PyMOL Wiki - User contributions [en]

Talk:LigAlign

2009-01-23T04:47:26Z

Aheifets:

* Great tool. I think this would be more useful for the users if they could load two objects into PyMOL and simply use it there. I had a session open with about 50 proteins and '''ligalign''' deleted everything!
[[User:Inchoate|Tree]] 09:15, 20 October 2008 (CDT)

* Thank you for the feedback! I am always interested in making LigAlign more useful and easier to use. The current version does reinitialize the PyMOL session: LigAlign aggressively caches computations to speed up the processing, and resetting all data structures between sessions ensures that we're properly re-computing for new proteins in the new session. I'll try to make version 0.02 more judicious in what it resets. Please feel free to email ligalign@cs.toronto.edu with any other requests or suggestions (and feel free to send complaints and bug reports, too). [[User:Aheifets|Abe]]

User:Aheifets

2009-01-23T04:45:42Z

Aheifets: New page: Hello, I am an author of LigAlign. For more information about me, please see [http://www.cs.toronto.edu/~aheifets my webpage].

Hello, I am an author of [[LigAlign]]. For more information about me, please see [http://www.cs.toronto.edu/~aheifets my webpage].

LigAlign

2008-10-03T22:49:50Z

Aheifets: ack, added tilde

===IMAGES===
<gallery>
Image:1xbb_proteins.png|Ligand-based alignment of 1XBB and 1OPJ
Image:mapping_example1.png|Atom-to-atom mapping of ligands
Image:heme18.png|Alignment of 1V07 and 1HBI using heme
</gallery>

===DESCRIPTION===
LigAlign is a tool to compare protein active-sites and investigate ligand binding. The active-site alignment is guided by the orientation of bound ligands in the protein active sites. LigAlign supports analysis of flexible ligand via automatic fragment-based alignment: first computing a natural fragmentation of the query ligand, aligning each fragment of the query independently against the baseline, and then permitting easy visualization of each active site subcavity. 

We use protein-ligand complexes to compare the active sites of several proteins which interact with a chosen ligand. Beginning with a user-specified protein-ligand structure, LigAlign gathers experimental structures of other proteins bound to the ligand from the Protein Data Bank. The tool then aligns the ligands bound in the structures to minimize the ligand-to-ligand RMSD. This transformation also aligns the active sites. Finally, the user can examine the aligned active sites to identify structural patterns, such as conserved steric hindrance or hydrophobicity. 

However, a flexible ligand can bend itself into different active sites, where the active site subcavities have different relative positions or orientations. Therefore, when comparing two active sites, a rigid RMSD-minimizing transform on docked flexible ligands may fail to align the correct portions of the active site. However, each subcavity should still exhibit chemical or geometric complementarity to the piece of the ligand which it binds. Please see [http://compbio.cs.toronto.edu/ligalign the website] for more information. 

LigAlign simplifies a number of protein analysis tasks. For example, LigAlign will align similar but distinct ligands which, in the context of structure-based drug discovery, permits the comparison of the docking of different ligands. Alternatively, if the user only specifies one protein-ligand complex, LigAlign will find chemically similar ligands automatically via [http://compbio.cs.toronto.edu/psmdb the Protein-Small Molecule Database]. Finally, LigAlign improves workflow by automatically fetching necessary data from the [http://www.rcsb.org Protein Data Bank]. 

LigAlign is contributed by [http://www.cs.toronto.edu/~aheifets Abraham Heifets] and [http://www.cs.toronto.edu/~lilien Ryan Lilien] at the University of Toronto. 

=== Additional Information ===
* '''[http://compbio.cs.toronto.edu/ligalign/downloads.html Downloads]'''
* '''[http://compbio.cs.toronto.edu/ligalign LigAlign Website]'''
* '''[http://compbio.cs.toronto.edu/ligalign/README.html Tutorial]'''

[[Category:Script_Library|LigAlign]]
[[Category:Structural_Biology_Scripts|LigAlign]]

Main Page

2008-10-03T22:45:38Z

Aheifets: Added link to LigAlign.

