PyMOL Frequently Asked Questions
There are no peer reviewed publications on PyMOL yet. So, if your journal is hip enough to allow URL citations, please cite PyMOL as:
The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.
You get the idea...and please don't forget to send us the reference for your article when it comes out so that I can add it to the list of publications which used PyMOL.Click to return to top
set bg_rgb=[1,1,1] # these are [red,blue,green] components
In version 0.61 or later, simply use the bg_color command.
Usually you're want to turn off depth cueing and fog too
set depth_cue=0 set ray_trace_fog=0Click to return to top
set ray_trace_fog = 0
By default, the ray-tracer applies depth-cue fog. This works great for dark backgrounds, but often isn't desirable with light ones.
In v0.61 or later, just disable "Depth Cue & Ray Trace Fog" from the Settings menu in the external GUI.Click to return to top
set spec_power = 200 # in range 20 - 250 set spec_refl=1.5 # in range 1.0 - 2.0
Note that the shadow options in the Display menu of the external GUI may modify these parameters.Click to return to top
The cartoon command just changes the type of cartoon, it doesn't make them visible. Try:
show cartoonClick to return to top
If you know Molscript, then you probably think in terms of specifying particular stretches of amino acids to be helix, sheet, or coil. PyMOL is slightly different: Secondary structure is considered an atomic property of the alpha carbon. To correctly indicate helices or sheets, you need to insure that these properties are correctly set.
PyMOL will interpret HELIX and SHEET records from PDB files if they are available, but you can specify or override these properties by using alter commands:
alter A/10:34/, ss='H' alter A/35:40/, ss='L' alter A/41:60/, ss='S' alter A/61/, ss='L' alter A/62:70/, ss='S' rebuild cartoon automatic show cartoon # is roughly equivalent to the following Molscript input plot ... helix from A10 to A34; coil from A34 to A41; strand from A41 to A60; coil from A60 to A62; helix from A62 to A70; ... end_plot
The best PyMOL practice is to start with secondary structure in the PDB as assigned by some reliable program (DSSP, etc.) and then just make minor tweaks using alter. You can try using util.ss but it is wrong quite often, so you'll need to do a lot of proofreading of its assignments.
Note that if you only use the cartoon command to explicitly define shapes over a particular region, then your results will be sub-optimal because PyMOL will not be able to properly prepare the geometry of the backbone trace for the corresponding secondary structure.Click to return to top
Use the "ss" atom selection operator (example below requires PyMOL 0.65+).
color red, ss h color yellow, ss s color green, ss l+''Click to return to top
This is no longer necessary since PyMOL now reads and normalizes CCP4 maps on the fly!
For older versions, use CCP4's interactive xdlmapman utility, or for command line convenience, use mapman in the RAVE package from Gerard Kleywegt at the Uppsula Software Factory.Click to return to top
The GLUT library does not work quite right on certain combinations of IRIX and SGI hardware, but you can work around this problem. I can't fix GLUT because it is not modifiable, redistributable open-source software.
Adopt the following technique when picking and/or dragging atoms on a SGI:
With practice, this will become automatic. The trick is to learn a fluid motion of pressing the modifier keys, pressing the mouse button, releasing the keys, dragging, and then releasing the button. If you remember not to move the mouse with SHIFT or CONTROL pressed on an SGI, then you'll be fine working with PyMOL on an uncooperative SGI.Click to return to top
PyMOL isn't yet suitable for building new main-chain coordinates for proteins, but that functionality is planned. Nevertheless, some people are already using PyMOL instead of "O" for limited model-building tasks. For example, modifying the conformations of existing side chains is simply a matter of switching the mouse into editing mode, picking the bond you wish to adjust, and then dragging the atoms around. Moving waters and ligands is also trivial. Just remember to set mouse into editing mode first!.
If you want to use PyMOL for crystallography right now, then my advice is:
CTRL-middle-click in the viewer window away from any atom.
In versions 0.60 or later, click the "unpick" button in the external GUI.
set internal_gui=0 # off (NOTE: versions 0.58+ only).
set internal_gui=1 # on.Click to return to top
if sys.platform[:5]=='linux': self.my_fw_font=('lucida console',7) elif sys.platform[:3]=='win': self.my_fw_font=('lucida console',8) # Courier 9 else: self.my_fw_font=('lucida console',10)