[Chimera-users] Selection of residues and superposition

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 24 11:21:40 PDT 2016


> Thank you so much Elaine! Very helpfull explanation about how to use match!
> Despite that, I have a problem with some match and selection.
> For some protein when I type for example:
> match #0:346 at n,ca,o,c #1:23 at n,ca,o,c
> to match those atoms in position 346 and 23, chimera tells me that the number of atoms is not the same.
> How this is possible?
> Thank again.
> -- 
> Alessandra Gastaldello

Hi Allessandra,
You’re welcome!  You would have to check specifically, but some reasons for different or unexpected numbers of atoms are:

(1) a model has multiple chains, so that if you just say residue 23, there might be residue 23 in chain A, residue 23 in chain B, … to avoid this, just specify the chain directly. You can see which chains you have by putting the mouse over the structure and it will be shown in the pop-up information. For residue 23 in chain A only: 
#1.23.A at n,ca,c,o

(2) one or more of the atoms is missing from a structure

(3) structure has alternate locations of atoms, e.g. two positions of the same atom.  If there were locations A and B, you could first delete all the “B” locations in all structures with:
delete @.b

(4) residue number is incorrect so it did not specify any atoms

Some ways to check are by trying to display all those atoms, for example:

~ribbon
disp #0:346 at n,ca,c,o #1:23 at n,ca,c,o

(hiding ribbon allows showing backbone atoms)
You can also try selecting either set of atoms, for example:

select #0:346 at n,ca,c,o
… and then see how many atoms are selected, such as by clicking the green magnifying glass in the bottom right corner to open the Selection Inspector.

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





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