[chimerax-users] [Chimera-users] matchmaker for more than one chain

[Elaine Meng]

Hi Mani,
There is a different e-mail address for ChimeraX questions:  it is chimerax-users at cgl.ucsf.edu CC'd here.

Responses below...

> On Sep 2, 2021, at 2:22 AM, manikandank via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi ChimeraX-users,
> I have used recently the mmaker cmd to align two pdb each have multiple chains as below.
>  
> mmaker #12/L,M,N to #5/S,A,B matrix  blosum-62 showAlignment true
>  
> But the sequence view shows only the alignment of chain L and S. 
> 
> 1. I would like to have aligned sequences of all chains used in mmaker alignement.

Your command above does not use all the chains for fitting, it only chooses the single pair of chains that gives the best sequence-alignment score to superimpose the two models.  The other chains might look superimposed but it is only because they moved along with the ones that were actually used for the fit.   To use all three pairs of chains, you need to also use the "pairing ss" option:

mmaker #12/L,M,N to #5/S,A,B matrix  blosum-62 showAlignment true pair ss

Then you would get three pairwise sequence-alignment windows:  L/S, M/A, and N/B.

matchmaker or mmaker command
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

pairing options
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options>
> 
> 2. Is it possible to open the saved RMSD header values in a file later just to color the pdb?

Yes, but with several steps so it may not be that convenient.  Probably easier just to save and restore the ChimeraX session (which includes the sequence alignment windows). Also remember if you move the structures relative to each other, the RMSD values will change.  However, if you really want to save the RMSD values to file after you showed sequence alignments and header, then you could save them as an attribute file (that could be reopened/applied later):
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes>

The attribute name is seq_rmsd as explained here:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers>

> 
> 3. Do mmaker align entire pdb based on selected chains and Can calculate RMSD for all residues in the pdb?

For the first question, 3A: yes, depending on the "pairing" option as explained above.

For the second question, 3B, I'm not sure what you want.  Remember that the main purpose of matchmaker is to superimpose the structures well, and then it happens to also give the RMSD over the positions that it chose to use, which are shown in the pinkish boxes on the sequence alignment.  By default it uses fit iteration and discards loops that don't superimpose well in space. Matchmaker only gives the RMSD over the positions it uses.  You could tell it to use all positions, but that would change the superposition.  If you like the default superposition (that does not use all of the positions), you can use a separate command "rmsd" to measure RMSD over any sets of atoms that you want, without moving the structures or changing the superposition.  Or, if you really want to use all of the positions in the sequence alignment for the fitting, you would have to use matchmaker option "cutoff none" ... but that usually does not give the best superposition.

cutoff option
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#cutoffDistance>

rmsd command (calculate RMSD in current positions, no fitting)
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html>

Matchmaker only gives alpha-carbon RMSD.  The rmsd command can give RMSD for any sets of atoms that you want, alpha-carbons only, or backbone only, or all atoms, as long as you give equal numbers of atoms from the two structures. However, it can be tricky to specify the correct sets of atoms if the residue numbering or residue types are different between the two structures.

So you might want to first use "mmaker" with whichever options give you the best superposition, and then to measure RMSD over all positions in the alignment (which might not be used in the matchmaker fit), use the "rmsd" command afterward.

> 
> 4. I also would like to change the displayed text for the sequence name. Presently it puts the filename as sequence name.
> 
>     [similar to 'Edit sequence name' in the sequence viewer in chimera]

Sorry, there is no way yet to change the displayed sequence name in ChimeraX.
> 
> Please let me know how this can be done. 
> thank you very much
> with kind regards
> Mani.

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