[PyMOL] Access to pymol commands from the terminal

Dear PyMol users! I'd like to find possibilities for running of some pymol commands from the terminal. For instance in my case I' d like perform 2 simple steps (both in terminal not in the pymol GUI) to remove water and ions from my target input pdb (typical I do it via gromacs editconf) superimpo

Re: [PyMOL] Access to pymol commands from the terminal

Hi James, You can use pymol -cd "pymolcommands". See http://www.pymolwiki.org/index.php/Command_Line_Options However, the first part is much easier with grep or sed. To remove all solvent molecules: grep -v "^ATOM.*SOL" in.pdb > out.pdb To remove NA+/CL- too grep -v "ATOM.*\(SOL\|NA+\|CL-\)" i

Re: [PyMOL] Access to pymol commands from the terminal

Hi Tsjerk, Thanks alot! Also I have the task to merge protein.pdb and lipids.pdb with some 1 line shell command ( like CAT) to obtain protein inserted in the lipids (the seccond file is consist of the whole which can locate the protein). My problem is that both protein.pdb and lipids.pdb consisted

Re: [PyMOL] Access to pymol commands from the terminal

Hi James, grep '^\(ATOM\|HETATM\|CRYST1\)' protein.pdb lipid.pdb > merged.pdb Oh, the joy one has from reading a sed/grep/awk tutorial :) Cheers, Tsjerk On Thu, Sep 4, 2014 at 12:19 PM, James Starlight wrote: > Hi Tsjerk, > > Thanks alot! > Also I have the task to merge protein.pdb and lip

Re: [PyMOL] Access to pymol commands from the terminal

(sed '1d' protein.pdb; sed '1d' lipid.pdb) > merged.pdb --or-- tail -q -n '+2' protein.pdb lipid.pdb > merged.pdb -David On Thu, Sep 4, 2014 at 6:19 AM, James Starlight wrote: > Hi Tsjerk, > > Thanks alot! > Also I have the task to merge protein.pdb and lipids.pdb with some 1 line > shell

Re: [PyMOL] Access to pymol commands from the terminal

one question :) could someone explain me the ussage the pymol commands from the shell on the example e.g i need to load 2 pdbs in pymol make its superimposition and than save one of the superimposed pdb like load ref.pdb tar.pdb super tar, ref save tar > tar_superimposed.pdb I've tried to do part

Re: [PyMOL] Access to pymol commands from the terminal

..and one question about grep (really didn't find it in the tutorial) using grep '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb |cat > merged.pdb I've obtained good pdb BUT each line prior to the ATOM the name of the pdb of the previous files have been added eg: tarr_se.pdb:ATOM 1 N A

Re: [PyMOL] Access to pymol commands from the terminal

Use the -h flag with grep to suppress the filename. Also, you don't need to pipe to cat, you can write directly to the file. grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb > merged.pdb On 09/04/2014 10:38 AM, James Starlight wrote: ..and one question about grep (really didn't find

Re: [PyMOL] Access to pymol commands from the terminal

thanks! and do I need to pipe the below command to smth grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb > merged.pdb if I need to change 'END' to 'TER' in the merged.pdb ? 2014-09-04 16:54 GMT+02:00 James Starlight : > thanks! > > and do I need to pipe the below command to smth > gr

Re: [PyMOL] Access to pymol commands from the terminal

You could make a python script that import pymol and does what you want from there. Some thing like this (untested); import __main__ __main__.pymol_argv = ['pymol','-cqk'] # Pymol: quiet and no GUI import pymol pymol.finish_launching() from pymol import cmd reffile = sys.argv[1] tarfile = s

[PyMOL] map color turns to gray after ray

Hello all, I am trying to show two electron density map with two colors. It works normally on the session. But after ray, all the mesh turns to gray, no matter which colors were chosen for the maps. Any suggestions? Many thanks. Yahui ---

Re: [PyMOL] map color turns to gray after ray

Hello, a bit more details. Pymol version: 1.3 in windows I did following: isomesh to show the maps on interested region(2F0-fc and anomalous map ), set mesh_width, 0.5 choose colors on the gui (colors can be shown correctly) ray (backbones still show as colors, but all the map mesh turns to gray

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Hi, is there an easy way to select by size (number of atoms) ? I know there is a count_atoms function, but I can't see how to use it for this. Ideally I'd need to do something like "select sele1, organic and *n_atoms* > 10" where *n_atoms* would be used to select only ligands with > 10 atoms. Xev

[PyMOL] PyMOL Open-Source Fellowship - Call for Applications

Greetings, I am excited to announce that the Warren L. DeLano Memorial PyMOL Open-Source Fellowship program is now accepting applications for the 2014--2015 term. The Fellowship is awarded by Schrӧdinger to supplement the income of an outstanding member of the PyMOL open-source community to dev