Re: [PyMOL] RMSD and color between two very similar structures

Dear Horacio -- On 21 Sep 2008, at 18:38, Horacio Sánchez wrote: Given two very similar pdb structures, do you know if it is possible to colour them in relationship with the RMSD between the 2 structures ? I guess it might be possible to do it by using the same trick as for the ConSurf rep

[PyMOL] pymol doing interesting things on windows

Hi again folks, I've been having some strange things happening with pymol starting on my windows machine (windows XP; NVIDIA GeForce 8400 GS; LG LCD screen; pymol version 1.1r). Attached is the most resent problem. Previously upon start up pymol decided to simply go very slowly when starting up

[PyMOL] RMSD and color between two very similar structures.

Hi, I think Leo's is the right way. In a little variant, you could change the b-factor value directly from pymol, instead of manipulating PDB. It should not be difficult prepare an script that ask for two selections (already superimposed and with the same number of residues) get the RMSDs and as

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

Dear all, Sorry for the late answer but I finally managed to find what the error is... First thing, I work on a Windows XP environment (nobody's perfect!!), and some of the problems were related to that. When I tried running everything from the command line (ie pdb2pqr and apbs) I did get the fi

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

Hello Gilles, The ObjectMapLoadDXFile-Error you are still having may sound familiar to us. Could you send us the following screenshots from your PyMOL APBS Tools? 1. A screenshot of the Main tab. 2. A screenshot of the APBS Location tab. 3. A screenshot of the Temporary File Locations tab. Wit

[PyMOL] displaying anisotropy ellipsoids in PyMOL v0.99rc6 running on Windows XP

Hi all, could someone advise me on the simplest way to display anisotropy ellipsoids in PyMOL v0.99rc6 running on Windows XP? Is there any script to do this? I haven't moved to the latest versions of PyMOL yet. Any help would be appreciated. Thanks in advance. Javier. -- Lic. Javier M. Gonzále

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

To follow up on one of Gilles least important questions: I was convinced that the PDB must contain structures for which there are more than two alternate conformations. I downloaded all structures with resolutions between 0.5 and 1.0A and with a bit of regexp grepping, quickly found the follo

Re: [PyMOL] displaying anisotropy ellipsoids in PyMOL v0.99rc6 running on Windows XP

Tim Fenn wrote something to do this a few years ago, but I don't think you can ray-trace them: http://www.stanford.edu/~fenn/pdb_aniso.py On Mon, Sep 22, 2008 at 2:48 PM, "Javier M. González" wrote: > Hi all, could someone advise me on the simplest way to display anisotropy > ellipsoids in PyMOL

[PyMOL] cmd equivalent of Display->Sequence On?

How can I turn sequence display on from a pymol script? 'help display' and 'help sequence' got me nothing Thanks! - Paul