[Chimera-users] color pdb based on rmsd

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 21 08:40:23 PDT 2021

Hi Mani,
You do not need to write any files.  It can be done by showing a sequence alignment with RMSD header, which automatically creates an attribute.

(1) When you use Matchmaker tool or command, turn on the option to "Show pairwise alignment(s)" (if command, the option is "show true").  However, that will create two pairwise sequence alignments, whereas you need all 3 structures to be associated with the same sequence alignment.  Keep both of those for now.

(2) In the menu of one of the pairwise sequence alignments, choose Structure... Associations and associate the third structure (the one that is not already associated) by checking option "associate with best match", Apply.  Even though the alignment only has two sequences, two structures can be associated with the same sequence, even if the structure has a slightly different sequence than the displayed sequence.  It only needs to be similar enough for the proper alignment to occur.  If that seems to occur without error (one of the sequence names will now have a dashed box around it to show that two structures are associated), just close/delete the other pairwise alignment... we were just keeping it in case you needed to try associating with that one instead.

(3) In the sequence alignment (with 3 structures associated) there is probably already an RMSD:ca histogram above the sequences.  That automatically creates for all 3 associated structures, residue attribute named mavRMSDca ("mav" because it comes from MultAlignViewer).  If that histogram is not already shown, show it using the Headers menu of the sequence alignment window. The attribute can be used in the rangecolor command for coloring, or in the Render by Attribute tool for display as colors or worms.

There is an alternative procedure for parts #1,2 above.  I gave the above since you were already using Matchmaker to superimpose the structures.  However, if you just have multiple proteins already superimposed, another way is to create a multiple sequence alignment with all of them associated in one step, using the Match->Align tool.  It may take a few minutes to calculate depending on how many proteins you have at the same time.  Three would probably not take too long.

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

> On Jul 21, 2021, at 5:35 AM, manikandank via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hi Chimera-users,
> I have aligned three pdbs using MatchMaker and would like to color one based on rmsd (per residue or per CA atoms).
> I see that i can use 'rmsd' to calculate CA-CA distance between two models, but i would like to write the distance difference in a file so that the file can be read 
> in 'attribute' coloring scheme. Please let me know how to do this.
> thanking you
> with kind regards
> Mani.

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