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

[Kim, Doo Nam]

Thank you all (Elaine, Tom, Eric).

"align #2-100/X:1 at ca,o,c,n to #1/X:1 at ca,o,c,n each structure"
worked perfectly!

Best,
Doo Nam

From: Eric Pettersen <pett at cgl.ucsf.edu>
Date: Monday, November 28, 2022 at 2:32 PM
To: Kim, Doo Nam <doonam.kim at pnnl.gov>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Align with specific atoms (but against all other molecules)
Check twice before you click! This email originated from outside PNNL.

Hi Doo Nam,
You should be able to use "align #2-100/X:1 at ca,o,c,n to #1/X:1 at ca,o,c,n each structure" to do this.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab



On Nov 26, 2022, at 1:49 PM, Kim, Doo Nam via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

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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