Hi,

I’ve used

align #2/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N

align #3/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N

align #4/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N

…

to align

#2 molecule against #1 molecule with backbone atoms

#3 molecule against #1 molecule with backbone atoms

#4 molecule against #1 molecule with backbone atoms

etc…

However, how can I align all rest molecules (e.g. #2~#100) against #1 molecule

with backbone atoms at once in chimeraX?

I’ve used

align all toAtoms #1 matchAtomNames true

align all toAtoms #1 matchNumbering true

to align all molecules to #1 molecule at once.

However, with this command, I cannot specify to use backbone atoms (e.g. CA,O,C,N) only when aligning.

I think that there should a 1 line command that aligns all molecules with specific atoms only

or there is chimeraX equivalent python script as

from chimera import runCommand as rc # use 'rc' as shorthand for runCommand

from chimera import replyobj # for emitting status messages

Best,

Doo Nam