Hi everyone, I have a question regarding the MMTK interfase. How complicate it is to get the hand on a the MMTK script and input files generated by chimera to perform the minimization ? Is it located in some subfolder? Is there a way to write it down so that I can perform further calculations outside the chimera environment? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic 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: Dimecres, Febrer 4, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 61, Issue 1
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Today's Topics:
1. alias menu (Richmond Timothy J.) 2. Re: alias menu (Elaine Meng) 3. Re: alias menu (Eric Pettersen)
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Message: 1 Date: Wed, 4 Feb 2009 14:09:53 +0100 From: "Richmond Timothy J." <richmond@mol.biol.ethz.ch> Subject: [chimera-dev] alias menu To: <chimera-dev@cgl.ucsf.edu> Message-ID: <874055BA140585479966DE1694AB0421F058B5@EX6.d.ethz.ch> Content-Type: text/plain; charset="iso-8859-1"
Dear Chimera Developers,
Perhaps I have missed it, but I would find a menu for selected aliases very useful. Having returned to Chimera from PyMol recently, it would be great to have an option for the alias command that allowed the particular alias to be listed in a separate window and ran the alias by clicking on the alias name listed there.
Best regards,
Tim
-------------------------
ETH Zurich
Prof. Timothy J. Richmond
Institute of Molecular Biology and Biophysics
HPK F 18
Schafmattstr. 20
8093 Z?rich
SWITZERLAND
richmond@mol.biol.ethz.ch
http://www.mol.biol.ethz.ch/groups/richmond
+41 44 633 24 70 phone
+41 44 633 11 50 fax
Chimera calls the MMTK Python API directly and does not generate any separate MMTK Python scripts. This is because there are a number of steps that Chimera needs to perform before MMTK can be used, eg adding hydrogens, assigning charges, etc. The main source code is in class MMTKinter in file CHIMERA/share/MMMD/MMTKinter.py. As for using MMTK outside of Chimera, you can certainly save the minimized structure as input for MMTK. The partial charges, however, may be a bit tricky. I've not used MMTK outside the context of Chimera so I'm not that familiar with all the different options available. Probably, the easiest way to get a usable MMTK configuration externally is to modify MMTKinter.py so to add an interface for calling MMTK.save() to save the Chimera-created universe to a file, and then use MMTK.load() in your script to read it back in. Conrad Jean Didier Pie Marechal wrote:
Hi everyone,
I have a question regarding the MMTK interfase. How complicate it is to get the hand on a the MMTK script and input files generated by chimera to perform the minimization ? Is it located in some subfolder? Is there a way to write it down so that I can perform further calculations outside the chimera environment? All the best, JD
Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic 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
participants (2)
-
Conrad Huang -
Jean Didier Pie Marechal