[chimerax-users] Aligning small molecules, ligands

[Elaine Meng]

Hi Heather,
You would specify the atoms directly in the command line.  How to specify atoms in commands is explained here:d
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

Actually if you would click the "matchatoms" or "refatoms" link in the help page for "align," it would show you that page anyway, which has several examples.   Did you try anything yourself?
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>

Issues I see are that 

(1) your model #1 has two copies of the PEG.  Which one are you trying to align with #2?   By holding the  mouse over some atom in each copy I can see that one is chain C (reported as #1/C in pop-up info balloon) and the other one is chain D.  All three of them have the same residue name, UNL.

(2) your model #2 has hydrogens but #1 does not.  You need to have equal numbers of "matchatoms" and "refatoms" so you would either need to delete the hydrogens or a use a specification that excludes them

Starting from your session I used these commands

delete H
align #2 to #1/C
[.... or to do it for the other copy ...]
align #2 to #1/D

None of this cares what is selected, i.e. those commands don't use the concept of selection.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 11, 2022, at 8:04 AM, Noriega, Heather via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> I hope you are well Elaine. I am wondering if there is a way to align my combined model UNL to my model 2. In hopes this could be a reference model of my docking done in Chimera for future builds. I did figure out the bonding, thank you. :)
> 
> I attached the session, and have read the align command. I am just unsure how to manipulate it to superimpose the ligand. 
> 
> align matchatoms (the whole model 2) toAtoms (UNL on model 1). 
> Thanks for your help.