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*
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