[Chimera-users] command line mode

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 4 14:00:53 PST 2008

Hi Snoze,
	I'm going to guess, like Elaine, that your purpose is to add partial  
charges.  If your 1000 compounds are in one big mol2 file, here is a  
script that would do the job:

from chimera import openModels, Molecule
from AddCharge import addNonstandardResCharges, estimateFormalCharge,  
mols = openModels.list(modelTypes=[Molecule])
log = open("errlog", "w")
for m in mols:
	residues = m.residues
	atoms = [a for r in residues for a in r.atoms]
	fc = estimateFormalCharge(atoms)
		addNonstandardResCharges(m.residues, fc)
	except ChargeError:
		print>>log, "Charge estimate (%d) or protonation wrong for %s (%s)"  
% (
			fc, m.name, m.oslIdent())
from WriteMol2 import writeMol2
writeMol2(mols, "output.mol2")

If you save the above in a file named script.py and your 1000  
compounds are in a file named input.mol2, then running:

	chimera --nogui input.mol2 script.py

will produce a file named output.mol2 with the charges included.  Any  
problems it had charging particular compounds will be saved in a file  
named errlog.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Feb 1, 2008, at 10:36 AM, Elaine Meng wrote:

> Hi Snoze,
> One of the main  uses of the ZINC database is to generate ligand sets
> for DOCK; I believe you can download mol2 format directly from ZINC,
> and that the molecules already have hydrogens and charges.  See
> http://zinc.docking.org/
> But maybe you wanted to use Antechamber inside of Chimera to get
> different charges.  If so, somebody else will have to answer the
> scripting part of your question!
> Best
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> On Feb 1, 2008, at 9:47 AM, snoze pa wrote:
>> Dear Chimera Users,
>>  How can I use chimera in --nogui mode to screen 1000 compunds from
>> ZINC database and save them in to mol2 format.
>> Is there any script so that I can convert preselected 1000 compound
>> from ZINC database and convert them  t o mol2 format so that I can
>> use them in DOCK program.
>> thanks in advance
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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