Hi
Is there a function in ChimeraX to calculate RMSD after matchmaking superimposition of structures?
Thank you

From: Elaine Meng <meng@cgl.ucsf.edu>
Date: Wednesday, October 8, 2025 at 11:23 AM
To: Vojo P Deretic <VDeretic@salud.unm.edu>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: tools for ligand-receptor interactions


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> On Oct 8, 2025, at 9:58 AM, Vojo P Deretic <VDeretic@salud.unm.edu> wrote:
>
> Hi
> How do I pose a question - via email or on the site?
> My question is: we have a Boltz/alphafold fitted organic molecule into a known structure.
> What are the tools for residue interactions in ChimeraX apart from H bonding and hydrophobic or charged surfaces?
> Thanks
> Vojo Deretic
>
Hi Vojo,
As per the Contact Us page <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/contact.html__;!!KXH1hvEXyw!e7f7-bCUI2LzHYm6mI2vMv6zWhxTYUgjCEzNlSIO_l3JrIzAr_uP0P_CTgYGx2gbvnsjPDcC_VfRBvuTzZGQ$ >

...to ask questions you would use the chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address, which is CC'd here so you don't need to send your questions again.  I don't know what you mean by "on the site" since there is no webform for questions, only this email address.

You already mentioned H-Bonds and coloring the receptor molecular surface by ESP (electrostatics) or MLP (lipophilicity).  That's most of it.  Certainly you can just visually evaluate what is nearby, but you could use the Contacts tool for a more objective approach:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html__;!!KXH1hvEXyw!e7f7-bCUI2LzHYm6mI2vMv6zWhxTYUgjCEzNlSIO_l3JrIzAr_uP0P_CTgYGx2gbvnsjPDcC_VfRBnU1sXZg$ >

See also the tutorial "Protein-Ligand Binding Sites"
<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html__;!!KXH1hvEXyw!e7f7-bCUI2LzHYm6mI2vMv6zWhxTYUgjCEzNlSIO_l3JrIzAr_uP0P_CTgYGx2gbvnsjPDcC_VfRBpb1Zk1n$ >

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

> On Oct 8, 2025, at 9:58 AM, Vojo P Deretic <VDeretic@salud.unm.edu> wrote:
>
> Hi
> How do I pose a question - via email or on the site?
> My question is: we have a Boltz/alphafold fitted organic molecule into a known structure.
> What are the tools for residue interactions in ChimeraX apart from H bonding and hydrophobic or charged surfaces?
> Thanks
> Vojo Deretic
>
> Sent from my iPhone with lots of typos and autocorrect nonsense - my apologies...
>