PyMOL Wiki - User contributions [en]

Talk:Plane Wizard

2011-06-07T20:30:42Z

Baker1:

I tried this out - it's pretty neat - good job!

Two minor comments:
- any plane created goes away when exiting the wizard. Is this intended?
- I found a typo in the code (spacing) on line 112 & corrected it

Hmm. For my purposes when I made it, cleaning up on exit was the right thing to do, but I guess other people might want it not to. Wizards are a little too simple for preferences...

If I ever manage to make plugins on OSX, then a plane (or geometry!) plugin would be more flexible.

---------------
So, if we don't want the planes to be removed on exit, how do we edit the code to prevent this?

Talk:Fog

2011-03-25T15:40:59Z

Baker1: Created page with "Perhaps this has a new function in v1.4? It looks like this actually controls fog thickness. So, "set fog_start,0.2" and "set fog, 0.8" makes a scene that has the fog starting ..."

Perhaps this has a new function in v1.4? It looks like this actually controls fog thickness. So, "set fog_start,0.2" and "set fog, 0.8" makes a scene that has the fog starting close to the camera, but the background does not fade into the background color completely.

Talk:Depth cue

2011-02-09T15:55:29Z

Baker1: Created page with "what is the difference between this setting and "fog"?"

what is the difference between this setting and "fog"?

Talk:Mutagenesis

2010-09-27T20:07:42Z

Baker1: Created page with '=== Questions === Any chance we could get bases added to the mutagenesis package in the next version?'

=== Questions ===
Any chance we could get bases added to the mutagenesis package in the next version?

Extend

2010-08-25T16:05:23Z

Baker1:

[[Extend]] is an API-only function which binds a new external function as a command into the PyMOL scripting language. In other words, when you write a function and want PyMOL to recognize the new command, you '''extend''' the command into PyMOL. Once extended, the function name is recognized like other function names (example below). Typically, '''extend''' is the last line of a PyMOL script.

===PYMOL API===
<source lang="python">
cmd.extend(string name,function function)
</source>

===PYTHON EXAMPLE===
<source lang="python">
def foo(moo=2): print moo
cmd.extend('foo',foo)
</source>

The following would now work within PyMOL:
<source lang="python">
PyMOL>foo
2
PyMOL>foo 3
3
PyMOL>foo moo=5
5
PyMOL>foo ?

Usage: foo [ moo ]
</source>

===NOTES===
For security reasons, new PyMOL commands created using "extend" are not saved or restored in sessions.

===SEE ALSO===
*[[Alias]]
*[[Api]]
*[[Category:Scripting]]

[[Category:Commands|Extend]]

<hr>
=== "extend" used in selections ===
"extend" can also be used in selection statements to grow a selection based on covalent bonds. This behavior is illustrated on residue 64 of PDB file 1KAO where we initially select one atom and then "extend" that selection by one and three covalent bonds.

<table border="1">
<tr>
<td>[[Image:Extend0.png|250px]]</td>
<td>[[Image:Extend1.png|250px]]</td>
<td>[[Image:Extend3.png|250px]]</td>
</tr>
<tr>
<td>select (resi 64 and n. cz)</td>
<td>select (resi 64 and n. cz) extend 1</td>
<td>select (resi 64 and n. cz) extend 3</td>
</tr>
</table>
<hr>

File:Extend3.png

2010-08-25T16:02:33Z

Baker1: select (1kao and resi 64 and n. cz) extend 3

select (1kao and resi 64 and n. cz) extend 3

File:Extend1.png

2010-08-25T16:02:20Z

Baker1: select (1kao and resi 64 and n. cz) extend 1

select (1kao and resi 64 and n. cz) extend 1

File:Extend0.png

2010-08-25T15:59:58Z

Baker1: select (1kao and resi 64 and n. cz)

select (1kao and resi 64 and n. cz)

Fetch

2010-05-04T21:30:18Z

Baker1:

'''Fetch''' retrieves a protein structure from the PDB and loads it into PyMOL. The PDB file is saved in the current working directory for PyMOL.

You can now fetch electron density maps using ''type=fofc'' or ''type=2fofc''. The map will be loaded if the electron density map exists on the [http://eds.bmc.uu.se/eds/ EDS] server.

=== Syntax ===
<source lang="python">
fetch PDB_ID [ ID2...IDN ] [, async = [0,1] , [ type=[fofc,2fofc] ]
</source>

To specify more than one PDB, just add its ID to the command line (without adding spaces).

=== Example ===
<source lang="python">
# fetch them singly
fetch 1kao
fetch 1ctq

# fetch them at once
fetch 1kao 1ctq

# fetch them at once, load them into PyMOL all at once (synchronously)
fetch 1kao 1ctq, async=0

# Example loading a protein and its electron density map
fetch 1cll
fetch 1cll, type=2fofc
# focus on residues 30-40
map_trim *, i. 30-40, 4
zoom i. 30-40
</source>

=== Example 2 ===
<source lang="python">
# fetch PDB files and process each of them
# using async=0, PyMOL will wait for fetch to finish before executing the next command
fetch 1kao, async=0
remove not (alt ''+A)
alter all, alt=''
save 1koa_clean.pdb,1koa
delete 1koa
fetch 1ctq, async=0
remove not (alt ''+A)
alter all, alt=''
save 1ctq_clean.pdb,1ctq
</source>

= See Also =
[[Fetch_Path]], [[Fetch_Host]]

[[Category:Commands|Fetch]]

Fetch

2010-05-04T21:29:46Z

Baker1:

'''Fetch''' retrieves a protein structure from the PDB and loads it into PyMOL. The PDB file is saved in the current working directory for PyMOL.

You can now fetch electron density maps using ''type=fofc'' or ''type=2fofc''. The map will be loaded if the electron density map exists on the [http://eds.bmc.uu.se/eds/ EDS] server.

=== Syntax ===
<source lang="python">
fetch PDB_ID [ ID2...IDN ] [, async = [0,1] , [ type=[fofc,2fofc] ]
</source>

To specify more than one PDB, just add its ID to the command line (without adding spaces).

=== Example ===
<source lang="python">
# fetch them singly
fetch 1kao
fetch 1ctq

# fetch them at once
fetch 1kao 1ctq

# fetch them at once, load them into PyMOL all at once (synchronously)
fetch 1kao 1ctq, async=0

# Example loading a protein and its electron density map
fetch 1cll
fetch 1cll, type=2fofc
# focus on residues 30-40
map_trim *, i. 30-40, 4
zoom i. 30-40
</source>

=== Example 2 ===
<source lang="python">
# fetch PDB files and process each of them
# using async=0, PyMOL will wait for fetch to finish before executing the next command
fetch 1kao, async=0
remove not (alt ''+A)
alter all, alt=''
save 1koa_clean.pdb,1koa
delete 1koa
fetch 1ctq, async=0
remove not (alt ''+A)
alter all, alt=''
save 1ctq_clean.pdb,1ctq

= See Also =
[[Fetch_Path]], [[Fetch_Host]]

[[Category:Commands|Fetch]]

Ideas

2010-01-20T17:40:18Z

Baker1:

=== Ideas for PyMOL Development ===

This page was originally developed for the 2008 Google Summer of Code competition, but seeing as PyMOL wasn't selected, this page can instead serve as a resource for ongoing PyMOL development efforts.

== Where to Start ==

Always start with Python and only delve down into the C code when absolutely necessary. Although PyMOL is mostly a C-based application, much of the that code is opaque, fragile, and unforgiving. Although C code refactoring is an important project goal, such work may not be ideal since once mistake could potentially to destabilize the entire platform.

