[Chimera-users] matchmaker for more than one chain

[manikandank]

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. 

2. Is it possible to open the saved RMSD header values in a file later
just to color the pdb? 

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

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] 

Please let me know how this can be done. 

thank you very much 

with kind regards 

Mani.
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