[chimerax-users] Use values printed from Log inside a script (e.g. RMSD)

[Eric Pettersen]

Hi Steven,

> On Oct 12, 2021, at 12:39 PM, Steven Truong via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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. 

Tony answered this.

> 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?

Do these chains have the same sequence?  Also, I'm a little uncertain what "map one chain to the other" means exactly.  At any rate, the matchmaker <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> command can be used to superimpose one chain onto another and report the backbone (CA or C4'/P) RMSD for the match.  By default matchmaker iterates its match, pruning off poorly matching regions and re-matching to get a good fitting "core" match, and will report RMSD values for both the core region and across the entire sequence.  You can turn off the iteration if desired with matchmaker's "cutoffDistance none" option.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> 
> Thank you,
> Steven Truong
> Cambridge University
> 
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