[Jmol-users] Color structural alignment by deviation "RMSD"?

[Eric M. <em...@mi...>]

For years, I have been frustrated by not knowing any way to color 
backbones in a structural alignment of two proteins by deviation _*in 
Jmol*_.

Jmol's *compare* command aligns two proteins, but I don't know any way 
to color one of the backbone alpha carbons by deviation from the other. 
Am I missing something?

Swiss-PdbViewer offers multiple methods to do structural alignments, and 
after aligning, will color the protein that was moved by deviation from 
the static reference structure. However, it offers no way to put the 
deviation values in e.g. the temperature column of the PDB file so they 
could be used for coloring by Jmol. (It does offer such a function, but 
one that works only when the two proteins have identical sequences.)

PyMOL can also align, and color by deviation ("RMSD") with its command 
colorByRMSD, but it is unclear to me whether the deviation values can be 
saved to a disk PDB file with those values in the B-factor/temperature 
column (which could then be used by Jmol). I have submitted a support 
request about this to Schrödinger.

If you'd like to see examples of structural alignments colored by 
deviation, take a look here: https://pymolwiki.org/index.php/ColorByRMSD

Thanks for any and all help, -Eric