[chimera-dev] Question regarding MMTK

Conrad Huang conrad at cgl.ucsf.edu
Wed Feb 11 11:59:11 PST 2009

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.


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 at uab.es

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