[Chimera-users] Visualizing Orientation of Side Chains

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 17 16:25:49 PST 2016

Hi Christian,
Not sure if by “visualize” you mean visualizing the actual 3D structures, or making some kind of RMSD plot.

If you’re just viewing the structures, no reason to make a trajectory.  Just open the structures and superimpose them in some way that you feel is appropriate (with match or matchmaker command), display the parts you want to see and undisplay the parts you don’t want to see.  Discussion of the different ways to superimpose structures:


To show per-residue RMSD as a histogram over the sequence for a large number of structures, you could just open them all and associate them with the same sequence.  Sounds like the structures are all the same sequence anyway, so you could just show the sequence for one of them and associate all the others with that sequence as well.  The basic steps are outlined in the previous post linked below, except now you have the choice of other RMSDs over more atoms, not just the CA-RMSD. Note, however, that they are not automatically symmetry-corrected… even though some Phe could look exactly superimposed, for example, if the atoms with the same names are on opposite sides of the ring, Chimera is not smart enough to calculate the lowest RMSD given the chemical equivalences (it uses the names only).  Also you’d still have to take care of the superposition yourself, since for different purposes one might want to use different atoms for the fitting.


That post also describes coloring any one of the structures to show this conformational variability. You can also write out the values using the File menu of the Render by Attribute dialog mentioned in step 4, or use Render by Attribute to show the values with worm fatness instead of or in addition to color.

The possible reasons to make a trajectory would be to run a per-frame script that does something to all the frames, and/or to automatically play through the different structures as if they were a time series.  You don’t have to put them all in one PDB file, you could also make serially numbered PDB files (see the multiple-PDB-files input option of MD Movie).  However, I don’t think it makes sense to put the correct structure into the trajectory.  Instead you could leave it separate and only put the predictions in the trajectory, and have the MD Movie per-frame script superimpose each frame (predicted structure) with the reference structure (which would be a separate model opened independently of the trajectory) and measure rmsd with the “rmsd” command.

MD movie, see “input” and “per-frame scripts” sections:

rmsd command:

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 17, 2016, at 3:44 PM, Christian Bock <cbock1 at uw.edu> wrote:
> Hello,
> I am new to Chimera and want to visualize how the side chain orientation for a specific residue changes in different structure predictions. Means I have a correct structure and several predictions and I want to see how different the orientations are among the predictions with reference to the correct structure. I was looking at the MD movie but I am not sure if it's smart to put the correct structure and all predictions into one .pdb file to make a movie. Does anyone has other suggestions? 
> Thanks,
> Christian 
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