[Chimera-users] Trajectory B-factors

[Eric Pettersen]

On Sep 15, 2014, at 2:47 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Actually, Chimera's tool for viewing trajectories, MD Movie, does "RMSD analysis" but that's somewhat different; it plots all-frame-by-all-frame RMSDs in a grid where each value is an RMSD over all specified atoms.  Basically, it's for comparing whole frames (MD timepoints, snapshots of the whole structure) to one another, not for evaluating local conformational variability.

…and related to that (but still not what you're asking for unfortunately) is that you can plot the RMSD of selected atoms against their position in a particular frame (usually the initial frame / starting position, but it doesn't have to be).

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


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