Fortunately, the Python interpreter and the PyMOL command and selection languages make it possible to extend PyMOL safely and quickly. Even when performance is critical, Python should be the interface between external C, C++, and Java code and PyMOL's internal C data structures.

== Choosing a Topic ==

The best open-source code is usually written by an end-users attempting to meet their own pressing needs. So if you have already have a specific need which relates to PyMOL, then we strongly encourage you to follow up on that first!

If you are looking for ideas, then try to seek out enhancements and/or integrations that will impact the largest potential user base. For example, imagine what new things might be useful to virtually all medicinal chemists, all structural biologists, all movie-makers, all paper-writers, and so forth.

The ideas below are organized by category. Right now, integration with other open-source projects seems like the approach most likely to yield significant benefit, so those ideas are first.

== Integration Ideas (Linking Out to Useful Open-Source Tools) ==

In most cases, depending on the need, integration can be accomplished through standalone Python scripts, through new PyMOL commands, through PyMOL Wizards, or via Tkinter plugins.

* APBS (electrostatics calculations): Improve the existing plugin. Michael Lerner is currently leading this effort. See [[APBS]]
* RDKit (cheminformatics, depiction, UFF cleanup, etc.): Lots of potential here, however C++ coding may be necessary for more advanced integration tasks. [http://www.rdkit.org RDKit home]
* GIMP (image manipulation): Streamline & document the process of exporting images from PyMOL into GIMP and preparing them for submission to scientific Journals.
* Jmol (publishing visualizations inside of web pages): Liason between PyMOL & Jmol projects to develop a shared molecular visualization data model compatible with both applications.
* Firefox (plugin): Develop an PyMOL plugin compatible with Firefox.
* MMTK (molecular mechanics -- Python/flexible): Develop the ability to round-trip molecular systems from PyMOL, into MMTK, and back.
* GROMACS (molecular mechanics -- C/fast) - Maybe some ideas can be shared with this guy. [http://www.kde-apps.org/content/show.php/Gromacs+GUI+?content=47665 Gromacs GUI]
* OpenOffice (escape Microsoft hegemony): Develop an PyMOL plugin.
* IPython integration (interactive shell): a robust alternative to the PyMOL command line?
* R (statistics): PyMOL a 3D viewer environment for visualizating & manipulating large statistical data sets?

Are there other key open-source packages we might specifically target for integration with PyMOL, either through GSoC or beyond?

== High-Level Enhancement Ideas (Mostly Python-oriented) ==

* Work on [[#More Ideas (Please add your own!)| MolViz]]
* Develop new plugins which automate routine tasks.
* Improve the Python API documentation.
* Flesh out the new "from pymol2 import PyMOL" instance-based PyMOL API.
* Develop alternate Tkinter "skins" (for custom OEM-like applications).
* Develop a Tkinter/TOGL widget which holds a PyMOL viewer instance.
* Develop a PyQt widget which holds a PyMOL viewer instance.
* Create a plugin-manager GUI in the style of Firefox, Rythmbox, Gedit, Eclipse. A GUI where it is easy to turn off/on plugins, configure them and see help-contents for them. Maybe also some way to paste a url to install a new Plugin.
* Add a plugin for a GUI window with the same functionality as the "Control Panel" window in SwissPDB Viewer.
* Extend and modify the PyMOL command language so as to be compatible with existing RasMol and/or Jmol scripts.
* Enhance the Mutagenesis Wizard in order to support Nucleic acids and/or Sugars.
* Streamline the process of creating movies out of Scenes.

== Low-Level Enhancement Ideas (Mostly C-oriented) ==

* Enable editing of displayed sequence alignments.
* Add multi-line textual annotations
* Support additional annotation object including: arrow, lines, and blobs.
* Add display of secondary structure into the sequence viewer.
* Enable per-object Z clipping (especially in the ray tracer)
* Hilite H-bonds, salt bridges, Pi-stacking, Pi-cations, etc.
* Build in a simple forcefield and energy minimizer suitable for use with Mutagenesis.
* Incorporate a suite of standard NMR visualizations (restraint violations, per-residue RMS, etc.)
* Enumeration and display of low-energy conformers.
* Automated structure grafting (poor-man's homology modeling).
* Import of alignment files.
* Implement IMD (Interactive Molecular Dynamics) Interface, see http://www.ks.uiuc.edu/Research/vmd/imd/

== Difficult C-level Code Refactoring Ideas ==

* Assemble a test suite which thoroughly exercises the existing code (a prerequisite to major refactoring).
* Catch & handle memory-allocation failures gracefully (instead of crashing).
* Replace PyMOL's memory management & custom containers with a simple runtime object model.
* Separate the View and the Controllers from the Model so that they can all run asynchronously (on multiple cores).
* Enable generalized undo of changes made to the Model.
* Clean up the internal matrix handling code.

== Ideas Involving Proprietary APIs ==

Since these involve closed-source APIs and infrastructure, they aren't suitable for open-source development efforts. However, such requests are noted here for the sake of complete coverage.

* Create a Windows port with "native" look & feel. <- Could this be done in PyQT or PyGTK?. Then it would look "native", but be cross-platform and not proprietary.
* Integrate directly via Mathematica via MathLink.
* Further enhance JyMOL (Java-JNI/wrapped PyMOL)
* Integrate with Matlab.

== More Ideas (Please add your own!) ==
* [http://molviz.cs.toronto.edu/molviz MolViz] is a project to incorporate head tracking input into [http://pymol.sourceforge.net/ PyMol]. This is accomplished through a [[ImmersiveViz]] script written in Python to control the molecule's position using the existing [http://www.pymolwiki.org/index.php/Category:Commands PyMol API]. Related projects would include:
** Improving the existing [[ImmersiveViz]] PyMol plugin for more precise control of the environment.
** Developing new input drivers for the Wiimote form of control. This would require some bluetooth hacking.
** Implementing some other forms of input for head tracking, such as fisheye head tracking, IR webcam tracking, etc (refer to the end of this [[http://www.youtube.com/watch?v=ncShaY4VSac video]] for a better description).
* Provide a 2D chemical depiction of the current 3D view.
* Spreadsheet view with additional information (e.g. IC50's).
* Create additional documentation, screen casts, & tutorials.
* Export 3D PDF images.
* <strike>Add extra "Single Word Selectors" like "nucleic", "protein", "water", "ions", "backbone" (for nucleic acids or proteins), "mainchain", "sidechain"</strike>
* Add functionality that allows you to select atoms based on their location (i.e. select (x_coordinate < 10) and (z_coordinate > 0))
* set pdb_mirror option to use PDB mirrors other than RCSB for fetching structures (PDBe, PDBj); the EBI mirror is much faster from Europe for example.
* have the ability to link the TK console to the viewer so that users don't have to constantly alt+tab between what they want
* have the ability to disable typing in the viewer and automatically type in the TK console (I like being able to cut/paste/home/end)
* I see a lot of "can pymol do this" threads - any ideas of a good UI for a page of "things PyMOL can do?"
* make an option where I can turn on a coordinate grid - perhaps an object that is a cuboid grid around any object in the view so I can still alter how it's rendered?

