PyMol

Useful Pymol Commands:

• >fetch PDBID (acquires a file from the data bank) or File>open to get one from the computer
• In the action pull-down menu, choose presets and render your molecule “pretty” or “publication”
• >sele name, PDBID and chain D+F will create a group on the right hand menu, defined by everything after the comma. The example shown defines an entire protein, then uses a boolean operator ("and", above) to further limit the considered protein to just two chain.
You may also use the select feature to identify residues by number (resi) or name (resn)
examples: >sele his, resn his selects any residue named histidine
>sele active, resi 98+101+198+46 selects 4 individual residues by number.
>sele helix, resi 14-22 selects a range of residues by number.
• >super Molecule1, molecule2 will superimpose two like-molecules one each other (it will work better the more selective you are with your selective groups: superimposing two chains on two chains for example)
• >show sticks, resn his -or- >show sticks, resi 208 will display the residue type or specific side chain indicated, respectively.
• >Ray will render the image in high resolution
• >png myimage.png saves an image of your working screen.
•>align prot1, prot2 will align proteins on pymol when they are in the same window.

[[Amendola June 4th 2014]]

For further information and significantly more commands and resources, see the Rowlett Wiki from Colgate University.
[[k.hoffmann 6/5/13]]

Advanced displays

Quick rotation movies in PyMol for Quicktime

ref: ikutti.com (iKutticom on YouTube)

Fetch and render the pdb structure to an appropriate starting position.

>mset 1, 180
>util.mrol 1, 180, 1
>set ray_trace_frames, 1
>set cache_frames, 0

From the file menu, pull down "save movie as...">Quicktime.

Choose 25 frames/second (more is faster rotation), key frame every 24 frame. Good quality is fine for classrooms, significant time will be required to ray trace, rotate and save each frame. Open in Quicktime or drag and drop into Powerpoint/Keynote. There used to be a need to save the movie file in the same folder as the presentation when you want to run the show.

Movies that transition between scenes

Fetch and render the pdb structure to an appropriate starting position. Under the scene menu, store as scene F1. Pan, zoom, recolor, slab, hide chains, or otherwise adjust the view to the end point of the transition you'd like in your movie, and store that as scene F2. Continue storing "scenes" representing particularly transitions in your movie, use scene>recall>F2 to go back to the stored scene, and store again if you want to adjust it at any point.

When the scenes are to your liking, recall scene F1, and pull down the movie menu>program>scene loop> steady or y-rock Y-rock will rock each set scene image for a few moments when you reach it. Steady will smoothly transition between scenes. I usually use 4 seconds each in transition between scenes.

Turn on ray_trace_frames from the pull down menu or the command line, and save the movie as a Quicktime .mov file (as above.)

[[k.hoffmann 2/1/13]]

Representing interfaces

Program representation of nonbonding interactions across the protein binding interfaces.
2D-GraLab: http://sourceforge.net/projects/gralab/

[[k.hoffmann 6/5/13]]