Re: [PyMOL] Binding pocket volume calculation

Sign, Sorry, PyMOL has no volume calculation capabilities at present. Cheers, Warren > -Original Message- > From: Kin Sing Stephen Lee [mailto:s...@chemistry.msu.edu] > Sent: Thursday, April 23, 2009 9:18 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Binding pocket volu

[PyMOL] Binding pocket volume calculation

Dear all, I'm just wondering is it possible to calculate the ligand volume and also the volume of the binding pocket from pymol? If no, do you have any program that allow me to do so? Thank you very much All the best, Sing

Re: [PyMOL] solvent accessibility with pymol

Folks, Please endeavor to be respectful, kind, and patient with one another. Toxic interactions on the mailing list hurt all of us, so please avoid such posts altogether or keep them private. Unfortunately, is appears that we can no longer rely on either SourceForge or Google to provide a PyMOL

Re: [PyMOL] solvent accessibility with pymol

Hi Warren, e.a., I agree that posts in which people react on the 'tone' of the communication of one another should in principle be kept private and settled thus. For me, there were three reasons to bounce this mail to the mailing list. First and for all, I had hoped for the response you gave rega

Re: [PyMOL] rms_cur, rms, fit - No atoms selected

(Sorry if this is dupe -- my email client is acting up...) the rms_* and fit commands required that the atoms in each selection to have matching identifiers: such as chain, resi, segi, resn, etc. You can use the "alter" command to set the identifiers to matching values before issuing such com

Re: [PyMOL] Roving detail and Roving density

On Wed, Apr 22, 2009 at 6:37 PM, Craig Smith wrote: > I was looking at the demos in pymol (wizard --> demo) and saw > interesting features called roving detail and roving density. I > looked in the manual on how to do this feature but couldn't find it. > Could anyone point me in the right direct

[PyMOL] rms_cur, rms, fit - No atoms selected

I'm new at pymol, and I'm trying to use the commands rms and rms_cur. I have two pdb files, with two proteins in each. First, I load the files > load 1acb_321000.pdb, c321 > load 1acb_dock.pdb, dock then I select the backbone of the B chain of each complex, > select lc, /c321//b//ca+c+n+o > sele

Re: [PyMOL] solvent accessibility with pymol

Hi Mehmet, > 1. I have just become a member today so I don't know who posted what 2 days > ago. and as far as I can see there is no search function on the archives. True, that's why I didn't answer 'search the archives', like I would on other lists. > 2. I do search the web before asking. I coul

[PyMOL] Roving detail and Roving density

Dear all, I was looking at the demos in pymol (wizard --> demo) and saw interesting features called roving detail and roving density. I looked in the manual on how to do this feature but couldn't find it. Could anyone point me in the right direction or show me how to interactively displ

[PyMOL] solvent accessibility with pymol

Hi all, I am looking for a way to figure out the solvent accessibility of a particular region on a protein. could anyone tell me if there is a command (or script) in Pymol that I can use to do it? thanks in advance.