Re: [PyMOL] weird visualization of a peptide structure

Annalisa, If bonds are not explicitly provided in the input file, then PyMOL infers bonding based on distance. Are the input coordinates valid? It looks like the atoms may be too close together in space... Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services

Re: [PyMOL] Mutating an Ion in Pymol and Displaying van der waals Radii

Buz, alter elem Na, elem='K' iterate elem K, print vdw show spheres, elem K alter elem K, vdw=1.4 rebuild iterate elem K, print vdw color yellow, elem K Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From:

Re: [PyMOL] surface properties

Mark, PyMOL does not have such abilities at present. Can such concepts even be defined in a precise, objective, and unambiguous fashion? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Mark Collins

Re: [PyMOL] adding python modules for MacPyMOL

Hi Ben, Current versions of MacPyMOL make use of the 2.3 version of the operating-system-provided Python interpreter. Future versions may behave differently. Officially speaking, if you need to integrate external native-code-containing Python modules, then DeLano Scientific's sole recommended

Re: [PyMOL] Ray Tracing A Protein Gallery

1. Use the grid_mode option (only available in the compiled from source pymols) FYI: grid_mode and many other enhancements will be present in the soon-to-be-available PyMOL 1.2 BETA builds. The annual PyMOL release cycle for official PyMOL builds has settled down as follows: - Summer: The

Re: [PyMOL] weird visualization of a peptide structure

Hi Andrew, thank you for your answer: now I have a clue! I knew that the structure is a NMR model, but what I didn't understand was that some atoms were repeated (with different coordinates). Now I have pruned my structure file and I can see a much more acceptable structure. Thank you very much,

Re: [PyMOL] weird visualization of a peptide structure

Hi Annalisa, Is the original coordinate file an NMR structure? It looks to me like there are several copies of each atom, which is consistent with the pdb file resulting from an NMR refinement. These will usually have several different models of the peptide, all consistent with the NMR data.

Re: [PyMOL] surface properties

Hi Mark, I remember that Kristian Rother's rTools could do hydrophobicity coloring: http://www.rubor.de/pymol_extensions.html it is some years ago, so maybe it needs some updateing.. Best, Andreas DeLano Scientific wrote: Mark, PyMOL does not have such abilities at present. Can such

[PyMOL] cmd.scene('*')

In a Python script I am working on I would like to get a list of the scenes that are defined. Unfortunately, cmd.scene('*') just prints the list to stdout, but doesn't return anything. That is, if I have a script test.py that looks like from pymol import cmd x = cmd.scene('*') print x

Re: [PyMOL] cmd.scene('*')

Malcolm, I believe the method you want is: print cmd.get_scene_list() Hopefully that method is present in the PyMOL build you are running! Cheers, Warren -Original Message- From: Malcolm E Davis [mailto:malcolm.da...@bms.com] Sent: Friday, December 19, 2008 3:46 PM To: