[Chimera-users] Trajectory analysis: RMSD

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 27 10:04:25 PST 2012

Hi George,
Chimera doesn't do fluctuation analyses across the whole trajectory, although you could (with some work) make many individual measurements that would let you calculate the fluctuations yourself.  So the short answer is you may want to use some other trajectory analysis capability, such as ptraj for AMBER.  Usually there is some analysis module associated with whatever software you are using to calculate the MD. I haven't done this myself, so I don't know the details.

In Chimera, here are a few related possibilities:
(a) "RMSD analysis" in MD Movie, which means all-by-all (all frames) RMSD calculations for a specified set of atoms.  The values are shown as a grayscale plot, and can be saved to a file.  However, this does not compare to some other structure, it only compares different frames in the trajectory, and you would have to do a separate calculation for each set of atoms (each residue).
See "RMSD Analysis" in the MD Movie docs:

(b) use a per-frame script with "rmsd" commands to measure RMSD values at each step.  The reference structure would also be open, and the commands would compare atoms in each frame to atoms in the reference structure.  However, again you'd have to specify each set of atoms, so you'd probably need another script to cycle through all residues, and at the end, you would still have to calculate the fluctuations from the raw RMSD values.
See "Per-Frame Scripts" in the MD Movie docs:

(c) to see a histogram of CA-CA distance per residue (trajectory structure to reference structure) at any given single trajectory frame, you could show the sequence of the trajectory structure, also associate the reference structure with it, and in the sequence window, show the RMSD header.  That calculation only uses CA atoms, so with only two structures the "RMSD" simply boils down to CA-CA distance.

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 27, 2012, at 7:21 AM, George Tzotzos wrote:

> Hi everybody,
> I'm wondering if there's a way to find out per-residue RMSD fluctuation in a trajectory. I'm trying to find the parts of the backbone that show the greatest RMSD fluctuation against a reference structure.
> A good weekend to you all
> George

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