[Chimera-users] Visualization Martini coarse grained model in Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 12 11:58:40 PST 2017


Dear Rahman,
Although we have not tried it ourselves, it must be possible because some other user has done it using version 1.10.2 or later, as mentioned in this previous post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-May/012295.html>

That user had the Martini trajectory in the Gromacs format, so I guess you would need to use that format too.   You would start the “MD Movie” tool (Tools… MD/Ensemble Analysis… MD Movie) and specify the input Gromacs files (.tpr file and .trr or .xtc file).

There are lots of features in MD Movie, see the manual:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.htmlL

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 8, 2017, at 9:04 PM, MOHD HOMAIDUR RAHMAN <rahmanhpu at gmail.com> wrote:
> 
> Dear All 
> 
> It is possible to visualize martini coarse grained bead of proteins and lipid in Chimera?
> if yes please guide me for same.
> 
> Thanks & regards
> Rahman




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