Hi Matthias, Yes absolutely. You just need all of the structure chains to be associated with the same sequence window, which might contain a single sequence or a sequence alignment, and then you can show an RMSD histogram above the sequence(s) which is then propagated as an attribute to the structures for coloring.

If I recall correctly, the video shows a specialized rarer case. Your case is the more common situation where the structures are homologous and may vary in structure, and you probably want to keep them superimposed.

If the sequences of the structure chains are fairly similar, you may be able to associate all of the structures with the same single sequence. I.e.,

(1) open all of the structures and superimpose them using your preferred method (matchmaker, align, ...) https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html

(2) show the sequence of only one of those structures (menu Tools... Sequence... Show Sequence Viewer, choose the chain for which you want to show the sequence) https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html

(3) use Sequence Viewer context menu (rt-click or Ctrl-click on that window depending on platform) Structure... Associations, add all of the relevant structure chains to the associations of that sequence https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#association

(4) use Sequence Viewer context menu Headers... Calpha RMSD to show RMSD histogram above sequence https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context

(4b) in the Sequence Viewer Settings, Headers section, you can choose backbone RMSD instead of Calpha RMSD if you prefer https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings

(5) then all of the associated structure chains get a residue attribute named seq_rmsd, and you can color any/all of them by that attribute using Render by Attribute (in menu under Tools... Depiction) or the "color byattribute" command https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html

(5b) Probably for nice-figure purposes you would only show/color one of the structures. For RMSD calculation purposes during coloring you need to keep the others open and superimposed but they could be hidden, e.g. by unchecking the shown checkboxes in the Model Panel.

If the structure sequences are very dissimilar, however, and don't associate properly with the sequence in the Sequence Viewer, instead of showing a single sequence you may need to generate a sequence alignment (outside of ChimeraX) of their sequences, and then open it in ChimeraX and make sure each structure is associated with some sequence in that alignment. Then proceed with (4) - (5) as above.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jul 4, 2023, at 7:02 AM, Vorländer,Matthias Kopano via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi all,

I would like to color proteins by the Ca-RMSD after aligning them, and found the Youtube tutorial on how to do this for proteins with identical sequence. However, I would like to compare structures from different species, as for example done in Figure 2 in this paper https://www.sciencedirect.com/science/article/pii/S0959440X16302408?via%3Dih... . Is this possible in ChimeraX?

Many thanks, Matthias

Hi Matthias,

I made a video showing how to color two aligned proteins by their C-alpha distances from each other.

https://youtu.be/XaTpB-UIxnU

Tom



On Jul 4, 2023, at 7:02 AM, Vorländer,Matthias Kopano via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi all,

I would like to color proteins by the Ca-RMSD after aligning them, and found the Youtube tutorial on how to do this for proteins with identical sequence. However, I would like to compare structures from different species, as for example done in Figure 2 in this paper https://www.sciencedirect.com/science/article/pii/S0959440X16302408?via%3Dih... . Is this possible in ChimeraX?

Many thanks, Matthias _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Manage subscription: