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, ChargeError
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)
try:
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")
log.close()

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

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu

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@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@cgl.ucsf.edu
http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users