[Chimera-users] Trajectory B-factors

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 15 14:47:41 PDT 2014


Hi George,
Chimera doesn't calculate measures of conformational variability at a position such as RMSF, RMSD, or B-factors directly from a trajectory.  The only way using Chimera alone that I can think of would be to save the trajectory to PDB, say a single multi-model file, then read it in as a regular ensemble PDB (not as a trajectory), superimpose the submodels if they aren't already, then follow the general multiple-structure procedure you mentioned:

<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009710.html>

We have made a minor improvement since then… if you get a recent daily build, you can associate all the ensemble models with the sequence with only a few steps, instead of the tedious one-by-one procedure mentioned in that earlier post.

However, that may still be very time- and space-inefficient, especially if you have a lot of frames to compare.   It would probably be better to use trajectory analysis software outside of Chimera (e.g. ptraj for AMBER, many others) to calculate the desired values, then if you want to display them in Chimera, reformat to an "attribute file" to map the values to atoms or residues .  Attribute file format is fairly simple:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile>

Unfortunately I don't know the details of trajectory analysis programs, so I don't have specific recommendations in that area.

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.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#rmsd>

Best,
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 Sep 15, 2014, at 1:09 PM, George Tzotzos <gtzotzos at me.com> wrote:

> Hi everybody,
> 
> Is there a way to calculate the B-factors of the backbone atoms of protein residues in a MD trajectory?
> 
> I checked earlier correspondence and saw that it can be done in Chimera with pdb structures.
> 
> Many thanks in advance for any suggestions
> 
> Regards
> 
> George




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