[chimerax-users] Matchmaker on a subset of residues

[Elaine Meng]

My previous answer failed to emphasize the main difference between Matchmaker and the other methods:  

Even when it uses restricted residue ranges, matchmaker will pair up the residues in the two structures by first doing a sequence alignment.  This means it is OK to give different total numbers of residues between the two structures, but it also means that what you specify in the command is not going to exactly control which residue in one structure is paired with which residue in the other structure.

In contrast, the other methods ("align" and "rmsd" commands) need to use the same numbers of atoms from each structure.  This can sometimes be difficult to specify correctly in the command line, but there are pairing options, for example "align" command "matchAtomNames" option to pair only atoms with the same names.  See the help page of each command for details.

I hope this helps,
Elaine


> On Feb 20, 2023, at 5:07 PM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Phillip,
> (1) If you mean you want to specify exactly which residues/atoms to use in fitting (and then get their best-fit RMSD reported in the Log at the end), see the "align" command.  
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
> 
> (2) Or, if you don't want to move the structures from their current positions, but simply to measure the RMSD between specified residues/atoms in their current locations, see the "rmsd" command.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html>
> 
> (3) You *can* use matchmaker on a subset of residues by specifying them in the command, see:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#restrict>
> 
> ... however, please note:
> - matchmaker will only use the alpha-carbon atoms of those residues in calculating the fit and RMSD.  If you want to use more atoms than one per residue, you have to use "align" or "rmsd" as mentioned above.
> -  by default it iterates the fit and prunes some of the residue pairs from the fit, unless you also give the option "cutoffDistance none"
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options>
> 
> The above relate to the "matchmaker" command since you said command.  However, if you're actually using the Matchmaker graphical interface (e.g. opened from the Tools menu), the same options are available.  To restrict matchmaker to only certain residues using the graphical interface, first select those residues and then check the option "Also restrict to selection"
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html>
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#pairing>
> 
> Making selections:
> <https://rbvi.ucsf.edu/chimerax/docs/user/selection.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 Feb 20, 2023, at 3:27 PM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Is it possible to use the Chimerax Matchmaker command to obtain the RMSD value between a subset or residues between two different proteins.
>> Phil McClean
> 
> 
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