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

[Eric Pettersen]

Hi Ryan,
	Unfortunately, coordinates are the only attribute that works on a per-frame basis.  We hope to remedy that in Chimera 2, but we are nowhere near even an alpha release of Chimera 2 so that isn't really relevant here.  If you only need this for movie recording and your machine has a lot of memory relative to the size of these trajectories, then what you can do is sort of a riff on your workaround 2:  open the trajectory both as submodels and with MD Movie and copy the anisoU attribute on an as-needed basis with the per-frame scripting capability of MD Movie (Per-Frame/Define Script).  Here's a Python script you could use in the Define Script dialog to do the copying:

from chimera import openModels, Molecule
mols = openModels.list(modelTypes=[Molecule])
for m in mols:
	if m.subid == mdInfo['frame']:
		for pdbAtom, trajAtom in zip(m.atoms, mdInfo['mol'].atoms):
			trajAtom.anisoU = pdbAtom.anisoU
		break

You could add an aniso command after the copy via the runCommand method:

from chimera import runCommand
runCommand("aniso args-you-want...")

	This is going to make trajectory playback sluggish, so is only really useful for movie recording I'd say.  Of course, showing the aniso surfaces was probably making playback sluggish anyway!

--Eric

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

On Nov 23, 2012, at 9:47 AM, Ryan Harrison wrote:

> 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



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