[chimerax-users] Question about pruned set in rmsd

[Elaine Meng]

Hi Chang Woon Jang,
I'm not sure if you are using Chimera or ChimeraX (this is the ChimeraX mailing list, but there is also one for Chimera, chimera-users at cgl.ucsf.edu).  Chimera's "match" command is different than the Chimera/ChimeraX "matchmaker" command.  

In Chimera, the "match" command has an "iterate" option (iteration = pruning) but it is turned off by default, 
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>

...so I'm guessing you are using "matchmaker" which has iteration turned on by default.   That means that the final fit only uses the "pruned" set of pairs, which are the residue pairs that fit better in space.  That way, if there are some loops or other parts that don't have a similar 3D shape, they do not interfere with a good superposition of the spatially conserved core.  This is explained in the help pages (e.g. links below), but I will try to summarize here:

"All" is all residue pairs that would be shown in the pairwise sequence alignment (there is an option to show this alignment).  The pruned set is the subset of these positions that are used for the final fit iteration, shown in light orange boxes on the sequence alignment.

If you don't want pruning you can turn off that option and simply use all positions in the sequence alignment for the fit.

In the ChimeraX matchmaker command, the option is "cutoffDistance" (details are different for the Chimera matchmaker command)
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options>

In the ChimeraX Matchmaker tool, it is in the Fitting parameters, "Iterate by pruning long atom pairs"
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#fitting>

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

> On Oct 14, 2021, at 9:38 AM, Chang Jang via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Chimera Users, 
> I want to understand a result from "match" command. There are two results for 1) pruned set and 2) across all. 
> What exactly is the pruned set in this calculation?
> Thanks,
> Chang Woon Jang