Ideas

2010-01-20T17:38:07Z

Baker1:

Ideas

2010-01-20T06:12:24Z

Baker1:

Talk:Ray

2009-10-05T23:34:22Z

Baker1:

== Thums in gallery ==

I've updated images (from performance part). But now the thumbs are not showing. What's wrong?
[[User:Davidov|Davidov]] 05:05, 13 March 2008 (CDT)

== Performance images ==

I loaded them with an image processing program. The images are offset outside of the viewable area. Please remake these images and try again. If this keeps happening you may have found a bug. [[User:Inchoate|Tree]] 07:57, 13 March 2008 (CDT)

:Thanks. It seems to be viewable area issue. [[User:Davidov|Davidov]] 05:47, 15 March 2008 (CDT)

== Cool idea ==

A script to automate this task would be really cool:

One of my tricks is to only show part of the structure at a time, ray each part individually
and the reassemble them in Photoshop. I do this all the time with the huge multi protein PyMol
sessions I have to work on. It depends on your orientation in the viewer though, be careful to
not cut anything off. With the ribo ou can hide the large or the small subunit, render each
separately, and then reassemble.

== surface outlines ==
I was wondering if folks could give tips on using 'set ray_trace_mode,1' with surface representations. Because of the contours involved you get black lines all over the surface, rather than just around the visible "edges." Inflating B-factors helps some. Any ideas as to how to improve these? [[User:Baker1|Baker1]]

User:Baker1

2009-09-03T16:41:55Z

Baker1:

I am a Ph.D. student in biophysics and bioinformatics (BCB). You can learn more about BCB at Iowa State University at the following:

<ul>
<li> [http://www.bioinformatics.iastate.edu/ L. H. Baker Center] </li>
<li> [http://www.bcb.iastate.edu/index.html BCB at ISU] </li>
<li> [http://lab.bcb.iastate.edu/ BCB Lab] </li>
</ul>

My personal web page is [http://michaelz.public.iastate.edu/ here].

User:Baker1

2009-09-03T16:41:09Z

Baker1:

Talk:Cealign

2009-09-03T16:39:00Z

Baker1:

The numpy zip file provided in the Windows section unzips with fatal errors.

Sean

: And the instructions to download NumpPy from sourceforge and install the folder into the /PyMol/modules/ folder result in an error when numpy is called (numpy shouldn't be called outside the source folder - apparently it needs to be called from inside the folder?) [I used Numpy-1.2.1.tar.gz - maybe I need to use the superpack installer?] [[User:Jedgold|Jedgold]] 17:41, 17 July 2009 (UTC)

:: I have no idea why it unzips with errors for some users! I am able to download an unzip it just fine on my Windows Vista (32-bit) system... Did you try downloading by doing 'Right click > Save As' and then opening the file using a third-party program like 7-zip from 7-zip.org ?? --[[User:Shiven|shiven]] 18:47, 17 July 2009 (UTC)

:: I wrote Cealign, but didn't do the Win32 packages. If I need to I can re-tar the files and provide that to folks (still attributing) Shiven, of course. [[User:Inchoate|Tree]] 23:28, 17 July 2009 (UTC)

== Disparity in description of first pair of figures ==

The atom count and rmsd value are different between the figure caption and the text in the preceding paragraph. This doesn't really have any effect on the message, but should be fixed by whomever posted the images.

-JMS

Thanks
[[User:Inchoate|Tree]] 17:54, 25 August 2009 (UTC)

== Return the residues used in the alignment ==

Is it possible to have cealign or fit return the residue (or atom) induces that it used in the fitting? By default it does tell you how many it used, so you can make a scanning window of that size and iterate through the sequences with align until you get the same answer, but that is pretty annoying to do (in my opinion). If I want the induces it decided to use, how do I get those printed out?
[[User:Baker1|Baker1]]

Talk:Line width

2009-08-06T18:15:34Z

Baker1:

I was wondering if it's possible to change the line_width for a selection. Say I want to have two line representations, one with most of a molecule at line_width,2 and a selection at 4, say. Doing the same with a sticks representation would be fine too if that's easier.

As of this writing, I can set different line_width values to different objects/selection, but it doesn't seem to make a difference.

Will update soon.

[[User:Inchoate|Tree]] 18:56, 6 July 2009 (UTC)

'''Update'''

You can do this in PyMOL. Do
<source lang="python">
set_bond line_width, 5, i. 1-10
</source>

The line that connects two atoms in PyMOL is bond, so use set bond.

=== question ===
what version of PyMol allows the functionality of set_bond? I have 0.99rc6 and when I run your examples using set_bond and variants of them I receive either "SyntaxError: invalid syntax" or "NameError: name 'set_bond' is not defined."

Talk:Line width

2009-08-06T18:01:48Z

Baker1:

I was wondering if it's possible to change the line_width for a selection. Say I want to have two line representations, one with most of a molecule at line_width,2 and a selection at 4, say. Doing the same with a sticks representation would be fine too if that's easier.

As of this writing, I can set different line_width values to different objects/selection, but it doesn't seem to make a difference.

Will update soon.

[[User:Inchoate|Tree]] 18:56, 6 July 2009 (UTC)

'''Update'''

You can do this in PyMOL. Do
<source lang="python">
set_bond line_width, 5, i. 1-10
</source>

The line that connects two atoms in PyMOL is bond, so use set bond.

---
what version of PyMol allows the functionality of set_bond? I have 0.99rc6 and when I run your examples using set_bond and variants of them I receive either "SyntaxError: invalid syntax" or "NameError: name 'set_bond' is not defined."

Category:FAQ

2009-07-17T04:13:52Z

Baker1:

==Overview==
Please post your FAQs here. I suggest you write a Q&A style list with a short answer. More involved answers should link to its own page. Just my suggestion. Should we have topics? Please note, not all AQ are FAQ. Also, many answers to frequently recurring problems are probably best sought by searching for your terms in the Wiki.

===Installation===
Q: I've installed PyMol_0_98, and recently my structures have stopped displaying. I've tried uninstalling PyMol_0_98 and installing PyMol_0_97, and yet i've ran into the same problem...my .pdb files no longer display, although it is evident that they are being loaded and I can edit them.

Does anybody have any clue as to what might be the problem?
Thanks, shebsmehr

----
===Startup===
Q: I've installed PyMol_0_98 correctly but I can't open my files in .mol2 or .pdb format from the menubar. Instead I can open them with the program. I can't even save the images I create in PyMol and obviously the mivie too.

Could you help me to solve these problems.
Thanks
Vittorio

A1: Vittorio, if I understand you correctly, then you need to (a) make sure you have the PDB file on your machine, say Desktop (or home directory, for *nix), then in the GUI click on, "File"->"Open" then use the dialog to find the file you want to load. You can save time if you know where the file is by just using PyMol's "load" command
load fileName, objectName
loads the fileName into a new object called objectName, for example,
load /tmp/1ggz.pdb, 1ggz

See [[Cmd load|load]],

A2: To save images you have a couple options. First, to save a quick raw screen dump type, "png fileName" to save a PNG image (IE and other programs can view these files). Or, secondly, if you prefer a higher quality image with ray-traced shadows and textures you can do, "ray" then, the above "png" command.

See [[Cmd ray|ray]], [[Cmd png|png]], [[:Category:Using_Pymol|Using PyMol]]

Hope this helps. If it didn't please restate your question to make it more clear.
----
Q: Hi I have a problem. For some reason PyMOl do not display certain areas (several loops) of my .pdb file (1DAN) when in cartoon. When I display the structure in "lines" or "sticks" everything is ok. Furthermore, other .pdb viewers dont have this problem. I have tried several things:
1. Upgraded to the newest version og PyMol.
2. Redefined secondary structure using the "alter command".
3. Imported the .pdb file into SwissViewer, saved as the imported structure as a .pdb file, and then imported into PyMOl.

