[Chimera-users] Ensemble models

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 20 15:35:22 PDT 2017


Hello Mohamed,
(A) Saving/restoring the display.  If you mean you want to be able to return to a specific display (what is shown, position, colors, style etc.), you can do that by saving a “scene”, for example, with command:

scene blah save

(where “blah” is whatever name you want to give that scene) …then later as long as you haven’t deleted atoms or closed models, return to it with:

scene blah reset

Scenes are also saved in session files, although they will increase their size.  There are also GUI ways of saving/restoring scenes.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/animation/animation.html#scenes>

Actually the “ribbons” preset (menu Presets… Interactive 1 (ribbons)) is quite similar to the default initial display, but some things like colors may be different.  You could try that and if it is OK for your purposes, you wouldn’t need to save/restore a scene.  You can also create your own custom presets.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets>

(B) RMSF, RMSD.  Chimera can calculate RMSD per residue over the ensemble, which I think is equivalent to RMSF.  The values can be written out, although not in CSV.  Assuming your ensemble is read in from a single multi-model file (like an NMR ensemble from the PDB, e.g. 1G1P) or as multiple separate files, the steps would be:

(1) open all the ensemble structures in Chimera
(2) superimpose them as desired for the RMSD calculation, if they aren’t already
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
(3) show Sequence of any one member of the ensemble (menu Favorites… Sequence)
(4) associate all ensemble members with that one sequence (sequence window menu Structure… Associations)
(5) in sequence window, show the RMSD histogram of interest (sequence window Headers menu: RMSD options are CA-only, backbone or full, but be aware “full” only uses atom names and does not equivalence atoms within symmetric sidechain groups)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers>
(6) write out the corresponding residue attribute (main menu Tools… Structure Analysis… Render by Attribute, in the resulting dialog choose File… Save Attributes, specify that the attribute is for “residues” not “atoms” and then choose the corresponding RMSD attribute, e.g. “mavRMSDbackbone")

This will produce a text file listing the residues and the values, but you’d have to postprocess it further to convert to CSV.  The file contents look something like this:

attribute: mavRMSDbackbone
recipient: residues
        :2.A    1.3780879732388507
        :3.A    0.35308333821132976
        :4.A    0.3016323720338901
        :5.A    0.25425002410246056
        :6.A    0.15787646490372187
        :7.A    0.16093274470085253
        :8.A    0.18328247884502627
        :9.A    0.22521810279034554
        :10.A   0.26080378520138037
[…etc…]

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 Mar 20, 2017, at 12:09 PM, Mohamed Noor <mohamed.noor at ul.ie> wrote:
> 
> Hello.
> I have an ensemble of models from phenix.ensemble_refinement. I notice that Chimera automatically loads the models and displays only a subset of atoms as "atoms/bonds". Can I save this as a preset while changing other settings manually so that I can go back to the automatic preset if I make a mistake somewhere?
> 
> Secondly, is it possible for Chimera to calculate rmsf of each residue and output the values to a CSV file? I would like to replot them in Excel.
> Thanks.
> Mohamed




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