[chimera-dev] gaussian interface: getting nuts with connectivity
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Fri Jul 17 08:01:08 PDT 2009
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 at uab.es
----- Missatge original -----
De: chimera-dev-request at cgl.ucsf.edu
Data: Dijous, Juliol 9, 2009 9:00 pm
Assumpte: Chimera-dev Digest, Vol 66, Issue 2
> Send Chimera-dev mailing list submissions to
> chimera-dev at cgl.ucsf.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
> or, via email, send a message with subject or body 'help' to
> chimera-dev-request at cgl.ucsf.edu
>
> You can reach the person managing the list at
> chimera-dev-owner at cgl.ucsf.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Chimera-dev digest..."
>
>
> 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)
>
>
> --------------------------------------------------------------------
> --
>
> Message: 1
> Date: Thu, 9 Jul 2009 17:32:22 +0200
> From: Davide Ba? <dbau at cipf.es>
> Subject: [chimera-dev] Generating images in chimera with the --nogui
> option
> To: chimera-dev at cgl.ucsf.edu
> Message-ID:
> <3e4b67ca0907090832r4e46b826i5dfe81842b58685a at 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 at cipf.es*
> Web: *http://sgu.bioinfo.cipf.es/dbau*
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://www.cgl.ucsf.edu/pipermail/chimera-
> dev/attachments/20090709/7ce22b79/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Thu, 9 Jul 2009 10:04:53 -0700 (PDT)
> From: Greg Couch <gregc at cgl.ucsf.edu>
> Subject: Re: [chimera-dev] Generating images in chimera with the
> --nogui option
> To: Davide Ba? <dbau at cipf.es>
> Cc: chimera-dev at cgl.ucsf.edu
> Message-ID: <Pine.OSF.4.63.0907090956280.1975366 at guanine.cgl.ucsf.edu>
> Content-Type: text/plain; charset="x-unknown"
>
> To generate chimera images with --nogui, you need to use a Headless
> chimera. Currently, they are only available as chimera daily
> builds and
> only for Linux and Linux 64-bit.
>
> - Greg
>
> On Thu, 9 Jul 2009, Davide Ba?? wrote:
>
> > 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 script
> > execute 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 at cipf.es*
> > Web: *http://sgu.bioinfo.cipf.es/dbau*
> >
>
> ------------------------------
>
> _______________________________________________
> Chimera-dev mailing list
> Chimera-dev at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
>
>
> End of Chimera-dev Digest, Vol 66, Issue 2
> ******************************************
>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ar.mol2
Type: chemical/x-mol2
Size: 2050 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-dev/attachments/20090717/7d5881db/attachment.bin>
-------------- next part --------------
El document original
ha estat eliminat per l'antivirus.
El motiu ha estat:
Fitxer adjunt amb extensió potencialment perillosa (vbs, vbe, js, jse,scr, exe, com, bat, lnk, ceo, htt, pif)
Per a més informació vegeu: http://www.uab.es/si/virus_correu/
More information about the Chimera-dev
mailing list