Dear Chimera team,

I've encountered a problem with atom.anisoU. Since class Atom is implemented in C++, and I don't have the technical sophistication or nerve to build chimera from scratch after the dire warning, [1] I seek council.

I'm using PDB ANISOU to store orientation information from a coarse grained model. Using PDB MODEL and PDB ENDMDL I output trajectory information. PDB atom coordinates and aniso change with each frame in the trajectory.

When visualizing a coordSet in the trajectory, atom.coord() updates as expected...
# m1 is a model with ANISO information
>>> m1.activeCoordSet = m1.coordSets[2]
>>> m1.atoms[1].coord()
chimera.Point(-0.268, 0.002, 0.08) # <~~~ As expected from PDB file
>>> m1.activeCoordSet = m1.coordSets[10]
>>> m1.atoms[1].coord()
chimera.Point(0.012, -0.276, -0.043) # <~~~ Changes as expected from PDB file

However, atom.anisoU does not update as expected [2, 3]. It is always the PDB ANISO information from the last model (last MD trajectory) in the file...
>>> m1.activeCoordSet = m1.coordSets[2]
>>> m1.atoms[1].anisoU # <~~~ ANISO for last model in PDB file, not model 2
array([[ 0.0296, 0.0182, 0.0201],
       [ 0.0182, 0.0844, -0.0055],
       [ 0.0201, -0.0055, 0.1258]], dtype=float32)
>>> m1.activeCoordSet = m1.coordSets[10]
>>> m1.atoms[1].anisoU # <~~~ Again, ANISO for last model in PDB file, not model 10
array([[ 0.0296, 0.0182, 0.0201],
       [ 0.0182, 0.0844, -0.0055],
       [ 0.0201, -0.0055, 0.1258]], dtype=float32)

The result is visualizations with proper coordinates (update properly for each frame in trajectory) but inaccurate ellipsoids (ANISO does not update; fixed as last frame / last model).

Work around 1 (Failed):
Since aniso takes spec atom-spec as an input, I tried specifying a model and position in trajectory. Unfortunately, this doesn't seem to be possible [4].

Work around 2 (Tedious):
Since aniso can take submodels, I import (cannot use nifty MD Movie tool) as sub-models instead of as a trajectory. I can then apply aniso to each submodel, which works as expected, and switch submodels on/off sequentially to make a movie (5). This is not ideal since I'm missing out on the ease of use of the MD Movie tool, and it's very cumbersome to move through a stack of submodels to emulate a trajectory.

Thank you for your time and please help!

Best,
Ryan

--
Ryan M Harrison
Wolfson College
University of Oxford
NIH-Oxford Graduate Partnership Program
http://graylab.jhu.edu/~ryan/
http://www.linkedin.com/in/rmharri