[Chimera-users] Selecting regions of a PDB structure

Eric Pettersen pett at cgl.ucsf.edu
Tue Jun 11 11:04:02 PDT 2013


One small additional note:  if your PDB is a standard PDB entry, you can use Tools->Sequence->PDB/UniProt Info to fetch the Uniprot sequence with regions of interest shown in a "region browser", including domains.  Selecting a region in the browser selects it on the sequence and on the structure (if that part of the sequence exists in the structure entry).

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jun 11, 2013, at 9:39 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Andy,
> There are many ways to select in Chimera, including:
> 
> (1) showing sequence of the chain of interest (Favorites… Sequence) and then in the sequence window, dragging a box to enclose the range of residues you want to select
> 
> (2) specifying model number, residue numbers and chains directly in the command line, for example:
> select #1:86-251.A,12-40.B
> 
> … although if you already know numbers and chain IDs, you might as well just do the coloring in the same command.  You can also use "alias" to give each set of residues a shorter name, which is more convenient if you want to act on them in multiple commands.  This earlier post has examples of aliasing and coloring residue ranges:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-July/007802.html>
> 
> (3) Ctrl-dragging in the main window to draw a box around around the residues you want to select (but it's hard to be precise with this method)
> 
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
> 
> After you select, you can use the menu (Actions… Color… etc., can choose color directly or first go to "all options" at the bottom of that menu for things like coloring only the ribbons and not atoms, or showing a bigger list of colors)
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#actcolor>
> 
> 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
> 
> 
> On Jun 11, 2013, at 12:55 AM, Anindito Sen <emailanindito at yahoo.co.in> wrote:
> 
>> Dear All,
>> I have a pdb file of a large protein complex. I want to select several regions and color them differently to show the various domains. How can I do that.
>> Thanks
>> Andy 
>> 
> 
> 
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