[chimerax-users] Pair-fitting in ChimeraX

[Elaine Meng]

Hi Rachael,
Sure, you can fit using any atoms that you want, using the "align" command.  The trick will be to specify them in the command, and specify the same numbers of atoms in the two structures.

align command (or just use command "help align" to see this page):
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>

specifying atoms in the command line:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>

Could be something like the following, but you'd have to use the correct chain/residue/atom specifiers for your own structures:

align #2/A:hem at c2,c3,c4,n1 to #1/A:hem at c2,c3,c4,n1

Matchmaker is different, it figures out biopolymer residue pairing by doing a sequence alignment, and then (for proteins) uses CA atoms only.

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

> On May 28, 2021, at 9:59 AM, Rachael Coleman <rec287 at cornell.edu> wrote:
> 
> Hello again,
> You guys were so helpful last time I figured I'd just ask for help again! I'm trying to do something that I know is a feature in PyMol but I'm not sure if it is a feature in ChimeraX (yet). In PyMol, there is a function to pair fit over specific atoms between two different structures. I have tried using the Matchmaker tool in ChimeraX to do this, but I think the dilemma is I'm trying to align the protein relative to the position of specific atoms in a heme cofactor across two different structures and that isn't something in the primary sequence of the protein. I also could just be doing something wrong in the matchmaker process. Do you know if there is an easy way to accomplish this in ChimeraX? 
> Best regards,
> Rachael Coleman