[PyMOL] selecting residues

Hi, I ran into a problem selecting nearby residues of one molecule regarding the binding partner. The "byres" command seems to work only with one single residue. It does not select the whole residue when using the molecule as reference. creat 4a, byres mol around 4 --- gives incomplete residue

[PyMOL] Visual Representation of Electrostatic Potentials

Does anyone know of a viewer that can not only visualize the electrostatic potentials, but also show the numerical values on top of the surface of the produced image? __ Do you Yahoo!? Read only the mail you want - Yahoo! Mail SpamGuard. http:

Re: [PyMOL] APBS binary location

Hi, I just checked the apbs download page and I couldn't find apbs binaries available for windows. The only way I've seen (through previous mailing lists posts) is to compile it using cygwin, but the performance is less than optimal. So if you or someone else has compiled apbs for windows, the bi

[PyMOL] APBS binary location

I've been trying to generate an electrostatic potential map of the surface of a protein using Pymol but haven't been successful. I'm working with the latest version of pymol (0.98, windows version), which brings the APBS plugin (I have as well installed the APBS plugin "apbs_tools.py") that is supp

RE: [PyMOL] cartoon_transparency: setting value for subset of residues in object

Kevin, The trick here is to use "create" instead of "select". Create makes new objects that can have independent settings. load mol_obj.pdb # transfer a piece of the molecule into a new object create new_obj, chain A remove mol_obj in new_obj # adjust trasparency for the new object set car

[PyMOL] cartoon_transparency: setting value for subset of residues in object

Hi all: I'd like to set a value for a selection of residues within an object --- which I think might be tough given the docs on the set command, but I'm open to suggestions. The particular case here is setting cartoon_transparency, which I'd like to use to make a subset of residues in a p

RE: [PyMOL] labelling using single letter codes

> 1. Add this to your $HOME/.pymolrc file: > > # start $HOME/.pymolrc modification > one_letter = {'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \ > 'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',\ > 'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',

[PyMOL] mesh represenation of surface

I am wondering where I can find mesh represenation of protein surface in PyMol API. -- Bingding Huang PhD student Bioinformatics group Biotec & Department of Computing Tazberg 47, 01307 TU Dresden, Germany Tel:0049 351 46340064 (Office) Tel:0049 351 4403368 (Home) Fax:0049 351 4634

Re: [PyMOL] labelling using single letter codes

andr...@biochem.utah.edu wrote: Hey Ramesh, for all sorts of labeling, image manipulation programs like photoshop or the gimp are superior. Convince yourself how simple it is even to adjust the z position of the label in a stereo picture by moving it (one partner of the stereo pair) horizontall

Re: [PyMOL] labelling using single letter codes

Ezequiel H Panepucci wrote: Hello Ramesh, use: label n. ca, one_letter[resn] Cheers, Zac Thanks Zac. that was indeed very useful. But I have one more problem. Doing thus gives me only the name of the aa, not its number. How to give the label command in order to give the number

Re: [PyMOL] labelling using single letter codes

Hello Ramesh, > Is it possible to do the labelling using single letter codes for the > amino acid residues rather than the three letter codes? Yes. 1. Add this to your $HOME/.pymolrc file: # start $HOME/.pymolrc modification one_letter = {'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q',

Re: [PyMOL] labelling using single letter codes

Hey Ramesh, for all sorts of labeling, image manipulation programs like photoshop or the gimp are superior. Convince yourself how simple it is even to adjust the z position of the label in a stereo picture by moving it (one partner of the stereo pair) horizontally. Andreas > Hi List! > > Is