jaimergp
commented
4 years ago get more information of mda_align.alignto() / Does MDA move the structure as part of the RMSD calculation?
mobile is transformed as part of the aligner, as per the docs here.
While looking up the docs, I realized MDAnalysis already provides helpers for sequence alignment! Read here. This mentions you can use fasta2select to detect the residue pairing automatically (you can even run the alignment there instead of using biotite!) and then feed the resulting dictionary to the AlignTraj class. Let's see if this solves some of our problems and, if that's the case, we will backport some of the fasta2select code into our routines.
[ ] We need to deal with the whole structure (residues atoms do not have the same length)
[ ] get more information of mda_align.alignto() / Does MDA move the structure as part of the RMSD calculation?
[ ] get superposed atomium model(s)