[Chimera-users] Visualizing Orientation of Side Chains

Christian Bock cbock1 at uw.edu
Tue Nov 22 13:31:02 PST 2016

Thanks for your response. It seems like the RMSD Plot makes more sense. I
was wondering what is actually calculated there? Could not find it in the
docu of the command. Is it just the proximity in the three dimensional


Elaine Meng <meng at cgl.ucsf.edu> schrieb am Do., 17. Nov. 2016 um 16:27 Uhr:

> 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:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> 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.
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009712.html>
> 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:
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html
> >
> rmsd command:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
> I hope this helps,
> Elaine
> ----------
> 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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