[chimerax-users] Align with specific atoms (but against all other molecules)

[Eric Pettersen]

Hi Doo Nam,
	You should be able to use "align #2-100/X:1 at ca,o,c,n to #1/X:1 at ca,o,c,n each structure" to do this.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Nov 26, 2022, at 1:49 PM, Kim, Doo Nam via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi,
>  
> I’ve used 
>  
> align #2/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N
> align #3/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N
> align #4/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N
> …
>  
> to align 
> #2 molecule against #1 molecule with backbone atoms
> #3 molecule against #1 molecule with backbone atoms
> #4 molecule against #1 molecule with backbone atoms
> etc…
>  
>  
> However, how can I align all rest molecules (e.g. #2~#100) against #1 molecule
> with backbone atoms at once in chimeraX?
>  
>  
> I’ve used
> align all toAtoms #1 matchAtomNames true
> align all toAtoms #1 matchNumbering true
>  
> to align all molecules to #1 molecule at once.
> However, with this command, I cannot specify to use backbone atoms (e.g. CA,O,C,N) only when aligning.
>  
>  
> I think that there should a 1 line command that aligns all molecules with specific atoms only
> or there is chimeraX equivalent python script as
>  
> from chimera import runCommand as rc # use 'rc' as shorthand for runCommand
> from chimera import replyobj # for emitting status messages
>  
> Best,
> Doo Nam
>  
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