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

James Starlight jmsstarlight at gmail.com
Fri Nov 25 11:48:25 PST 2016

update - on screen is the result which I have composed using morphing
(B): [image:
Встроенное изображение 1]
my question - is it possible to select one of the conformer from the
ensemble (assuming that all are merged within one model) end changes its
popersties regardless of others? E.g I want to select "the middle" state,
making it visual state as solid (call it reference) and set transparency to
others states, eventually producing impression of the deformation of the
reference state (shown as solied) where rest conformers (shown as
transparent) indicate the collective directions of it.


2016-11-25 0:22 GMT+04:00 James Starlight <jmsstarlight at gmail.com>:

> 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/e
>> nsemblecluster/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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