[chimera-dev] Linking Chimera with our molecular simulation tool-kit

[Lianheng Tong]

Dear Chimera developers,

I am a postdoc research associate working with Prof. Lev Kantorovich of King’s College London. I am currently a full time developer for the ab initio atomic simulation code CP2K, and as a part of our project funding, we are looking to develop a tool kit that would improve user friendliness that would allow the users to construct various bulk or molecular structures in an intuitive and graphically way.

We currently have a quite extensive tool-kit (tetr) developed by Prof. Kantorovich for generating, modifying structures—especially tailored for periodic systems, as well as post processing utilities on volume data (such as generating STM images etc).  It is written in FORTRAN, and currently is command based only, with the user input being either interactive or by a batch file.   The goal, is to be able to link to a visualisation package like Chimera, so that: 

a) one is able to automatically update the visualisation when the user uses the tool interactively
b) allow the user to select atoms and fragments and use these selections as an input to the tool-kit.

Ideally, the took-kit can run as an independent code, with the extension providing an interface between Chimera and the tool-kit. The user would then control the tool-kit from within the Chimera command interface.

I have used Chimera a lot during my PhD, however, I have not yet written any extension for it. I do, however, have quite a number of years experiences with code development, especially in Fortran and in Python.  I am wondering:

1)  If you would mind if we develop an extension to link our took-kit with Chimera
2)  If the functionalities I mentioned above would be possible to achieve

Any suggestions from you would be great. Thank you very much for your time, and I look forward to hearing from you soon.

Best regards,

Lianheng

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Lianheng Tong
Room S4.02, Strand Building
Department of Physics
Kings College London
Strand, London WC2R 2LS, U.K.
Tel: +44 20 7848 2064
Fax: +44 20 7848 2420
lianheng.tong at kcl.ac.uk
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