[chimerax-users] Align command; designating the positions to align

[McClean, Phillip]

Hi,

I have been trying to properly code the align command.  I would like to use the command to determine the RMSD value between corresponding sections of two highly homologous proteins.  Here are the details:

Model 1 is to be aligned to Model 2; each model only has one chain
Model 1 positions (residues=amino acids) 11-323
Model 2 positions ( residues=amino acids) 24-336

When I pair each of the amino acids that are being aligned, everyone of the pairs has the same number of atoms.

Here is what I thought would work:

align #1:11-323 to_atoms #2:24-336

Here is the error message:

Unequal number of atoms to pair, 2483 to 2371

I am still trying to understand the nomenclature for understanding residues and atoms.

Thanks for any help you can provide.

Phil McClean
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