[chimera-dev] atom.anisoU does update as expected for MD trajectories

[Ryan Harrison]

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<http://www.cgl.ucsf.edu/chimera/sourcecode.html>]
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<http://www.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007246.html>,
3<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-December/003377.html>].
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<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
].

*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<http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003800.html>).
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
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