[chimerax-users] Align with specific atoms (but against all other molecules)

[Kim, Doo Nam]

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

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