[chimerax-users] comparison of 2 similar models

[Elaine Meng]

Hi Dmitry,
When you open an atomic structure (at least for PDB entries from RCSB) there will be tables of information like what chains and nonstandard residues are present.  
<https://rbvi.ucsf.edu/chimerax/docs/user/modelinfo.html>

But maybe you are interested in comparing exactly which residues are in the protein and/or nucleic chains.

(A) for simple counts of atoms and residues per model, an easy way is to just select a whole model, e.g.

select #2

...and then the total number of atoms, residues, ... will be reported briefly in the status line, or you can click the green magnifying glass icon in the top toolbar to raise the Selection Inspector which also lists those things. Then you can repeat with other model(s), "select #1" etc.

(B) if you want to omit waters, ions, ligands, you could be more specific:

select #2 & protein
or 
select #2 & nucleic

(C) Then you can get a list of the selected residues in the Log with "info" e.g.

info residues sel
or 
info atoms sel

See "info"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues>

(D) If you care mostly about biopolymer residues and the sequences are similar enough to align pretty well, for an easier visual, I like to just use matchmaker and show a pairwise sequence alignment of a chain in one model with a chain in the other model.  Then you can see the "missing" residues outlined in black boxes.   For example

open 7ljd
open 5wiv
preset ribbons/slabs
view
mm #2/A to #1/R show true
view
color #1/R gold

Screenshot of Sequence Viewer window attached.  Black outline boxes are residues with missing coordinates.  The orange boxes are just what were used in the final matchmaker fit.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#show>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings-regions>

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




> On Sep 17, 2022, at 3:10 AM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear colleagues,
> I want to compare two similar PDB structures.
> I suspect one structure has fewer residues than the other.
>  
> Is there a way to get the list of all components of the PDB structure, including residues, in the txt/doc file?
>  
> Or what is the alternative way to do that? 
> Thank you.
> Kind regards,
> Dmitry

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