Thanks Osvaldo for your suggestion .
I will work it out and let you know if any issues raises .
Regards
On Mon, Aug 24, 2015 at 5:17 PM, Osvaldo Martin
wrote:
> Dear Vinod,
>
>
> One option is to call PyMOL function from Python script.
>
> import __main__
> __main__.pymol_argv = ['pymol','-q
Dear Vinod,
One option is to call PyMOL function from Python script.
import __main__
__main__.pymol_argv = ['pymol','-qc']
import pymol
from pymol import cmd, stored
pymol.finish_launching()
cmd.set('dot_solvent', 1)
cmd.set('dot_density', 3)
cmd.load('pdb.file') # use the name of your pdb fil
I am very unsure of your question, but I believe you're asking if you have
a PDB id, how to load that into pymol. For that, you can use the fetch
command ( http://www.pymolwiki.org/index.php/Fetch )
You type:
fetch 1acb
into the pymol interface and it will download pdb id 1acb and load it into
the
I will try this
thank you for your input
Sent from my iPhone
> On Sep 9, 2014, at 12:00, David Hall wrote:
>
> I am very unsure of your question, but I believe you're asking if you have a
> PDB id, how to load that into pymol. For that, you can use the fetch command
> ( http://www.pymolwiki
Hi,
> Just a small doubt
> cmd.load("pdb%04d.pdb"%ener1)
> cmd.load("pdb%04d.pdb"%ener2)
> so if
> ener1 =0001
> ener2 =0002
> The program will understand the pdb0001 and pdb0002 in
> v = cmd.fit("pdb0001 and name CA", "pdb0002 and name CA") or not ?
> or would I need to assign them some names
Hello,
> I am quite new to python and more specifically to PYTHON ,PYMOL interface
> hence I urgently need a help from you.
Welcome! This list has about 1500 people on it and is accepting of
new users. A couple hints to get you started. First, you can type
"help commandName" in PyMOL to help o
Hi Aaron,
> I am somewhat new to PYMOL and was trying to create a selection of atoms.
> What I need to do is select all atoms of a protein that are within 5
> angstroms of an inhibitor (the protein and inhibitor are separate
> molecules). I cannot figure out how to do this from the examples in t
Thanks to the previous responders! In addition, versions 0.82 and beyond
support a more intuitive distance selection phrase:
"... within ... of ..."
For example:
load lig.pdb
load prot.pdb
select site,prot within 6 of lig
show surface, site
Note that if the ligand and protein are in the same
Hello Aaron,
* aaron.b.mil...@gsk.com [2002-10-11 15:36] wrote:
> Hello,
>
> I am somewhat new to PYMOL and was trying to create a selection of atoms.
> What I need to do is select all atoms of a protein that are within 5
> angstroms of an inhibitor (the protein and inhibitor are separate
> mole
select ligands, (byres gmp expand 5 and psd)
selects whole residues from molecule psd within 5 A from gmp
aaron.b.mil...@gsk.com wrote:
Hello,
I am somewhat new to PYMOL and was trying to create a selection of atoms.
What I need to do is select all atoms of a protein that are within 5
angstro
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