None of these things have solved the problem. Help please! (I would hate to have to start using another pdb-viewer!!)
Cheers
Kasper

----

Q: Can the startup settings be edited so that MacPyMol starts with a One-Button Mouse mode? Please advise.
A: echo "config_mouse one_button" >> ~/.pymolrc

----
Q: What I should write into the .pymolrc (Mandriva Linux) to be able open PyMol with .pdb or .pml from shell? I was able to run pymol *.pdb with old 0.99rc6 version, but then I upgraded Mandriva Linux and this option is not working anymore.

===Settings===
Q: I am wondering how to change the default settings for a color "spectrum". I would like to color by b-factor but not with the default spectrum but from white-to-red.

A: See [[Color#Color_by_Spectrum_Example]].
----
Q: I would like the distance labels generated with the 'distance' command to be single-digit only, e.g. 2.8 instead of 2.77. How can I do this? Thanks, MindFrog

A: Setting startup settings and python commands can be done in a file: ~/.pymolrc
E.g. command in there: cmd.set('label_distance_digits',1)
On my windows machine this is in C:\Documents and Settings\jurgen.WHELK.000\.pymolrc
===Commands===
Q: I want to move one object while keeping another fixed. How do I do this?

A: Load the proteins as separate objects, put the mouse into 3-button editing mode, then shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. (Warren DeLano answer)
----
Q: I'd like to select residues that are in contact with a surface, or else be able to select buried/non-buried residues, is there any way to do this ? [[User:Xevi|Xevi]] 03:52, 16 Jun 2006 (CDT)
: I'm also looking for this (e.g. to see available lysines' -NH2 or cysteines' -SH on the surface), could one maybe cover the protein with an additional layer of new atoms, and then select all protein atoms close to these? Edit: there is now a simple solution for proteins displayed as non-transparent surfaces: [[Displaying_Biochemical_Properties#Residues_with_functional_groups]] -- [[User:Moino|moino]] 19:35, 7 October 2008 (CDT)
----
Q: After using the usual mset command to rotate an object, states/frames are loaded into that object. However, using the "frame" command has odd behaviour (in comparison to loading a molecular dynamics trajectory into the state in which the "frame" command behaves normally). Can anyone explain this?

----

Q: How do I suppress the 'ExecutiveRMS' output while running cmd.pair_fit()?

----

Q: How does cmd.rms() choose a mapping between atoms in the selections? Exhaustive search over all possibilities?

----
Q: How do I select (especially, iterate through a set of) bonds? The existence of [http://www.pymolwiki.org/index.php/Cycle_Valence cycle valence] seems to imply that it can be done. Is this possible via the API?
----

===Export/Import===
Q: Is there any way to export PyMol models onto CAD standards (autocad, archicad) or 3D modeling software (blender, 3DStudio, Maya)? Thanks a lot.
----
Q: I am doing some MD simulations using CHARMM (not AMBER) and would like to visualize the .dcd files output by CHARMM. I understand that PyMol can open .trj files from AMBER but is there a way to open up these .dcd files and if not, are there any plans to implement this? Thank you for your time!

A: Answering my own question here. See: [[Load_Traj]]

===Others===
Q: I was wondering what the percentage given under the mutengensis wizard means? Thanks...
----
Q: Some of the bases in RNA helices are missing (not all in any given helix) when I am showing them in the CARTOON mode. How should I set it to get them shown? I tried the Secondary Structure Assignment commands, they did not work.
----
Q: Why does PyMol run version 2.3 of Python when I have Python 2.5 installed? How do I tell it to switch?
----
Q: How do I cite PyMOL?

A: DeLano, W.L. The PyMOL Molecular Graphics System. (2008) DeLano Scientific LLC, Palo Alto, CA, USA. http://www.pymol.org

----
Q: What is the status of the VMD plugin for Pymol? How does one install it? Is it installed by default? Will it appear in the plugins list? I compiled from source and changed several configuration files, but I cant't seem to be able to get the VMD plugins working properly. Thanks!

----
Q: If I want to ask a question to the PyMol Wiki community, how do I do that? Is there a page for PyMol usage questions?

Category:FAQ

2009-07-17T04:13:15Z

Baker1:

==Overview==
Please post your FAQs here. I suggest you write a Q&A style list with a short answer. More involved answers should link to its own page. Just my suggestion. Should we have topics? Please note, not all AQ are FAQ. Also, many answers to frequently recurring problems are probably best sought by searching for your terms in the Wiki.

===Installation===
Q: I've installed PyMol_0_98, and recently my structures have stopped displaying. I've tried uninstalling PyMol_0_98 and installing PyMol_0_97, and yet i've ran into the same problem...my .pdb files no longer display, although it is evident that they are being loaded and I can edit them.

Does anybody have any clue as to what might be the problem?
Thanks, shebsmehr

----
===Startup===
Q: I've installed PyMol_0_98 correctly but I can't open my files in .mol2 or .pdb format from the menubar. Instead I can open them with the program. I can't even save the images I create in PyMol and obviously the mivie too.

Could you help me to solve these problems.
Thanks
Vittorio

A1: Vittorio, if I understand you correctly, then you need to (a) make sure you have the PDB file on your machine, say Desktop (or home directory, for *nix), then in the GUI click on, "File"->"Open" then use the dialog to find the file you want to load. You can save time if you know where the file is by just using PyMol's "load" command
load fileName, objectName
loads the fileName into a new object called objectName, for example,
load /tmp/1ggz.pdb, 1ggz

See [[Cmd load|load]],

A2: To save images you have a couple options. First, to save a quick raw screen dump type, "png fileName" to save a PNG image (IE and other programs can view these files). Or, secondly, if you prefer a higher quality image with ray-traced shadows and textures you can do, "ray" then, the above "png" command.

See [[Cmd ray|ray]], [[Cmd png|png]], [[:Category:Using_Pymol|Using PyMol]]

Hope this helps. If it didn't please restate your question to make it more clear.
----
Q: Hi I have a problem. For some reason PyMOl do not display certain areas (several loops) of my .pdb file (1DAN) when in cartoon. When I display the structure in "lines" or "sticks" everything is ok. Furthermore, other .pdb viewers dont have this problem. I have tried several things:
1. Upgraded to the newest version og PyMol.
2. Redefined secondary structure using the "alter command".
3. Imported the .pdb file into SwissViewer, saved as the imported structure as a .pdb file, and then imported into PyMOl.

None of these things have solved the problem. Help please! (I would hate to have to start using another pdb-viewer!!)
Cheers
Kasper

----

Q: Can the startup settings be edited so that MacPyMol starts with a One-Button Mouse mode? Please advise.
A: echo "config_mouse one_button" >> ~/.pymolrc

----
Q: What I should write into the .pymolrc (Mandriva Linux) to be able open PyMol with .pdb or .pml from shell? I was able to run pymol *.pdb with old 0.99rc6 version, but then I upgraded Mandriva Linux and this option is not working anymore.

===Settings===
Q: I am wondering how to change the default settings for a color "spectrum". I would like to color by b-factor but not with the default spectrum but from white-to-red.

A: See [[Color#Color_by_Spectrum_Example]].
----
Q: I would like the distance labels generated with the 'distance' command to be single-digit only, e.g. 2.8 instead of 2.77. How can I do this? Thanks, MindFrog

A: Setting startup settings and python commands can be done in a file: ~/.pymolrc
E.g. command in there: cmd.set('label_distance_digits',1)
On my windows machine this is in C:\Documents and Settings\jurgen.WHELK.000\.pymolrc
===Commands===
Q: I want to move one object while keeping another fixed. How do I do this?

