atom.anisoU does update as expected for MD trajectories
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*
m1.activeCoordSet = m1.coordSets[2] m1.atoms[1].anisoU *# <~~~ ANISO for last model in PDB file, not model 2
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... * 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
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
participants (2)
-
Eric Pettersen -
Ryan Harrison