[PyMOL] help needed

hi all, I am writing this email with regards to the following problem. Statement of the problem: I have around 19,200 unique PDB files. Each of them have one or more ligands in it. For each ligand, I have to extract a zone which contains complete residues within 4.5Angstroms of the ligand [ i.e.

Re: [PyMOL] Mutate residues in batch mode

And to save it, add this python block python for PDB in PDBs: cmd.save("%s-K.pdb"%PDB,"%s"%PDB) python end Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/9/22 Troels Emtekær Linnet > # Firs load files in

Re: [PyMOL] Mutate residues in batch mode

# Firs load files in dirextory with: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ # load_sep.py # Load multiple PDB files into a multiple PyMOL objects # e.g. load_sep prot_*.pdb, prot # will create objects with names, prot1, prot2, prot3, etc. # Now the rest cd /home/tlinnet/Desktop #

Re: [PyMOL] Write in a file the number of water at a distance from a

Thanks Marius With the second it works A bientot Stephane -Message d'origine- De : Marius Retegan [mailto:marius.s.rete...@gmail.com] Envoyé : jeudi 22 septembre 2011 18:02 À : intra\sa175950 Objet : Re: [PyMOL] Write in a file the number of water at a distance from a Hello Stephan

[PyMOL] Write in a file the number of water at a distance from a

Hi All, With the help of Thomas Holder (thanks to him), now I can show and obtain the number of water in the first shell of my six peptides (an amyloid fibrils). However, I have a little problem with the command count_atoms in my script Below my script (*.pml) for Pymol 1.3 : mstop dss hide al

[PyMOL] Mutate residues in batch mode

Hi Pymolers, I need to perform a batch operation but I need a help with script modification. A have a set (~100) of pdb files that I would like to mutate all residues to lysine. I modified mutate02.py script in pymol to perform this task, but I would need two extra "features": 1) the script would

Re: [PyMOL] Using Volumes

On 12 sept. 2011, at 14:20, Jason Vertrees wrote: > Greetings, > > One chance encounter at ACS couple weeks ago turned into a multi-day > discussion about using the new volume visualization for presenting > field data. Leroy Laverman from UCSB now has some example movies > showing how the electr

[PyMOL] RE : Write in a file the number of water at a distance from a protein surface

Thank you for your response, i will try your suggestion A bientot Stephane De : Thomas Holder [ad...@thomas-holder.de] de la part de Thomas Holder [spel...@users.sourceforge.net] Date d'envoi : jeudi 22 septembre 2011 11:14 À : ABEL Stephane 175950 Cc : p

Re: [PyMOL] Write in a file the number of water at a distance from a protein surface

Hi Stephane, you can select those waters using the "within" or "gap" selection operators. "within" measures from the atom centre, whereas "gap" takes the VDW radius into accout but selects everything beyond instead of near. Have a look at those examples: # use '... within ...' select firstshel