A: Load the proteins as separate objects, put the mouse into 3-button editing mode, then shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. (Warren DeLano answer)
----
Q: I'd like to select residues that are in contact with a surface, or else be able to select buried/non-buried residues, is there any way to do this ? [[User:Xevi|Xevi]] 03:52, 16 Jun 2006 (CDT)
: I'm also looking for this (e.g. to see available lysines' -NH2 or cysteines' -SH on the surface), could one maybe cover the protein with an additional layer of new atoms, and then select all protein atoms close to these? Edit: there is now a simple solution for proteins displayed as non-transparent surfaces: [[Displaying_Biochemical_Properties#Residues_with_functional_groups]] -- [[User:Moino|moino]] 19:35, 7 October 2008 (CDT)
----
Q: After using the usual mset command to rotate an object, states/frames are loaded into that object. However, using the "frame" command has odd behaviour (in comparison to loading a molecular dynamics trajectory into the state in which the "frame" command behaves normally). Can anyone explain this?

----

Q: How do I suppress the 'ExecutiveRMS' output while running cmd.pair_fit()?

----

Q: How does cmd.rms() choose a mapping between atoms in the selections? Exhaustive search over all possibilities?

----
Q: How do I select (especially, iterate through a set of) bonds? The existence of [http://www.pymolwiki.org/index.php/Cycle_Valence cycle valence] seems to imply that it can be done. Is this possible via the API?
----

===Export/Import===
Q: Is there any way to export PyMol models onto CAD standards (autocad, archicad) or 3D modeling software (blender, 3DStudio, Maya)? Thanks a lot.
----
Q: I am doing some MD simulations using CHARMM (not AMBER) and would like to visualize the .dcd files output by CHARMM. I understand that PyMol can open .trj files from AMBER but is there a way to open up these .dcd files and if not, are there any plans to implement this? Thank you for your time!

A: Answering my own question here. See: [[Load_Traj]]

===Others===
Q: I was wondering what the percentage given under the mutengensis wizard means? Thanks...
----
Q: Some of the bases in RNA helices are missing (not all in any given helix) when I am showing them in the CARTOON mode. How should I set it to get them shown? I tried the Secondary Structure Assignment commands, they did not work.
----
Q: Why does PyMol run version 2.3 of Python when I have Python 2.5 installed? How do I tell it to switch?
----
Q: How do I cite PyMOL?

A: DeLano, W.L. The PyMOL Molecular Graphics System. (2008) DeLano Scientific LLC, Palo Alto, CA, USA. http://www.pymol.org

----
Q: What is the status of the VMD plugin for Pymol? How does one install it? Is it installed by default? Will it appear in the plugins list? I compiled from source and changed several configuration files, but I cant't seem to be able to get the VMD plugins working properly. Thanks!
---
Q: If I want to ask a question to the PyMol Wiki community, how do I do that? Is there a page for PyMol usage questions?

Talk:Line width

2009-07-06T16:44:16Z

Baker1: Created page with 'I was wondering if it's possible to change the line_width for a selection. Say I want to have two line representations, one with most of a molecule at line_width,2 and a selecti...'

Talk:Huge surfaces

2009-03-31T22:33:59Z

Baker1:

I have appreciated learning to work with these objects and make more coarse grained images as you describe. The command 'as spheres' has caused my pyMol to crash every time. If I just leave it out I still seem to get the same result, but I was curious if anyone knows why that command would consistently make PyMol crash. If I do 'hide everything' then 'show spheres' it also works just fine.
--[[User:Baker1|Baker1]] 17:33, 31 March 2009 (CDT)

Talk:Huge surfaces

2009-03-31T22:33:34Z

Baker1: New page: I have appreciated learning to work with these objects and make more coarse grained images as you describe. The command 'as spheres' has caused my pyMol to crash every time. If I just le...

Symexp

2008-11-21T19:42:32Z

Baker1:

=== DESCRIPTION ===
'''symexp''' is used to reconstruct neighboring asymmetric units from the crystallographic experiment that produced the given structure. This is assuming the use of a [http://www.rcsb.org/pdb/home/home.do PDB] file or equivalent that contains enough information to reproduce the lattice. 

From the PyMOL developers:
"'symexp' creates all symmetry related objects for the specified object
that occurs within a cutoff about an atom selection. The new objects
are labeled using the prefix provided along with their crystallographic
symmetry operation and translation."

=== USAGE ===
In general: 
symexp(prefix,object,selection,cutoff) 

For one protein: 
symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance 

* ''name_for_new_objects'' (prefix) - PyMOL will generate a number of new objects corresponding to copies (rotated and translated) of the given asymmetric unit with the given name (prefix) appended with a numerical counter
* ''asymmetric_name'' (object) - this is the name of the loaded asymmetric unit that you wish to reproduce neighboring crystal partners for; the source of the symmetry operators
* ''(asymmetric_name)'' (selection) - the same name, but with parentheses around it if you are reproducing a crystal from its asymmetric unit - the source of atom coordinates
* ''distance'' (cutoff) - in Angstroms; reproduce any other unit that has any part of it falling withing ''distance'' Angstroms from the original asymmetric unit

=== EXAMPLE ===
load any .pdb file into PyMOL (here we use 1GVF). 

[[Image:1GVF_assym.png]]

At the PyMOL command prompt type the following: 
>> symexp sym,1GVF,(1GVF),1 
produces three new objects. We now have four objects corresponding to two biologic units (the functional protein in a cell).

[[Image:1GVF_1A.png]]

>> symexp sym,1GVF,(1GVF),5 
If we color all of the sym* cyan we will produce the following: 

[[Image:1GVF_5A.jpeg]]

As you can see, we can begin to understand the crystal environment of our asymmetric unit. Increasing ''distance'' will reveal more of the crystal lattice, but will place in increasing demand on your computer's rendering ability. 

NOTE: My PyMOL likes to crash if I ask it to ray trace or make a .png of anything that is too large. ''Too large'' varies, but (for instance) I was not able to ray trace the above picture using the default settings. Just making a .png image without the extra visual niceties rarely creates problems.

--[[User:Baker1|Baker1]] 13:41, 10 November 2008 (CST)

[[Category:Commands|symexp]]

Symexp

2008-11-10T19:50:11Z

Baker1:

=== DESCRIPTION ===
'''symexp''' is used to reconstruct neighboring asymmetric units from the crystallographic experiment that produced the given structure. This is assuming the use of a [http://www.rcsb.org/pdb/home/home.do PDB] file or equivalent that contains enough information to reproduce the lattice.

=== USAGE ===
symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance 

* ''name_for_new_objects'' - PyMOL will generate a number of new objects corresponding to copies (rotated and translated) of the given asymmetric unit with the given name appended with a numerical counter
* ''asymmetric_name'' - this is the name of the loaded asymmetric unit that you wish to reproduce neighboring crystal partners for
* ''(asymmetric_name)'' - the same name, but with parantheses around it - my guess is that the first is the source of atom coordinates and this is the source of the symmetry operators, but that is only a guess.
* ''distance'' - in Angstroms; reproduce any other unit that has any part of it falling withing ''distance'' Angstroms from the original asymetric unit

=== EXAMPLE ===
load any .pdb file into PyMOL (here we use 1GVF). 