__NOTOC__
{| align="center" width="90%"
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
|-
| style="padding: 3px 5px 10px 15px;"| &diams; New logo for the wiki. It's DNA. You can easily see the major/minor grooves. If you don't see it, force a reload of the page (CTRL-F5, usually).
|-
| style="padding: 3px 5px 10px 15px;"| &diams; New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; Information about PyMOL and [[Stereo_3D_Display_Options|Stereo 3D Displays]].
|-
| style="padding: 3px 5px 10px 15px;"| &diams; Massively restructured the [[TOPTOC]] and make the [[OLD_TOPTOC]] for the older version. Still need to add more content to the [[TOPTOC]].
|-
| style="padding: 3px 5px 10px 15px;"| &diams; Added a simple script for [[removeAlt|removing specific alternately located atoms]].
|-
| style="padding: 3px 5px 10px 15px;"| &diams; Added a starter gallery of PyMOL-created Journal [[Covers]].
|-
| style="padding: 3px 5px 10px 15px;"| &diams; Added some information on how PyMOL handles [[Nonstandard_Amino_Acids]].
|-
| style="padding: 3px 5px 10px 15px;"| &diams; Downtime: The PyMOLWiki underwent some downtime due to FS problems. There are also upgrades planned for this week, so we may expect a little downtime for that. We've been very fortunate to have hosting from [http://www.bitgnome.net/ BitGnome.Net]; they've done an incredible job!
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| style="padding: 3px 5px 10px 15px;"| &diams; [[Gallery]] -- Did you make a [[:Image:Ccp4_map.png|cool image]]? Pop it into the PyMOLWiki Gallery with the PyMOL command you used. Looking for a particular representation--start here (new!).
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|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:070920nature.pdf.jpg|125px]] Sample Cover from the [[Covers]] gallery.
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
|-
| style="padding: 3px 5px 10px 15px;"| &diams; PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[group]] command has been added.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; The truly awesome [[grid_mode]] setting has been added.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[Ellipsoids]] representation added for drawing thermal ellipsoids.
|}
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Gm1.png|125px]] Screenshot of [[grid_mode|Grid Mode]] in action.
|}
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{|style="background-color: transparent;" width="100%"
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts & Plugins
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[LigAlign]] -- Ligand-based active site alignment and comparison.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[ImmersiveViz]] -- Headtracking user interface for PyMOL (watch the video)!
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [http://ase-web.rit.edu/~ez-viz/ProMOL_dl.html ProMOL] plugin added. Catalytic site prediction, other tools. Redirects to website.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[EMovie]] plugin added. Easy movies in PyMol using a GUI.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[DYNMAP]] plugin page created. Check it out!
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[EZ-Viz]]
|}
|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:COLORAMA-screenshot.jpg|125px]] Screenshot of [[Colorama]].
|}
|}

Category:Structural Biology Scripts

2008-10-03T22:43:18Z

Aheifets: Added link to LigAlign. Alphabetized script descriptions.

This page is a sub-category of scripts for Structural Biology Applications.

* [[CreateSecondaryStructure]] -- Grow a helix,strand or loop from ends of proteins
* [[DynoPlot]] -- Generic dynamic plotting utility; Interactive Ramachandran Plots.
* [[LigAlign]] -- Ligand-based active site alignment and comparison.
* [[Rotamer Toggle]] -- Toggle through the most common side chain rotamers and/or color by rotamer probability (Dunbrack's Backbone-depenedent library)

[[Category:Script_Library]]

Category:Script Library

2008-10-03T22:41:31Z

Aheifets: /* Descriptions */

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

= Descriptions =

* [[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).

[[Category:Scripting|Script Library]]

LigAlign

2008-10-03T22:38:40Z

Aheifets:

===IMAGES===
<gallery>
Image:1xbb_proteins.png|Ligand-based alignment of 1XBB and 1OPJ
Image:mapping_example1.png|Atom-to-atom mapping of ligands
Image:heme18.png|Alignment of 1V07 and 1HBI using heme
</gallery>

===DESCRIPTION===
LigAlign is a tool to compare protein active-sites and investigate ligand binding. The active-site alignment is guided by the orientation of bound ligands in the protein active sites. LigAlign supports analysis of flexible ligand via automatic fragment-based alignment: first computing a natural fragmentation of the query ligand, aligning each fragment of the query independently against the baseline, and then permitting easy visualization of each active site subcavity. 

We use protein-ligand complexes to compare the active sites of several proteins which interact with a chosen ligand. Beginning with a user-specified protein-ligand structure, LigAlign gathers experimental structures of other proteins bound to the ligand from the Protein Data Bank. The tool then aligns the ligands bound in the structures to minimize the ligand-to-ligand RMSD. This transformation also aligns the active sites. Finally, the user can examine the aligned active sites to identify structural patterns, such as conserved steric hindrance or hydrophobicity. 

However, a flexible ligand can bend itself into different active sites, where the active site subcavities have different relative positions or orientations. Therefore, when comparing two active sites, a rigid RMSD-minimizing transform on docked flexible ligands may fail to align the correct portions of the active site. However, each subcavity should still exhibit chemical or geometric complementarity to the piece of the ligand which it binds. Please see [http://compbio.cs.toronto.edu/ligalign the website] for more information. 

