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

[Cardiff Jiang]

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: image.png]

Best regards,
Zichen "Cardiff" Jiang
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