[[Image:1GVF_assym.png]]

At the PyMOL command prompt type the following: 
>> symexp sym,1GVF,(1GVF),1 
produces three new objects. We now have four objects corresponding to two biologic units (the functional protein in a cell).

[[Image:1GVF_1A.png]]

>> symexp sym,1GVF,(1GVF),5 
If we color all of the sym* cyan we will produce the following: 

[[Image:1GVF_5A.jpeg]]

As you can see, we can begin to understand the crystal environment of our asymmetric unit. Increasing ''distance'' will reveal more of the crystal lattice, but will place in increasing demand on your computer's rendering ability. 

NOTE: My PyMOL likes to crash if I ask it to ray trace or make a .png of anything that is too large. I'm not sure how large too large is, but be aware of this.

--[[User:Baker1|Baker1]] 13:41, 10 November 2008 (CST)

[[Category:Commands|symexp]]

File:1GVF 5A.jpeg

2008-11-10T19:47:13Z

Baker1: result of symexp on 1GVF; shows all crystal neighbors within 5A

result of symexp on 1GVF; shows all crystal neighbors within 5A

File:1GVF 1A.png

2008-11-10T19:45:11Z

Baker1: Result of symexp on 1GVF with a 1A distance; shows 2 biologic units

Result of symexp on 1GVF with a 1A distance; shows 2 biologic units

File:1GVF assym.png

2008-11-10T19:44:16Z

Baker1: A picture produced in PyMOL of the crystallographic asymmetric unit of 1GVF

A picture produced in PyMOL of the crystallographic asymmetric unit of 1GVF

Symexp

2008-11-10T19:41:20Z

Baker1: New page: === DESCRIPTION === '''symexp''' is used to reconstruct neighboring asymmetric units from the crystallographic experiment that produced the given structure. This is assuming the use of a ...

=== DESCRIPTION ===
'''symexp''' is used to reconstruct neighboring asymmetric units from the crystallographic experiment that produced the given structure. This is assuming the use of a [http://www.rcsb.org/pdb/home/home.do PDB] file or equivalent that contains enough information to reproduce the lattice.

=== USAGE ===
symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance 

* ''name_for_new_objects'' - PyMOL will generate a number of new objects corresponding to copies (rotated and translated) of the given asymmetric unit with the given name appended with a numerical counter
* ''asymmetric_name'' - this is the name of the loaded asymmetric unit that you wish to reproduce neighboring crystal partners for
* ''(asymmetric_name)'' - the same name, but with parantheses around it - my guess is that the first is the source of atom coordinates and this is the source of the symmetry operators, but that is only a guess.
* ''distance'' - in Angstroms; reproduce any other unit that has any part of it falling withing ''distance'' Angstroms from the original asymetric unit

=== EXAMPLE ===
load any .pdb file into PyMOL (here we use 1GVF). 

add image of 1GVF

At the PyMOL command prompt type the following: 
>> symexp sym,1GVF,(1GVF),1 
produces three new objects. We now have four objects corresponding to two biologic units (the functional protein in a cell).

add image of 1GVF_1A

>> symexp sym,1GVF,(1GVF),5 
If we color all of the sym* cyan we will produce the following: 

add image of 1GVF_5A

As you can see, we can begin to understand the crystal environment of our asymmetric unit. 

NOTE: My PyMOL likes to crash if I ask it to ray trace or make a .png of anything that is too large. I'm not sure how large too large is, but be aware of this.

I will try to learn how to upload pictures soon.
--[[User:Baker1|Baker1]] 13:41, 10 November 2008 (CST)

[[Category:Commands|symexp]]

PyMOLWiki talk:Community Portal

2008-11-10T18:45:10Z

Baker1:

PyMOL wiki folks, 
I am new to the wiki community and am wondering how I create a new page. I would like to contribute an explanation of the symexp command and link it to the 'PyMOL commands' page. Where do I go start this new page? 
Thanks.

PyMOLWiki talk:Community Portal

2008-11-10T18:45:00Z

Baker1:

PyMOLWiki talk:Community Portal

2008-11-10T18:44:49Z

Baker1:

PyMOL wiki folks,
I am new to the wiki community and am wondering how I create a new page. I would like to contribute an explanation of the symexp command and link it to the 'PyMOL commands' page. Where do I go start this new page?
Thanks.

User:Baker1

2008-11-08T20:27:14Z

Baker1:

User:Baker1

2008-11-08T20:26:17Z

Baker1:

I am a Ph.D. student in biophysics and bioinformatics. You can learn more about BCB at Iowa State University at the following:

<ul>
<li> [http://www.bioinformatics.iastate.edu/ Baker Center] </li>
<li> [http://www.bcb.iastate.edu/index.html ISU BCB] </li>
<li> [http://lab.bcb.iastate.edu/ BCB Lab] </li>
</ul>

User:Baker1

2008-11-08T20:24:32Z

Baker1: New page: I am a Ph.D. student in biophysics and bioinformatics. You can learn more about BCB at Iowa State University at the following: [http://www.bioinformatics.iastate.edu/ Baker Center] [http...

I am a Ph.D. student in biophysics and bioinformatics. You can learn more about BCB at Iowa State University at the following:

[http://www.bioinformatics.iastate.edu/ Baker Center]
[http://www.bcb.iastate.edu/index.html ISU BCB]
[http://lab.bcb.iastate.edu/ BCB Lab]

Cealign plugin

2008-11-08T20:14:33Z

Baker1:

== Introduction ==

'''Go directly to [[Cealign#Version_0.8-RBS|DOWNLOAD]]'''

This page is the home page of the open-source CEAlign PyMOL plugin. The CE algorithm is a fast and accurate protein structure alignment algorithm, pioneered by Drs. Shindyalov and Bourne (See
References). There are a few changes from the original CE publication (See Notes).

The source code is implemented in C with the rotations finally done by Numpy in Python. Because the computationally complex portion of the code is written in C, it's quick. That is, on my machines --- relatively fast 64-bit machines --- I can align two 400+ amino acid structures in about 0.300 s with the C++ implementation.

This plugs into PyMol very easily. See [[Cealign#The_Code|the code]] and [[Cealign#Examples|examples]] for installation and usage.

== Comparison to PyMol ==
'''Why should you use this?'''

PyMOL's structure alignment algorithm is fast and robust. However, its first step is to perform a sequence alignment of the two selections. Thus, proteins in the '''twilight zone''' or those having a low sequence identity, may not align well. Because CE is a structure-based alignment, this is not a problem. Consider the following example. The image at LEFT was the result of CE-aligning two proteins (1C0M chain B to 1BCO). The result is '''152''' aligned (alpha carbons) residues (not atoms) at '''4.96 Angstroms'''. The image on the RIGHT shows the results from PyMol's align command: an alignment of '''221 atoms''' (not residues) at an RMSD of '''15.7 Angstroms'''.

<gallery>
Image:cealign_ex1.png|Cealign's results (152 aligned; 4.96 Ang.)
Image:pymol_align.png|PyMol's results (763 atoms; 18.4 Ang. )
</gallery>

== Examples ==
=== Usage ===
==== Syntax ====

CEAlign has the semantic, and syntactic formalism of
<source lang="python">
cealign MASTER, TARGET
</source>
where a post-condition of the algorithm is that the coordinates of the '''MASTER''' protein are unchanged. This allows for easier multi-protein alignments. For example,
<source lang="python">
cealign 1AUE, 1BZ4
cealign 1AUE, 1B68
cealign 1AUE, 1A7V
cealign 1AUE, 1CPR
</source>
will superimpose all the TARGETS onto the MASTER.

