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.