[Chimera-users] selecting a specific residue

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 19 08:44:33 PDT 2013


On Sep 18, 2013, at 8:53 PM, Serina Doolittle <serinadoolittle at me.com> wrote:

> Hi again, 
> 
> So now i have another question... 
> I have selected the ligand because that is what my research mentor and I are interested in (the active site and ligand binding etc.) however, when i select "ligand" it also high lights other molecules around the protein, more around the surface, like butanol - how can i just select the ligand NADPH and not have to select the other small molecule ligands that are not part of the active site of the protein? can i do that?
> 
> Serina Doolittle 
> Thanks!
> 

Hi Serina,
The "ligand" detection uses automatic rules and won't always get what you expect, but there are many other ways to select a specific residue. For example, you can select by residue name and/or number, or with the mouse in the Chimera window.  

With mouse: Ctrl-click on some atom selects it, and then keyboard up arrow will promote the selection to the whole residue.

With command: specify residue name or number, e.g.

select :nad
select :254.a

… would select residue named NAD, or residue 254 in chain A respectively.  How do you find out the residue name or number?  One way is by hovering the mouse over some atom or bond in the residue, which will pop up a balloon that shows atom name, residue name, and residue number.

With menu: Select… Residue… allows selecting by name (all the residue names present will be listed in the menu).  NADPH might have residue name NAP, NAD or something like that, since PDB files have 3-letter residue names.   That would select all residues of that type, so you'd probably want to use one of the other methods if there are multiple NADPH molecules and you only wanted to select a particular one.

Manual pages on selection and command-line atom specification:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

Also, you may want to look through the "getting started" tutorial to become more familiar with Chimera.
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>

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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