[Chimera-users] Visualizing Orientation of Side Chains

Christian Bock cbock1 at uw.edu
Tue Nov 29 11:41:55 PST 2016

Hi Elaine,
thanks for that. I was trying to load the reference and predicted
structures into a trajectory but run into an error: Residue 1 not in first
model on line 2857 of someTmp.pdb. I guess there are problems with aligning
the predicted structure to the reference? Does the residue sequence number
in the .pdbs have to be the same?


Elaine Meng <meng at cgl.ucsf.edu> schrieb am Di., 22. Nov. 2016 um 15:34 Uhr:

> Hi Christian,
> I still don’t know whether you want the per-residue RMSD histogram or
> overall-structure single RMSD values, but I see I messed up the last part
> of my previous reply:
> MD Movie (trajectory viewer) does allow plotting of the RMSD of every
> frame against a reference frame, so it would work to put both the actual
> structure and predicted structures all into one trajectory, and you
> wouldn’t have to generate the plot outside of Chimera.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#plotting
> >
> If all the structures are NOT in a trajectory but they contain exactly the
> same set of atoms with the same names (although their positions may be
> different)  and there aren’t too many predictions (more than a couple
> dozen) you could use Ensemble Match instead.  You’d still have to put all
> the predictions into one mult-MODEL PDB file, though, optionally also with
> the actual structure.
> The MD Movie and Ensemble Match approaches only give one RMSD per
> predicted structure vs the actual structure, using whatever atoms you
> specify.
> I hope this helps,
> Elaine
> > On Nov 22, 2016, at 2:29 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi Christian,
> > The RMSD histogram above a sequence (or sequence alignment) with
> multiple associated structures is described here:
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers
> >
> >
> > The histogram bar height relates to the RMSD among the structure
> residues associated with that position in the sequence, with options ca (CA
> atoms only), backbone, or full.  So yes, it is their proximity in 3D
> space.  If the structures aren’t superimposed, the values will be large.
> >
> > How this RMSD histogram over the sequence differs from other RMSD
> measurements in Chimera is that it is per residue, so you can see how the
> variability in space is different for different parts of the structure.
> >
> > If instead you want a single RMSD over  different conformations of the
> whole structure (or some specific set of atoms you specify), then you would
> use one of the other types of RMSD calculations in Chimera, of which there
> are many:  the all-by-all square RMSD plots from MD Movie (trajectory
> viewer), Ensemble Match pairwise RMSDs, “rmsd” command, etc. … most
> described in links from the superposition page:
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> >
> > If you wanted just a single RMSD for each predicted structure vs. the
> actual structure, you might still want to make all of the predicted
> structures into a trajectory (read in via MD Movie either as serially
> numbered PDB files or as a single multi-MODEL PDB file), open the actual
> structure as a separate model, and then use a trajectory per-frame script
> to calculate the RMSD of each frame (prediction) vs. the actual structure.
> That would not do the plotting for you, you’d have to extract the values
> from the Reply Log and plot it yourself.  The command you’d use to
> calculate rmsd depends on whether they are already superimposed with the
> actual structure.  If they were already superimposed you could just use
> “rmsd” but if not, then you’d have to use the “matchmaker” command or
> “match” (not the same as “matchmaker”, see superposition page linked above)
> command depending on how you want to superimpose them.
> >
> > 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 22, 2016, at 1:31 PM, Christian Bock <cbock1 at uw.edu> wrote:
> >>
> >> Elaine,
> >> 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
> space?
> >> Thanks,
> >> Christian
> >>
> >> 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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