Distances measurement for NMR ensemble
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
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: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h...> 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 ---------- 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@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
Thanks so much Elaine ! I love Chimera !! James 2016-07-14 22:48 GMT+02:00 Elaine Meng <meng@cgl.ucsf.edu>:
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: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h...>
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 ---------- 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@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
participants (2)
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Elaine Meng -
James Starlight