[PyMOL] RE : Pymol Scripts for Coarse grained for non-protein molecules

2013-03-01 Thread ABEL Stephane 175950
Hi Tsjerk, Many thanks for your help, once again ;0 It works and it gives what i want. cool !! Stephane De : Tsjerk Wassenaar [tsje...@gmail.com] Date d'envoi : vendredi 1 mars 2013 13:56 À : ABEL Stephane 175950 Cc: pymol-users@lists.sourceforge.net

Re: [PyMOL] Pymol Scripts for Coarse grained for non-protein molecules

2013-03-01 Thread Tsjerk Wassenaar
Hi Stephane, You can convert a Gromacs run input file (.tpr) to a pdb file with CONECT records using the Gromacs tool 'editconf' with the '-conect' flag. The CONECT records will be set according to the bonds in the topology. Pymol will read the CONECT records and set the bonds. If you have a

[PyMOL] AttributeError: 'module' object has no attribute 'lock_api'

2013-03-01 Thread Jonathan Soffer
Hi all, I have a question about lock_api? The program was running perfectly for months and when I tried to open the program today I got the error below. It worked fine two days ago so I am a little confused on where to begin and I was unable to find an answer that matched this issue in the

[PyMOL] How to visualize an active site pocket using specific residues?

2013-03-01 Thread Yarrow Madrona
Hello, I have some output from the CASTp server-pymol plugin. I have the residues selected surrounding an active site pocket. I would like to make a shape with these atoms as vertices that I can color transparent from the atom selection. Is there a way to do this in pymol? Thank you. -- Yarrow