LigAlign simplifies a number of protein analysis tasks. For example, LigAlign will align similar but distinct ligands which, in the context of structure-based drug discovery, permits the comparison of the docking of different ligands. Alternatively, if the user only specifies one protein-ligand complex, LigAlign will find chemically similar ligands automatically via [http://compbio.cs.toronto.edu/psmdb the Protein-Small Molecule Database]. Finally, LigAlign improves workflow by automatically fetching necessary data from the [http://www.rcsb.org Protein Data Bank]. 

LigAlign is contributed by [http://www.cs.toronto.edu/aheifets Abraham Heifets] and [http://www.cs.toronto.edu/~lilien Ryan Lilien] at the University of Toronto. 

=== Additional Information ===
* '''[http://compbio.cs.toronto.edu/ligalign/downloads.html Downloads]'''
* '''[http://compbio.cs.toronto.edu/ligalign LigAlign Website]'''
* '''[http://compbio.cs.toronto.edu/ligalign/README.html Tutorial]'''

[[Category:Script_Library|LigAlign]]
[[Category:Structural_Biology_Scripts|LigAlign]]

File:Heme18.png

2008-10-03T22:24:29Z

Aheifets:

File:Mapping example1.png

2008-10-03T22:24:16Z

Aheifets:

File:1xbb proteins.png

2008-10-03T22:24:01Z

Aheifets:

LigAlign

2008-10-03T22:12:31Z

Aheifets: Describing the LigAlign tool

===IMAGES===
<gallery>
Image:1xbb_proteins.png|Ligand-based alignment of 1XBB and 1OPJ
Image:mapping_example1.png|Atom-to-atom mapping of ligands
Image:heme18.png|Alignment of 1V07 and 1HBI using heme
</gallery>

===DESCRIPTION===
LigAlign is a tool to compare protein active-sites and investigate ligand binding. The active-site alignment is guided by the orientation of bound ligands in the protein active sites. LigAlign supports analysis of flexible ligand via automatic fragment-based alignment: first computing a natural fragmentation of the query ligand, aligning each fragment of the query independently against the baseline, and then permitting easy visualization of each active site subcavity. 

We use protein-ligand complexes to compare the active sites of several proteins which interact with a chosen ligand. Beginning with a user-specified protein-ligand structure, LigAlign gathers experimental structures of other proteins bound to the ligand from the Protein Data Bank. The tool then aligns the ligands bound in the structures to minimize the ligand-to-ligand RMSD. This transformation also aligns the active sites. Finally, the user can examine the aligned active sites to identify structural patterns, such as conserved steric hindrance or hydrophobicity. 

However, a flexible ligand can bend itself into different active sites, where the active site subcavities have different relative positions or orientations. Therefore, when comparing two active sites, a rigid RMSD-minimizing transform on docked flexible ligands may fail to align the correct portions of the active site. However, each subcavity should still exhibit chemical or geometric complementarity to the piece of the ligand which it binds. Please see [http://compbio.cs.toronto.edu/ligalign the website] for more information. 

LigAlign simplifies a number of protein analysis tasks. For example, LigAlign will align similar but distinct ligands which, in the context of structure-based drug discovery, permits the comparison of the docking of different ligands. Alternatively, if the user only specifies one protein-ligand complex, LigAlign will find chemically similar ligands automatically via [http://compbio.cs.toronto.edu/psmdb the Protein-Small Molecule Database]. Finally, LigAlign improves workflow by automatically fetching necessary data from the [http://www.rcsb.org Protein Data Bank]. 

LigAlign is contributed by [http://www.cs.toronto.edu/aheifets Abraham Heifets] and [http://www.cs.toronto.edu/~lilien Ryan Lilien] at the University of Toronto. 

=== Additional Information ===
* '''[http://compbio.cs.toronto.edu/ligalign/downloads.html Downloads]'''
* '''[http://compbio.cs.toronto.edu/ligalign LigAlign Website]'''
* '''[http://compbio.cs.toronto.edu/ligalign/README.html Tutorial]'''

[[Category:Script_Library|LigAlign]]
[[Category:Structural_Biology_Scripts|LigAlign]]

Category:FAQ

2008-06-25T20:39:02Z

Aheifets: /* Overview */

==FAQ==

===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.

----------

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 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 was wondering what the percentage given under the mutengensis wizard means? Thanks...

----
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: 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

----
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: 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)

----
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]]

----
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
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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.
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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

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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?

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

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

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Q: Why does PyMol run version 2.3 of Python when I have Python 2.5 installed? How do I tell it to switch?

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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?

Category:FAQ

2008-06-24T01:47:02Z

Aheifets: /* Overview */

Category:FAQ

2008-06-24T01:46:40Z

Aheifets: /* Overview */

Category:FAQ

2008-06-24T00:12:23Z

Aheifets: /* Overview */

Category:FAQ

2008-06-24T00:10:30Z

Aheifets: /* Overview */