On Jun 25, 2023, at 7:21 AM, Vaibhav Anand dvaibhav@iitk.ac.in wrote:

Respected Mam, I hope this email finds you well. I am seeking your assistance in resolving a problem I am currently facing.

I have performed the Molecular dynamic simulation of the UBA domain (PDB ID - 1OQY), and for analysis, I've extracted the 11 PDB structures at [500ns - 1000ns with steps of 50ns], and I've one reference structure (em.gro - energy minimized structure).

I want to superimpose 11 structures with respect to my reference structure and compute the RMSD corresponding to helical residues (162-172, 177-187, 192-197).

I am aware that in Chimera, an in-built tool called Matchmaker can perform the superimposition for multiple structures, but it doesn't have an option for selecting required (helical) residues.

I've tried using the command line but cannot select the C-alpha atoms of helical residues. I've used the following commands -

...

...

mm #0:162-172, 177-187, 192-197@CA #1-11:162-172, 177-187, 192-197@CA (Error - "Invalid atom specifier syntax: '177-187,'")

...

...

mm #0:162-172, 177-187@CA #1-11:162-172, 177-187@CA (Error - "Invalid atom specifier syntax: '177-187@CA'")

However, the following command is running well -

...

...

mm #0:162-172@CA #1-11:162-172@CA (Output - "RMSD between 11 pruned atom pairs is 0.607 angstroms; (across all 11 pairs: 0.607)")

I've also checked the atom specifications from the documentation for further guidance. - Atoms specifications

I kindly request your assistance in resolving this issue. Thank you for your attention. Regards, Vaibhav Anand

Dear Vaibhav Anand, Questions about using Chimera should be sent to chimera-users@cgl.ucsf.edu CC'd here. https://www.rbvi.ucsf.edu/chimera/docs/feedback.html

If you want to specify the exact atoms to use yourself, then the command is "match" (not "matchmaker" or "mm"). See "match" and also the discussion of different superposition methods. https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html

You are also giving wrong atom specifications. They should not have spaces after the commas.

I.e. should be something like the following.

match #0:162-172,177-187,192-197@CA #1-11:162-172,177-187,192-197@CA

Command-line specification: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco