[chimerax-users] Aligning atoms

[Elaine Meng]

Hi Heather,
With "align" you can superimpose two models using any sets of atoms, but it has to use the same number of atoms from each model.  If you get that message it means exactly what it says: whatever command you were using didn't specify the same number of atoms from each model.  I don't know what you tried, but you will probably need to list residue and atom names in the command, in the order in which you want them paired.  Label to show the residue and atom names and then look carefully to decide which atoms to pair with which.  You will probably need to write it down, and it may be a tedious process.

To hide protein and display the atom and residue names of the remainder

hide protein targ ar
label ~protein height 2 color red
label ~protein
hide H

See "align" and its options
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>

....and how to specify models/residues/atoms in the command line:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy>

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

> On Dec 17, 2022, at 5:06 PM, Noriega, Heather via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> 
> I have a question about the alignment. Is there a way to get the glycans to align, one has a PEG docked to it and I was hoping to place the PEG and delete the glycan #2. I am unsure if it is possible. It gives me an error because the number of atoms are not equal. I attached the session. Thanks in advance.
> 
> Thank you,
> 
> Heather Noriega
> PhD-Pharmaceutical Science student 
> Howard University
> heather.noriega at bison.howard.edu
> 520-203-1883
> <Trast_glycan_align.cxs>