[Chimera-users] On the adding of the dynamics effect on the static structure

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 21 09:41:56 PST 2016


Hi James,
(A) If you have only one conformation of the structure, Chimera does not include any simple way of producing additional conformations that show its structural fluctuations.  To do that, people often use some kind of “normal mode analysis," for which there are several web servers, e.g.

elNemo <http://www.sciences.univ-nantes.fr/elnemo/>
ANM web server <http://anm.csb.pitt.edu/cgi-bin/anm2/anm2.cgi>
WEBnma <http://apps.cbu.uib.no/webnma/home>

… and probably many others.  I don’t have experience using them, I just know of their existence and that they produce various different kinds of output and show results in different ways.

In Chimera, one possibility is to just color the structure and/or use “worm” fatness to show its B-factor.  Of course, for that you would need to have a crystal structure that includes B-factor values.  This type of coloring and showing worms is done with Render by Attribute (in menu under Tools… Structure Analysis), and for coloring ribbons and showing worms (which are special ribbons), you would need to use the residue attribute “average bfactor” (average value from the atoms in the residue).   Here is an example image of PDB 2gbp with average bfactor per residue shown with ribbon colors and worms:


(B) if you have two conformations of the structure, you can calculate a morph trajectory in Chimera with Morph Conformations (in menu under Tools… Structure Comparison).  Essentially it interpolates and makes additional structures that are intermediates between the two input structures.  Then if you save the trajectory as multiple PDB files (or a single multi-model PDB file) you can superimpose the starting structures with one or more of the intermediate structures, as I did when making the figure shown in the Morph Conformations manual page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html>
(if it is just a trajectory in the MD Movie tool, you can only see one conformation at a time, that’s why you’d have to save as PDB and reopen to see multiple conformations together)

See also general discussion of how to superimpose structures:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

There is also a “ViewMotions” web server that will take the two structures as input, calculate intermediate structures, and show them all together as a rainbow.  It creates a Chimera session, so you can open the results in Chimera and change the view etc. as you like before saving an image.
<http://viewmotions.bc.edu/>

(C) if you already have multiple conformations of the structure, such as from a NMR ensemble multi-model PDB file, then there are a few different possibilities:
i) just superimpose them or a subset of them (see also Ensemble Cluster for identifying representatives if there are too many to show all at once) 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html>
The MD Movie tool also includes a similar clustering function to identify representatives from a trajectory.

ii) just show one representative but (similar to the B-factor stuff above) color and/or worm it to show the structural variability from the whole set of conformations.  You would do this by superimposing all of the conformations, then associating all of them with a single sequence, hiding all of the conformations except one, and then using the per-residue RMSD values along the sequence to color/worm that structure.  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 RMSDs including sidechain atoms are not automatically symmetry-corrected… even though some phenylalanine ring 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).

<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009712.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 19, 2016, at 1:22 PM, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> Dear Chimera Users!
> 
> I am interesting whether it possible to add some impression of the
> dynamics to some static elements of the pdb? Assuming that I am
> working with the visualisation of static x-ray structure and would
> like via some vizualisation trick to add some element of the
> conformational dynamism (like what can be obtained from the md
> trajectory or nmr ensemble) to the selected fragment of the structure
> (e.g loops or alpha-helix) eventually making impression of the several
> conformers superimposed on the structure?
> 
> Thanks so much for any suggestions!
> 
> James

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