[Chimera-users] selection of multiple atoms in a session with multiple pdb structures

Kenward Vaughan kay_jay at earthlink.net
Sun Sep 9 10:09:08 PDT 2012

On Sun, 9 Sep 2012 22:54:57 +0800 (SGT)
Anindito Sen <emailanindito at yahoo.co.in> wrote:

> Dear All,
> I have a Chimera session where 4 different atomic structures  (pdb
> files)  are docked in the computed density map of a macromolecular
> complex. I need to select multiple amino acids positioned at
> different places of the different docked atomic structures.
> To explain the situation-
> Say the 4 docked Atomic structures are A, B, C & D
> I need to select 276aa of A, 15aa of B, 246aa of C and so on...
> How can I do that ?
> Thanks

Hi Anindito!

Just playing around with the select command on a session with 2 loaded
pdb files gave me the following:

select #0:105.a #1:77.c #1:82 #:5

In other words, spaces between the different residues being picked
allows you to pick from multiple models on the same line.

With this command, I selected 
  residue 105 on chain A of model 0, 
  residue 77 on chain C of model 1,
  residue 82 on all chains of model 1,  and
  residue 5 on all chains on both models.

Since you label your pdb files as A, B, C, ...  I assume that these
would be numbered as 0, 1, 2, ...  by Chimera, depending on the order
they were read into the session.  You would then enter the following:

select #0:276 #1:15 #2:246 ...

While I have not played with such situations, the origin of your
particular set of pdb structures may have Chimera classify the chains
as submodels of one large model, instead of distinctly different
molecules. If that is true, then I believe the above becomes:

select #.0:276 #.1:15 #.2:246 ...

This is explained (much) more fully on the Atom Specification page of
the help system.

Final thought: if you know which residues you want to grab because
you can see them in the structure, and this is a one time sort of
thing, I'd honestly just select the residues with the mouse (with a
cleared selection, Ctrl-Shift click on an atom of each residue,
then up-arrow the results to grab the whole residues) ...

Hope this works for you!

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