[Chimera-users] Opening DESMOND trajectories in Chimera,

[Eric Pettersen]

Hi Shriyash,
	Chimera can read Maestro files, but not as a trajectory — I believe you will get a very large number of separate models.
	Using VMD as an intermediary looks like if would work.  You can write a DCD file as per:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/12717.html <http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/12717.html>

You can also write the corresponding PSF with Extensions  Modeling  Automatic PSF Builder, though you might need to have started from a PDB file — i’m not sure.  There’s a tutorial here:

Generating a Protein Structure File (PSF) <http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node6.html>

—Eric


	Eric Pettersen
	UCSF Computer Graphics Lab




> On Jul 27, 2017, at 9:46 AM, Shriyash Upadhyay <shriyash.upadhyay at gmail.com> wrote:
> 
> Hello,
> 
> I am a researcher using DESMOND to run molecular dynamics simulations of protein-DNA interactions. However, I and others in my lab are most comfortable viewing trajectories and creating images in UCSF chimera. Is there a way to export DESMOND trajectories in a format that Chimera can open, either from maestro or some intermediate program like VMD?
> 
> Thanks,
> Shriyash Upadhyay
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170728/d5281d7c/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: img17.png
Type: image/png
Size: 131 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170728/d5281d7c/attachment.png>