[chimerax-users] ChimeraX sequence alignment score?

[Elaine Meng]

> On Oct 27, 2022, at 4:46 PM, Budayr, Omar Mahdi <obudayr at vols.utk.edu> wrote:
> 
> Dear Dr. Meng,
> 
> I looked through the documentation for ChimeraX and I still cannot figure out what the value for sequence alignment score indicates. I aligned two b-adrenergic receptors from PDB (2RH1 and 3NH8) and it gives a value of 2423.9. What does this value actually represent? The documentation refers to it but never gives specifics besides the parameters in the table that matchmaker generates
> 
> Sincerely,
> Omar Budayr

Dear Omar Budayr,
The value itself is not at all important.  The reason to have a score is that the alignment process tries to maximize it for the pair of sequences that it is given.  By changing parameters for scoring you can change the relative importance of the different parts of the score, and thus what is most important for the alignment method to align.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. we recommend sending questions to the chimerax-users at cgl.ucsf.edu address (CC'd here) so that others can benefit from the answers and/or help to answer the questions - thanks!