=====Examples=====
<source lang="python">
cealign 1cll and i. 42-55, 1ggz and c. A
cealign 1kao, 1ctq
cealign 1fao, 1eaz
</source>

=====Multiple Structure Alignments=====
Use the '''alignto''' command, now provided with cealign. Just type,
<source lang="python">
alignto PROT
</source>
to align all your proteins in PyMOL to the one called, '''PROT'''.

=== Results ===
See '''Changes''' for updates. But, overall, the results here are great.

<gallery>
Image:v7_1fao_1eaz.png|EASY: 1FAO vs. 1EAZ; 96 residues, 1.28 Ang
Image:v7_1cbs_1hmt.png|EASY: 1CBS vs. 1HMT; 128 residues, 2.01 Ang
Image:v7_1a15_1b50.png|MODERATE: 1A15 vs 1B50; 56 residues, 2.54 Ang.
Image:v7_1oan_1s6n.png|EASY: 1OAN vs. 1S6N (state 1); 96 residues aligned to 3.83 Ang. RMSD.
Image:v7_1rlw_1byn.png|HARD: 1RLW to 1BYN; 104 residues; 2.21 Ang.
Image:v7_1ten_3hhr.png|HARD: 1TEN vs. 3HHR; 80 residues, 2.91 Ang.
Image:v7_2sim_1nsb.png|HARD: 2SIM vs. 1NSB; 272 residues, 4.93 Ang.
Image:v7_1cew_1mol.png|HARD: 1CEW vs. 1MOL; 80 residues, 4.03 Ang.
</gallery>

== Installation ==

===Mac OS X (10.5)===
[[Image:Cealign mac os x.png|300px|thumb|center|CEAlign running on Mac OS X (10.5)]]
* Install PyMOL under fink.
* Install Numpy for fink:
<source lang="bash">
/sw/bin/fink install scipy-core-25
</source>
* Install cealign
<source lang="bash">
sudo /sw/bin/python setup.py install
</source>
* In PyMOL, run the two scripts needed for cealing: "cealign.py" and "qkabsch.py".
* Voila!

===Windows systems===
This is a quick and dirty method to get it working on Win32 right now, more details coming soon.
====Requirements====
* Latest PyMol, installed on your system
* Numpy for python 2.4 -- quick download of just what's needed: http://users.umassmed.edu/Shivender.Shandilya/pymol/numpy.zip
* Pre-compiled ccealign.pyd python module: http://users.umassmed.edu/Shivender.Shandilya/pymol/ccealign.zip
* Modified pymolrc: http://users.umassmed.edu/Shivender.Shandilya/pymol/pymolrc
* cealign.py and qkabsch.py from the Cealign-0.8-RBS package: download below

====Directions====
# Unzip the numpy.zip file, which will give you a folder named '''numpy'''
# Move this entire folder to: C:\Program Files\DeLano Scientific\PyMOL\modules\ (or the corresponding location on your system)
# Unzip ccealign.zip, which will give you a file called '''ccealign.pyd'''
# Move this pyd file to: C:\Program Files\DeLano Scientific\PyMOL\py24\DLLs\ (or the corresponding location on your system)
# Copy the downloaded '''pymolrc''' file to: C:\Program Files\DeLano Scientific\PyMOL\ (or the corresponding location on your system)
# Extract and copy the files cealign.py and qkabsch.py from the Cealign-0.8-RBS package to: C:\Program Files\DeLano Scientific\PyMOL\py24\Lib\ (or the corresponding location on your system)
# Run PyMol and load some molecules
# Run this command in Pymol: '''cealign molecule1, molecule2'''
# Enjoy!

===*nix systems===
====Requirements====
* C compiler
* Python 2.4+ with distutils
* Numpy
** for User-compiled PyMOL: <source lang="python">python setup.py install</source>
** for the precompiled version of PyMOL <source lang="python">python setup.py install --prefix "" --root /DIR_TO/pymol/ext/</source>

====Directions====
# uncompress the distribution file '''cealign-VERSION.tgz'''
# cd cealign-VERSION
# sudo python setup.py install # if you installed by PyMOL by hand
## python setup.py install --prefix "" --root /DIR/TO/pymol/ext/ # if you are using the precompiled binary download
# insert "run DIR_TO_CEALIGN/cealign.py" and "run DIR_TO_CEALIGN/qkabsch.py" into your '''.pymolrc''' file, or just run the two Python scripts by hand.
# load some molecules
# run, '''cealign molecule1, molecule2'''
# enjoy

=====Pre-compiled Hackish Install=====
For those people that prefer to use the pre-compiled version of PyMOL, here are the basics for your install. '''This is a poor method of installing Cealign. I suggest users compile and install their own PyMOL.''' The final goal is to get
# '''ccealign.so''' module into '''PYMOL/ext/lib/python2.4/site-packages'''
# numpy installed (get the numpy directory into (or linked into) '''PYMOL/ext/lib/python2.4/site-packages'''
# and be able to run cealign.py and qkabsch.py from PyMOL.
If you can do the above three steps, '''cealign''' should run from the pre-compiled PyMOL.

In more detail, on a completely fictitious machine --- that is, I created the following commands from a fake machine and I don't expect a copy/paste of this to work '''anywhere''', but the commands should be helpful enough to those who need it:
<source lang="python">
# NOTES:
# This is fake code: don't copy/paste it.
#
# PYMOL='dir to precompiled PyMOL install'
# CEALIGN='dir where you will unpack cealign'
# replace lib with lib64 for x86-64
# install numpy
apt-get install numpy

# link numpy to PyMOL
ln -s /usr/local/lib/python2.4/site-packages/numpy PYMOL/ext/lib/python2.4/site-packages

# download and install Cealign
wget http://www.pymolwiki.org/images/e/ed/Cealign-0.6.tar.bz2
tar -jxvf Cealign-0.6.tar.bz2
cd cealign-0.6
sudo python setup.py build
cp build/lib-XYZ-linux/ccealign.so PYMOL/ext/lib/python2.4/site-packages

# run pymol and try it out
pymol
run CEALIGN/cealign.py
run CEALIGN/qkabsch.py
fetch 1cew 1mol, async=0
cealign 1c, 1m
</source>

== The Code ==
Please unpack and read the documentation. All comments/questions should be directed to Jason Vertrees (javertre _at_ utmb ...dot... edu).

'''LATEST IS v0.8-RBS'''. (Dedicated to Bryan Sutton for allowing me to use his computer for testing.)

=== Version 0.8-RBS ===
* '''Download: [[Media:Cealign-0.8-RBS.tar.bz2|CE Align v0.8-RBS]] (bz2)'''
* '''Download: [[Media:Cealign-0.8-RBS.zip|CE Align v0.8-RBS]] (zip)'''

=== Beta Version 0.9 ===
Use at your own peril. Please report any problems or inconsistent alignments to this discussion page, or to me directly; my email address all over this page.

'''Improvements/Changes''':
* All C++
** So, faster
** comes with the dependencies built in
* No numpy

''' Download: [[Media:Cealign-0.9.zip|CE Align v0.9]] (zip)'''

== Coming Soon ==
* Windows binary
* Linux Binaries (32bit, x86-64)
* Better instructions for precompiled distributions
* Optimization

== Updates ==

=== 2008-03-25 ===
Pure C++ code released. See the beta version above.

=== 2007-04-14 ===
v0.8-RBS source updated. Found the bug that had been plaguing 32-bit machines. This should be the last release for a little while.

