[Chimera-users] Distances measurement for NMR ensemble

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 14 13:48:43 PDT 2016

Hi James,
MD Movie plotting includes distances, angles, dihedrals, and/or RMSDs from the trajectory, and you can dump the values to a file.  See the “Plotting” section:

You can open a single multiple-model PDB file (such as used for NMR ensembles) as a trajectory with MD Movie and then use the plotting.  PDB input as a trajectory does not require any other files.  See the “Startup and Input” section of the link above.

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

> On Jul 14, 2016, at 7:04 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> Dear Chimera Users!
> I wonder to ask whether it possible to calculate distances between two
> selected atoms by means of the Chimera's Distance measurement tool
> providing as input NMR-ensemble consisted of 20 snapshots (without any
> additional files like topology!) or alternatively small md trajectory,
> obtaining also some elementrary statistics (E.g RMSD etc)
> Thanks!
> James

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