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

Eric, You made my day 5 hour shorter. Yeah..I want to get good charges using chimera. Thanks a lot for your help. s On Feb 4, 2008 4:00 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

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, In the Python language, indentation is significant. It seems you didn't preserve the indentation levels when you copied what I sent. In particular, I'm guessing that line 6 ("residues = m.residues") and all following lines lack indentation. I have _attached_ a copy of the script so that when you use it the indentation will be correct. --Eric On Feb 26, 2008, at 12:24 PM, snoze pa wrote:

Hi Eric, The scripts is not working.. It is giving me following error message. Is it possible to call the minimization step inside the script so that i can use the bcc charges? Thanks a lot for your help.

chimera --nogui x.mol2 script.py Sorry: IndentationError: ('expected an indented block', ('script.py', 6, 8, 'residues = m.residues\n'))Opening x.mol2...Compiling script.py...Compiling script.py succeededExecuting script.py... Traceback (most recent call last): File "/usr/local/chimera/share/_ _main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 350, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1378, in open File "CHIMERA/share/chimera/__init__.py", line 865, in _openPython IndentationError: expected an indented block (script.py, line 6) Error while processing script.py: IndentationError: expected an indented block (script.py, line 6) (see reply log for Python traceback info)

On Mon, Feb 4, 2008 at 4:00 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: 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