[PyMOL] depiction of ligands

Hi all I would like to know, how we can show the ligands in pymol. Although i can see the non-bonded atoms ( HOH) automatically, eacept other nonbonded atoms l;ike sulphate and metal ions. I will appreciate the suggestions. Thanks in advance Thomas

[PyMOL] Rosetta Academic Training Webinar

The Rosetta Design Group is proud to present the first webinar in the Rosetta Academic Workshop Series. For the first webinar, we have selected to focus on Protein-Protein Docking based on the answers to the interest poll. We hope this will be the first in a line of helpful and inspiring

Re: [PyMOL] Rosetta Academic Training Webinar

On Wed, Mar 25, 2009 at 5:07 PM, Nir London n...@rosettadesigngroup.com wrote: Pleas note: This is not a promotional webinar. Rosetta is open-source and freeware for academic and non-profit organizations and can be downloaded here from University of Washington's TechTransfer Digital Ventures.

[PyMOL] Showing only part of a surface around a ligand

Hi all, this question may be resolvable by sufficient RTFMing, but maybe there is someone out there to help me... I am trying to generate a figure in which I want to show only a part of the protein surface around a ligand - pretty much like preset -- ligand sites -- solid surface I have

Re: [PyMOL] Showing only part of a surface around a ligand

Wulf, suppose you have this scenario: Protein in chain A Ligand in chain I Then create b-site, byres chain A within 5 of chain I show sticks, chain I show surface, b-site should get you close. HTH Carsten BTW If you replace the create command with select your surface will be

Re: [PyMOL] Showing only part of a surface around a ligand

Wulf, The source code for presets can be found in modules/pymol/preset.py, but there is object, method, and housekeeping stuff in there that distracts from its understandability. show surface, polymer within 5 of organic May be all that you really need. # example use load $TUT/1hpv.pdb

Re: [PyMOL] depiction of ligands

Hi Thomas, You're not really specific here, so I'll give the most general reply: show spheres, hetatm By the way, these compounds will definitely be drawn either as sticks or as nonbonded upon loading of the structure. You may not easily see them, but if they're in the file, they'll be drawn.

Re: [PyMOL] depiction of ligands

Hi there, There are many ways to do this. You can also try Actionpresetligands. This will show the ligands (hetatms) and their interactions. Unfortunately this doesn't highlight metal ions everytime (unless it interacts with the ligands). You can usually view this using the sequence option.