[chimerax-users] How to Align Chromosome Models with Different Number of Atoms?

[Elaine Meng]

Hi Cardiff,
It is impossible to tell from a picture what the atoms are named or how the residues are numbered.  You have to figure out how to specify an equal number of "atoms" from the two files, based on how the atoms are named and how the residues are numbered.  Matchmaker is for biopolymers (proteins or nucleic acids made of real atoms, not your chromosome models), so you would need to use "align" after figuring out how to specify equal numbers of "atoms."  

You might need to look at your PDB files in a text editor to understand its naming/numbering.  Do they really contain 40 residues?  Or is each one really a single residue with 40 atoms?  

"#1:1-40" specifies residues numbered 1-40 in model #1 because the colon symbol ":" means residues. Command "select #1:1-40" will report how many "atoms" that specifies.  It might be 0 atoms if the specification is wrong.  If you really meant "atoms" numbered 1-40 (not residues) the atom specification should instead be "#1@@serial_number>=1 & #1@@serial_number<=40"

How to specify atoms in the command line, where # : @ are symbols for hierarchical levels model residue atom, and @@ refers to atom attributes:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

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

> On Mar 27, 2021, at 11:45 AM, Cardiff Jiang <z8jiang at ucsd.edu> wrote:
> 
> Dear ChimeraX User List,
> 
> How can I compare two chromosome 3D models (PDB files) that have different numbers of "atoms"?
> 
> Matchmaker tool reports, "Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'align' command to superimpose small molecules/ligands." align #1 toAtoms #2 reports, "Unequal number of atoms to pair, 49 and 63." align #1 toAtoms #2 matchNumbering true reports, "Pairing dropped 49 atoms and 63 reference atoms. No atoms paired for alignment." align #1:1-40 to #2:1-40 reports, "No atoms paired for alignment."
> 
> How should I compare two chromosome 3D models below? Thank you.
> <image.png>
> 
> Best regards,
> Zichen "Cardiff" Jiang
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