[PyMOL] how to use pymol functionalities from a python script ?

Is it possible to use PyMOL from a Python script without lunching a GUI. When I do : "import cmd from pymol" in a Python program it automatically lunch Pymol. The only solution I've found was to write a Python script and to execute it from PyMOL with “-c” option. (pymol -c my_script.py) Thank

RE: [PyMOL] How to apply state-specific colours?

Hubert, The trick for doing this is to load each state into a "discrete" object, which maintains separate atoms for each state. load $TUT/1hpv.pdb, discrete=1 load $TUT/1hpv.pdb, discrete=1 color red, state 1 color blue, state 2 Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D

[PyMOL] surface inner color

Hi all, Is it possible to edit the color of the inner side of a surface? I want to show some waters filling a cavity. To do this I have clipped the image near the cavity and given some transparency to the surface. This is fine, but the inner side of the surface is just black (or very dark) I

Re: [PyMOL] How to apply state-specific colours?

Hubert, You need to use the mdo command, e.g. cmd.mclear() cmd.mset("1 x10") # Set all residues to white cmd.mdo(1, "color white") # Colour a residue cmd.mdo(2, "color red, (i;51)") # Clear colour of previous residue, and highlight a new one cmd.mdo(3, "color white, (i;51); color red, (i;184)

[PyMOL] "Flying" residues

Hi to all I created a protein in cartoon tube fashion and want now to display on a few residues in ball and stick. Evertything is fine but my problem is that the residues seem to "fly" above the protein tube since they are linked to it actually. How could I manage to connect the tube and the residu

[PyMOL] How to apply state-specific colours?

Dear all! I would like to prepare a an animation in which I would like to follow one certain residue on its journey through an enzyme in a stepwise manner. To do so, I would like to color a certain residue, say, red in state one and grey in all other frames. In frame 2, the next residue shoul

[PyMOL] RE: PyMOL-users digest, Vol 1 #717 - 12 msgs

-Original Message- From: pymol-users-requ...@lists.sourceforge.net [mailto:pymol-users-requ...@lists.sourceforge.net] Sent: 13 October 2004 23:45 To: pymol-users@lists.sourceforge.net Subject: PyMOL-users digest, Vol 1 #717 - 12 msgs Send PyMOL-users mailing list submissions to p