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

James Starlight jmsstarlight at gmail.com
Thu Nov 24 12:22:53 PST 2016


Hi Elaine and thank you so much for the interesting ideas!
(B) should works for me, however I will also play with NMR ensemble of
another protein and write here whether (C) is also works for my case.

Regarding (A): I like visualisation in worm-style at least from the visual
perspective, however it will be great idea to include in future Chimera
realize some built-in Normal mode tool to i) calculate Hessian for
specified structure ii) obtain normal modes via it diagonalisation and
finally iii) deform initial structure along chosen sub-set of normal modes
to obtain it alternative conformers which iv) after superimposition against
reference might be interesting concept to produce perception of NMR
ensemble.

James

2016-11-21 21:41 GMT+04:00 Elaine Meng <meng at cgl.ucsf.edu>:

> 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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