Steven,

I can't answer the second part of your question, but the RMSD can be obtained from the "run" function in python:

```
from chimerax.core.commands import run

value = run(session, "rmsd #1 to #2")
if value > 2:
    # do stuff
```

Best,

Tony
From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Steven Truong via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: Tuesday, October 12, 2021 3:39 PM
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] Use values printed from Log inside a script (e.g. RMSD)
 
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


Dear ChimeraX Admins,

I was hoping to use the “rmsd” command in ChimeraX to measure distances between models within a .py script.

Is there a way to use the output of “rmsd” (or generally any other output in Log) within the script? For example, if rmsd > 2 Angstroms, then do X.

Ultimately, I am attempting to align chains between models. Because my protein is asymmetric, chain A on Model #1 might actually be chain B on Model #2. I was hoping to use “rmsd” to map one chain to the other. Is it a better idea to do this in another program and re-write chain IDs in the .PDB file? If so, what other program would be better at making RMSD calculations between .PDB chains?

Thank you,
Steven Truong
Cambridge University

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