Hi Abhilash, My way of doing it is to run the mm command for each chain separately. This assigns the rmsd score for each alpha-carbon in the selected chains and updates it after each new mm. The command look something like that: matchmaker #2/A to #1 show true matchmaker #2/B to #1 show true matchmaker #2/C to #1 show true color byattribute seq_rmsd #1 palette rainbow Best Rémi R. ----- Mail original ----- De: "Abhilash Padvannil via ChimeraX-users" <chimerax-users@cgl.ucsf.edu> À: chimerax-users@cgl.ucsf.edu Envoyé: Mardi 29 Août 2023 03:15:55 Objet: [chimerax-users] Coloring by Ca-RMSD Hello, I am working with a multi-subunit protein. I aligned current structure with a previously determined structure using mm command. I am trying to color my protein using RMSD. Chimerax is however, coloring only one-subunit by RMSD, the other chains have default colors. Is there a way to color the whole molecule with RMSD attribute. Thanks Abhilash. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Thank you very much. The suggestions helped. Regards Abhilash.

On Aug 29, 2023, at 8:45 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Abhilash, In agreement with Rémi, you will need some way of showing the sequence alignment for each chain (each subunit) in the complex. Using the option in matchmaker to show the sequence alignment is a good way because it will automatically also show the RMSD header above the sequences.

One thing for both of you to consider, however, is which parts of the multiprotein complex you actually want to use for fitting. In Rémi's method, the final fit is based only on #2/C to #1. Even though the two other fits before that showed the previous two sequence alignments, the RMSD in all three of them will change as the fit (the superposition) changes.

If you had #2 with chains A,B,C that you want to fit to #1 chains E,F,G then the matchmaker command to use all three pairs at the same time and show their sequence alignments would be:

matchmaker #2/A,B,C to #1/E,F,G pairing ss show true

See matchmaker help for the explanation of options. The "pairing ss" option means to use all pairs of specified chains for the fit at the same time, in this case, A with E, B with F, and C with G.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

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

...

On Aug 29, 2023, at 1:36 AM, Rémi RUEDAS via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Abhilash,

My way of doing it is to run the mm command for each chain separately. This assigns the rmsd score for each alpha-carbon in the selected chains and updates it after each new mm. The command look something like that:

matchmaker #2/A to #1 show true matchmaker #2/B to #1 show true matchmaker #2/C to #1 show true color byattribute seq_rmsd #1 palette rainbow

Best

Rémi R.

----- Mail original ----- De: "Abhilash Padvannil via ChimeraX-users" <chimerax-users@cgl.ucsf.edu> À: chimerax-users@cgl.ucsf.edu Envoyé: Mardi 29 Août 2023 03:15:55 Objet: [chimerax-users] Coloring by Ca-RMSD

Hello,

I am working with a multi-subunit protein. I aligned current structure with a previously determined structure using mm command. I am trying to color my protein using RMSD. Chimerax is however, coloring only one-subunit by RMSD, the other chains have default colors. Is there a way to color the whole molecule with RMSD attribute.

Thanks

Abhilash.

_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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