Hi Doo Nam, You should be able to use "align #2-100/X:1@ca,o,c,n to #1/X:1@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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>