[chimerax-users] Align Structures at Specific Residues

[Elaine Meng]

Hi Cameron,
Thomas is right that you can specify residue ranges in matchmaker to limit the calculation.  Also, an alternative is the "align" command, which can use any atoms that you specify.  The help for each command tries to explain the differences when crossreferencing the other, but I'll try to summarize here:

Matchmaker tries to make it easy for you by figuring out the residue pairing between the structures (by aligning their sequences "under the hood" although there is an option to show that alignment).  You can limit the range of residues used as Tom said, but it will still then try to sequence-align those residues and it will only use the CA atoms for fitting. Matchmaker only works to align biopolymer-containing structures  (protein or nucleic acid).
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

The "align" command can be used to fit any atoms of all types of atomic structures, but requires specifying equal numbers of atoms from the two models. For example, you could use all peptide backbone atoms N,CA,C,O if you give equal numbers of residues from the two structures. It also has some options to try to make specification easier if the two structures have the same residue numbering or atom names.  Take a look:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>

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 9, 2022, at 10:47 PM, Thomas Mulvaney via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Cameron,
> 
> Most of the commands work using the ChimeraX atomspec [0], which lets you create selections of parts of a structure.
> 
> If for example you are using matchmaker and want to align residues 50-100 of model #1 to model #2 you can do:
> 
> ‘mm #1:50-100 to #2’ 
> 
> Hope that helps,
> 
> Tom
> 
> [0] https://www.cgl.ucsf.edu/chimerax/docs/user/commands/atomspec.html
> 
> 
> 
>> On 10. May 2022, at 06:07, Cameron Larson via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hello,
>> 
>> I would like to know how to align structures at specific residues. For example, how do I align an ion channel at the selectivity filter instead of aligning the entire structure?
>> 
>> Does this ability exist with chimeraX?
>> 
>> -Thanks
>> 
>> CL