Color protein conformations using ChimeraX

I show how to color a homo-octamer protein complex to highlight where the 8 proteins differ in shape using ChimeraX 1.5.

[@JuNiNh008]

Thanks for the video!
I cannot access the header Ca RMSD when I right click on the sequence, any idea why?

[@ucsfchimerax8387]

I used ChimeraX 1.5 in the video (from November 2022). Maybe you are using an old ChimeraX? The version is listed at the top of the Log panel when you start the program. To report the C-alpha RMSD the sequence has to be associated with more than one copy of the structure. Right click on the sequence shows a menu with an entry Structure / Associations that lets you associate multiple structures with the shown sequence if it is not done automatically. ChimeraX tries to associate the sequences automatically but if the sequences differ enough you sometimes have to do it manually.

[@diyajoshi1689]

sir how to reduce surface on protein,we are doing docking results analysis,the protein cover the whole ligand,I am not able to saw the ligand in pocket,I have to reduce the protein bulk so clearly visualize the ligand,if you made one video on it,it would be great help professor.
Kind regards
Kavita

[@ucsfchimerax8387]

Best to ask on the ChimeraX mailing list [e-mail]. You probably want to show just the protein side-chains near the ligand to get the clearest views. Another method would be to use clip planes.

[@diyajoshi1689]

@@ucsfchimerax8387 sir you make a video on that please,thankyou for kind reply,I need less surface of protein around ligand when analyse result of docking.on transparency option also does not work for me because protein is so bulky and ligand is not visible through the bulk sir,please help.
Kind regards,
Kavita

[@ucsfchimerax8387]

Please ask on the ChimeraX mailing list. Your question is not related to the content of this video.