Hi JD, I don't think you attached the right file. The file you attached is just a Mol2 file. Nonetheless, from the format description you provided I think you just want to loop through Molecule.atoms and then for each atom its bondsMap in order to write your file. The major stumbling block is that Chimera doesn't compute bond orders. The mol2 module guesstimates them using a few heuristics, but could certainly get them wrong in complex situations. You could just conscript the half page of code that does the estimation into your own module if you felt that it was "good enough". Otherwise you're going to have to write some code to generate bond orders consistent with the atoms' types. If the systems you work with aren't too large that would be feasible (though non-trivial) but for large systems would likely be slow unless you coded it in a compiled language (urg!). At any rate, assuming that you've obtained bond orders for bonds somehow, the template for writing the format you need would be: # may need to fetch m.atoms and sort it into Gaussian order # instead of using m.atoms directly... for a in m.atoms: # 'identifer' dictionary maps atoms to Gaussian name print>>outf, identifer[a], for nb, b in a.bondsMap.items(): print>>outf, identifier[nb], order[b], print>>outf On Jul 17, 2009, at 8:01 AM, Jean Didier Pie Marechal wrote:

Dear all,

I am trying to make chimera an interface for the quantum mechanical program gaussian. Pretty much everything seems to go smooth but I am getting crazy (stupid?) because I can't reproduce the geometry connectivity gaussian wants. I used tools of chimera I know for bond mapping and connectivity. But I can't get to the right connectivity format.

I join you here an input file of gaussian (a ARG-ALA dipeptide). If you look at the file, the connectivity between the atoms is at the end and is in the following form:

atom 1, atom 2, bond_order, atoms 3, bond_order (etc for all atoms linked to atom 1) ...

atom 31 (to 37 = all terminal atoms).

I have been using the different atoms attributes I know like neighbors, bonds and bondMap, but I can't see how to proceed neither I see how to use the bond order calculations as in the mol2 module. If you have time and can give me a hint, I would be extremely greatful

Thank you very much,

best JD

Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es

----- Missatge original ----- De: chimera-dev-request@cgl.ucsf.edu Data: Dijous, Juliol 9, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 66, Issue 2

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Today's Topics:

1. Generating images in chimera with the --nogui option (Davide Ba?) 2. Re: Generating images in chimera with the --nogui option (Greg Couch)

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Message: 1 Date: Thu, 9 Jul 2009 17:32:22 +0200 From: Davide Ba? <dbau@cipf.es> Subject: [chimera-dev] Generating images in chimera with the --nogui option To: chimera-dev@cgl.ucsf.edu Message-ID: <3e4b67ca0907090832r4e46b826i5dfe81842b58685a@mail.gmail.com> Content-Type: text/plain; charset="utf-8"

Hi,

my name is Davide and I'm currently working on Marc Marti-Renom's group. I'm trying to generate an image using chimera with the --nogui option:

chimera --nogui --nostatus --script cmd.py

The file cmd.py contains the following lines:

from chimera import runCommand

...

runCommand('open input.cmm') runCommand('copy file image.png png')

but I keep getting the following error message:

Traceback (most recent call last):

...

File "/usr/src/chimera/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 384, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1344, in open File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython File "cmd.py", line 3, in <module> runCommand('copy file image.png png') File "CHIMERA/share/chimera/__init__.py", line 2025, in runCommand File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand File "CHIMERA/share/Midas/midas_text.py", line 563, in doCopy File "<string>", line 1, in <module> File "CHIMERA/share/Midas/__init__.py", line 908, in copy File "CHIMERA/share/chimera/printer.py", line 1182, in saveImage AttributeError: '_chimera.NoGuiViewer' object has no attribute 'pilImages'> Error while processing cmd.py: AttributeError: '_chimera.NoGuiViewer' object has no attribute 'pilImages'> (see reply log for Python traceback info)

cmd.py was generated from within chimera using the "record" command of chimera's "command line". If I delete the line "runCommand('copy file image.png png')", the scriptexecute with no error.

Is it possible to generate images using the --nogui option?

Thanks a lot for your help!

Best regards, Davide

____________ *Davide Ba?* Structural Genomics Unit Bioinformatics & Genomics Department, Prince Felipe Research Center Avda. Autopista del Saler, 16 , 46012 Valencia, Spain Tel: +34 96 328 96 80 (ext. 1021) Fax: +34 96 328 97 01 Email: *dbau@cipf.es* Web: *http://sgu.bioinfo.cipf.es/dbau*