Thank you all (Elaine, Tom, Eric). "align #2-100/X:1@ca,o,c,n to #1/X:1@ca,o,c,n each structure" worked perfectly! Best, Doo Nam From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Monday, November 28, 2022 at 2:32 PM To: Kim, Doo Nam <doonam.kim@pnnl.gov> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@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@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<mailto: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://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fmailman%2Flistinfo%2Fchimerax-users&data=05%7C01%7Cdoonam.kim%40pnnl.gov%7Ceae8b899c9064cc3f98e08dad19065a5%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C638052715367370676%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CoT5qldSz2ofWkwUBb9tKVXUpmxtytXBcr3VnpT80qk%3D&reserved=0>