-drag'' on an atom
#* ''ctrl-right-click'' on a bond, then ''ctrl-left-click-and-drag'' about that bond.

You can adjust the radius and cushion using the blue pop-up menus.

Right now I'm not sure the sculpting feature is more than entertainment, but my expectation is that it will become part of PyMOL's crystallographic model building system in the future.

[[Category:Modeling_and_Editing_Structures|Molecular Sculpting]]

Mutagenesis

2010-05-17T14:51:10Z

Orbeckst: added sectioning and explanation of colour codes (as found in an email message by WDL)

= Mutagenesis =
PyMol has a '''Mutagenesis Wizard''' to make mutagenesis very easy for the end user.

== Walk-through ==
To mutate a residue follow these easy steps:
<OL>
<LI>Load a PDB file 

[[Image:Mutag1.png|180px|none]]
<LI>Under the '''Wizard''' menu select '''Mutagenesis''' 

[[Image:Mutag2.png|180px|none]]
<LI>In the PyMol viewer window select a residue 

[[Image:Mutag3.png|180px|none]]
<LI>Select '''No Mutation''' and select resultant residue 

[[Image:Mutag4.png|180px|none]]
<LI>Selecting the rotamer you think better fits your structure. 

Several side chain orientations (rotamers) are possible. You can use
the back-and-forth movie controls (lower right corner) to display (in white) each of the rotamers available for
this residue in PyMOL, whose current and total numbers are shown in the (green) Frame info. The rotamers
are ordered according to their frequencies of occurrence in proteins, shown as a red percentage at the mutation
object, which exists while mutagenesis is being performed. 

<LI>Select Apply
<LI>Select Done
</OL>

== Explanation of colour codes ==

From [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06196.html]:

The visible disks & colors in the Mutagenesis Wizard indicate pairwise overlap of atomic van der Waals radii. The intent is to provide a qualitative feedback regarding contacts and bumps.

Short green lines or small green disks are shown when atoms are almost in contact or slightly overlapping. Large red disks indicate signficant van der Waals overlap. Everything else lies between those extremes.

[[Category:Tutorials|Mutagenesis]]

Ls

2010-05-15T23:02:03Z

Orbeckst: typo corrected

'''ls''' lists contents of the current working directory. PyMOL comes with a few commands that allows the user to traverse a directory structure and list files. This is a powerful tool if you have many directories full of files --- you don't have to quit PyMOL, you can just '''cd''' to the directory and '''ls''' to find the contents.

===USAGE===
<source lang="python">
ls [pattern]
dir [pattern]
</source>

===EXAMPLES===
<source lang="python">
# list all files in the current directory
ls

# list all files ending in, pml, in the current directory.
ls *.pml
</source>

===SEE ALSO===
[[Cd]], [[Pwd]], [[System]]

[[Category:Commands|Ls]]

MAC Install

2010-05-15T22:56:02Z

Orbeckst: pymol is also in MacPorts; also reformatted trouble shooting to use definition lists

[[Category:Installation|Mac]]

__TOC__

=Installing MacPyMOL=
===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.

----

===PyMOL and Fink===
Fink is a subsystem that was created to bring the full power of Linux open-source to the Darwin (Apple) platform. It is essentially a full working Linux system integrated with the Apple OS. Even X11 applications can be run. To use PyMOL with fink, you will first need to install [http://fink.sourceforge.net/ fink]. This usually takes a while, but is straightforward.

Once fink is installed, you have two options: (1) use the PyMOL package setup by [[User:wgscott|wgscott]], which might be old, but easier to install; or, download the PyMOL source and build. As usual, it comes down to ease of install vs. new features.

==== PyMOL Directly from Fink ====
To install PyMOL directly from fink, type:
<source lang="bash">
fink install pymol-py25
</source>

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.

=====Notes and Possible Issues =====
* 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:
<source lang="bash">
sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.
</source>
You might need to create the latter directory if it doesn't already exist, i.e., issue the command
<source lang="bash">
sudo mkdir -p /sw/fink/dists/local/main/finkinfo
</source>
* 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:
<source lang="bash">
export DISPLAY=":0.0"
</source>
Do NOT set the DISPLAY variable for 10.5+, as God does this for you automatically. If for some reason you don't want to set DISPLAY, launch X11 manually (Applications/Utilities) then start a login shell with 'xterm -ls' (note default xterm is not a login shell so will not read .bashrc) and finally issue 'pymol'
* Fink pymol also reads ~/.pymolrc in your home directory.
* 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.

==== PyMOL Install from Source, Using Fink ====
If the above didn't work, of you really want the latest PyMOL code, then
* Download the latest PyMOL source and unpack it.
* Ensure that you have installed, in Fink:
** python-2.5 pmw-py25
** mesa mesa-shlibs
** libpng3 libpng3-shlibs
** freetype2 freetype2-deve
** freeglut freeglut-shlibs
* Change directory into the new PyMOL dir, eg. ''cd pymol''
* Then, install PyMOL with,
<source lang="bash">
/sw/bin/python setup.py install
</source>

=====Notes and Possible Issues=====
* If you get an error about '''-Wno-long-double''' then your gcc is mismatched. I fixed this by pointing the symbolic link ''/usr/bin/gcc'' from ''/usr/bin/gcc-4.2'' to ''/usr/bin/gcc-4.0''. Or, in code,
<source lang="bash">
# These command are commented out to stop people from copy/pasting b/c
# these are possibly dangerous for your system. Ensure that /usr/bin/gcc
# is a symbolic link and not a real binary. If so, I used the following
# to fix the -Wno-long-double error.
# sudo rm /usr/bin/gcc
# sudo ln -s /usr/bin/gcc-4.0 /usr/bin/gcc
</source>
* If you get an error about something like ''GL_PALETTE_TEXTURE'' then you need to comment out those few lines in the code that throws the error. Read the output.

====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-openmpi 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.

===PyMOL in MacPorts===

Recent versions of [http://www.macports.org/ MacPorts] (at least 1.8.2) also include a hybrid PyMOL and also apbs. One can install it with
sudo port install pymol apbs apbs-mpi

===Troubleshooting===

; When selecting atoms with the mouse, no matter how well one aims, the atoms selected are actually those far from the ones wanted: This is a known problem. Select "Millions of Colors" in '''System Preferences->Display'''.
; There seems to be a race condition between the Tk window and the openGL window. (The focus for the windows are very quickly flashing back and forth.): This is a well-known problem. The blame here is circular: Apple blames developers, developers blame Apple. Regardless, it appears to have been fixed with the latest Mac OS X (10.6) release. Upgrade to 10.6 and this problem goes away.
;When using multiple displays, the OpenGL window flickers; moving the window between displays crashes the whole session [https://trac.macports.org/ticket/24895]: If you don't need stereo then start PyMOL in mono mode with <pre>pymol -M</pre>If you need stereo then you probably need to wait for a fix in the graphics driver.

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

PyMOL Wiki - User contributions [en]

Molecular Sculpting

Mutagenesis

Ls

MAC Install