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
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
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
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
(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
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
..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
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
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
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
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
---
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
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
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 SchrÓ§dinger to supplement the income of an outstanding
member of the PyMOL open-source community to dev
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