[chimerax-users] Matchmaker on a subset of residues

Wed Feb 22 08:12:30 PST 2023

Hi Phil,
First of all, are you sure you should even be using matchmaker?  My first reply discussed which situations in which you would want to use other methods such as the "align" or "rmsd" command instead.  I'm not convinced that matchmaker is what you want to use in your situation, but if you read that and are still convinced matchmaker is what you need:

Exactly as I suspected and described in my previous reply, it looks like you don't have any residues selected in the tan structure, or else those residues would also be highlighted in green in the sequence view.  When you dragged a box in the second sequence to select the blue structure, it erases the selection in the tan structure.

There are lots of ways to select
<https://rbvi.ucsf.edu/chimerax/docs/user/selection.html>

... but if dragging in the sequence window is the only way you know how to select the residues, here is how to select in both structures at the same time.  

(A) First drag a box in one sequence, and it will show a select command in the Log, e.g. something like:
select #1/A:100-158
(B) Then drag a box in the other sequence, which will erase the first selection but also show a select command in the Log, e.g. something like:
select #2/A:32-88

These commands in the log show the model, chain, and residue identifiers you would need to write your own select command that selects all of them at the same time.  Carrying on from the examples above, you would enter in the command line:
select #1/A:100-158 #2/A:32-88

Finally, you have to check the two boxes "Also restrict..."  which you do not have checked in your screenshot.  Matchmaker help:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html>

How to save a session: use menu File.... Save, choose Files of type: ChimeraX session, -OR- use the save command: save myfilename.cxs
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session>

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 22, 2023, at 6:51 AM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> Attached is a screenshot of the situation I am confronting.  The "shaded brown" / "shaded green" reference refers to the sequence boxes on the right panels.  I also have the Matchmaker GUI box open; it shows what I face when I try to be sure I am selecting the proper reference and match sequences.
> 
> I used the screenshot approach because I don't know how to capture the session.
> 
> Phil
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Tuesday, February 21, 2023 3:33 PM
> To: McClean, Phillip <phillip.mcclean at ndsu.edu>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Matchmaker on a subset of residues
>  
> Hi Phil,
> I can't tell from your description what is wrong.   I also don't understand "shaded brown" and "shaded green" ... selection means shown with a green outline in the 3D window, not drawing a box on the sequence, although the act of drawing the box would select some residues in the 3D window.  When you try to run matchmaker, is there a selection in both structures at the same time, or did the selection from one structure get cleared when you made a selection on the other structure?  That is my only guess of what might have happened.
> 
> If you want to send (just) me a session of when you think there is a selection in both structures, maybe that would help.
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> > On Feb 21, 2023, at 12:33 PM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > 
> > Hi Elaine,
> > 
> > I have tried to us the GUI Matchmaker interface for this comparison.  I loaded the two models into the same window; the reference model was loaded first and the model that was to be matched to that reference was loaded second.  I loaded each sequence, and selected the residues to be paired using the mouse.  The first (reference) is shaded brown and the second is shaded green.  I open the GUI interface and select "also restrict to selection" for both the reference and selection to match.  Both the reference and model to match the reference are shaded grey.  Then I click apply and receive the follow message:
> > 
> > No "to" model specified
> > 
> > I have tried this multiple times and the same result.
> > 
> > Any ideas on how to get past this error message.
> > 
> > Phil
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > Sent: Monday, February 20, 2023 7:07 PM
> > To: McClean, Phillip <phillip.mcclean at ndsu.edu>
> > Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> > Subject: Re: [chimerax-users] Matchmaker on a subset of residues
> >  
> > 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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