[chimera-dev] Does chimera support molecules from MMTK

Eric Pettersen pett at cgl.ucsf.edu
Wed Jun 18 13:24:38 PDT 2014

Hi JD,
	Are you asking whether Chimera can read those files and display a molecule from them?  If so, the answer is no -- there are no coordinates in those files.  They are essentially topology files with charge and atom type information.
	If what you need is the atom types and charges from the file added to an existing structure it wouldn't be hard to whip up a Python script that read that format and spit out 'defattr' files that could be used to set the 'charge' and 'gaffType' attributes of the corresponding atoms.  Of course in such a case you might as well cut out the middleman and write out the defattr files yourself directly from whatever data source you are getting the charges and atom types.
	Maybe I'm misunderstanding your question?  If so, please explain more…


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Jun 18, 2014, at 3:21 AM, Jean-Didier Maréchal <jeandidier.marechal at uab.cat> wrote:

> Dear all,
> I would like to avoid gaff assignation with the dock prep interface (basically, I need to work with some organometallic compounds) and I was wondering if chimera accepts MMTK molecules ( as can be found in lib/site-packages/MMTK/Database/Molecules).
> I believe this would be of the best way to expand the force field inside chimera.
> Cheers,
> JD
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