Also, I provide the option of aligning based solely upon RMSD or upon the better CE-Score. See the '''References''' for information on the '''CE Score'''.

== Troubleshooting ==

Post your problems/solutions here.

=== Unicode Issues in Python/Numpy ===
'''Problem''': Running/Installing cealign gives
<source lang="python">
Traceback (most recent call last):
File "/home/byron/software/pymol_1.00b17/pymol/modules/pymol/parser.py",
line 308, in parse
File "/home/byron/software/pymol_1.00b17/pymol/modules/pymol/parsing.py",
line 410, in run_file
File "qkabsch.py", line 86, in ?
import numpy
File "/usr/lib/python2.4/site-packages/numpy/__init__.py", line 36, in ?
import core
File "/usr/lib/python2.4/site-packages/numpy/core/__init__.py", line 5, in ?
import multiarray
ImportError: /home/byron/software/pymol/ext/lib/python2.4/site-packages/numpy/core/multiarray.so:
undefined symbol: _PyUnicodeUCS4_IsWhitespace
</source>
where the important line is
<source lang="python">
undefined symbol: _PyUnicodeUCS4_IsWhitespace
</source>

This problem indicates that your Numpy Unicode is using a different byte-size for unicode characters than is the Python distribution your PyMOL is running from. For example, this can happen if you use the pre-built PyMOL and some other pre-built Numpy package.

'''Solution''': Hand-install Numpy.

=== LinAlg Module Not Found ===
'''Problem''': Running CE Align gives the following error message:
<source lang="python">
run qkabsch.py
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/parser.py", line 285, in parse
parsing.run_file(exp_path(args[nest][0]),pymol_names,pymol_names)
File "/usr/lib/python2.4/site-packages/pymol/parsing.py", line 407, in run_file
execfile(file,global_ns,local_ns)
File "qkabsch.py", line 86, in ?
import numpy
File "/usr/lib/python2.4/site-packages/numpy/__init__.py", line 40, in ?
import linalg
ImportError: No module named linalg
</source>

'''Solution''': You do not have the linear algebra module installed (or Python can't find it) on your machine. One workaround is to install [http://www.scipy.org/ Scientific Python]. (on debian/ubuntu this can be done by: sudo apt-get install python-scipy) Another is to reinstall the Numpy package from source, ensuring that you have the necessary requirements for the linear algebra module (linpack, lapack, fft, etc.).

=== CCEAlign & NumPy Modules Not Found ===
'''Problem''': Running CE Align gives the following error message:
<source lang="python">
PyMOL>run cealign.py
Traceback (most recent call last):
File "/home/local/warren/MacPyMOL060530/build/Deployment/MacPyMOL.app/pymol/modules/pymol/parser.py", line 297, in parse
File "/home/local/warren/MacPyMOL060530/build/Deployment/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 408, in run_file
File "/usr/local/pymol/scripts/cealign-0.1/cealign.py", line 59, in ?
from ccealign import ccealign
ImportError: No module named ccealign
run qkabsch.py
Traceback (most recent call last):
File "/home/local/warren/MacPyMOL060530/build/Deployment/MacPyMOL.app/pymol/modules/pymol/parser.py", line 297, in parse
File "/home/local/warren/MacPyMOL060530/build/Deployment/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 408, in run_file
File "qkabsch.py", line 86, in ?
import numpy
ImportError: No module named numpy
</source>

'''Solution''': This problem occurs under [http://www.apple.com/macosx Apple Mac OS X] if (a) the Apple's python executable on your machine (/usr/bin/python, currently version 2.3.5) is superseded by [http://fink.sourceforge.net/ Fink]'s python executable (/sw/bin/python, currently version 2.5) and (b) you are using [http://delsci.com/rel/099/#MacOSX precompiled versions of PyMOL] (MacPyMOL, PyMOLX11Hybrid or PyMOL for Mac OS X/X11). These executables ignore Fink's python and instead use Apple's - so, in order to run CE Align, one must install NumPy (as well as CE Align itself) using Apple's python. To do so, first download the [http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=175103 Numpy source code archive] (currently version 1.0.1), unpack it, change directory to numpy-1.0.1 and specify the full path to Apple's python executable during installation: <tt>sudo /usr/bin/python setup.py install | tee install.log</tt>. Then, donwload the [http://www.pymolwiki.org/index.php/Cealign#The_Code CE Align source code archive] (currently version 0.2), unpack it, change directory to cealign-0.2 and finally install CE Align as follows: <tt>sudo /usr/bin/python setup.py install | tee install.log</tt>.
[[User:Lucajovine|Luca Jovine]] 05:11, 25 January 2007 (CST).

=== The Function SimpAlign() is not found ===
'''Problem''': Running CE Align gives the following error message:
<source lang="python">
PyMOL>cealign 1CLL,1GGZ
Traceback (most recent call last):
File "C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\pymol\parser.py", line 203, in parse
result=apply(kw[nest][0],args[nest],kw_args[nest])
File "py24/Lib/cealign.py", line 177, in cealign
curScore = simpAlign( matA, matB, mol1, mol2, stored.mol1, stored.mol2, align=0, L=len(matA) )
NameError: global name 'simpAlign' is not defined
</source>
I am running PyMOL v. 0.99rc6 on Win XP Professional x64 edition version 2003 sp2 and have followed the windows install procedure as described above.

=== Short Alignments Don't Work ===
If you are trying to align fewer than 16 residues then use [[align]], [[super]], or [[optAlign]]. CE uses a window size of 8; and to build a path of more than one window, you need 2*8=16 residues. I will insert some code to re-route small alignments to one of the aforementioned alignment algorithms.

=== It Worked A Second Ago! ===
[[Image:Rewind.png|thumb|right|Showing the rewind button to rewind to state 1.]]

If you were using cealign (or alignto) and now the commands don't work -- that is, they return an RMSD, but don't actually superimpose the objects, then you have a simple problem dealing with states. Most likely the cause of this oddness was (1) when you issued "cealign prot1, prot2" one of them was actually an ensemble of states or (2) you are trying to align to proteins with only one state, but are not looking at state one (because the last protein you were considering had more than one state and you quit editing that protein on a state that's not state 1). To fix this, use the rewind button to get the proteins back into state 1 & reissue the cealign/alignto command.

== References ==
Text taken from PubMed and formatted for the wiki. The first reference is the most important for this code.

# Shindyalov IN, Bourne PE. '''Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.''' ''Protein Eng.'' 1998 Sep;11(9):739-47. PMID: 9796821 [PubMed - indexed for MEDLINE]
# Jia Y, Dewey TG, Shindyalov IN, Bourne PE. '''A new scoring function and associated statistical significance for structure alignment by CE.''' ''J Comput Biol.'' 2004;11(5):787-99. PMID: 15700402 [PubMed - indexed for MEDLINE]
# Pekurovsky D, Shindyalov IN, Bourne PE. '''A case study of high-throughput biological data processing on parallel platforms.''' ''Bioinformatics.'' 2004 Aug 12;20(12):1940-7. Epub 2004 Mar 25. PMID: 15044237 [PubMed - indexed for MEDLINE]
# Shindyalov IN, Bourne PE. '''An alternative view of protein fold space.''' ''Proteins.'' 2000 Feb 15;38(3):247-60. PMID: 10713986 [PubMed - indexed for MEDLINE]

== License ==
The CEAlign and all its subprograms that I wrote, are released under the open source Free BSD License (BSDL).

[[Category:Script_Library]]
[[Category:Structure_Alignment|Cealign]]

Cealign

2008-11-08T20:14:33Z

Baker1: