[Chimera-users] cavity cropped view

[Elaine Meng]

Hi Randy,
You can use a "zone" specification, either with commands or via the  
menu.  An example of the command approach:

show ligand zr<5
    or
show :glc zr<5

The first example would show all residues [with any atom] within 5  
angstroms of what is considered "ligand" ... in the second example, I  
gave a specific residue name.  GLC is the residue name of glucose in  
the PDB entry 2gbp.  You could also use a residue number or range of  
numbers. "za" instead of "zr" would just the atoms within the cutoff  
rather than their whole residues, and > instead of < gets the  
complementary set.  The "show" command (unlike "display") undisplays  
everything that is not specified, so you don't have to undisplay  
anything beforehand.

See the "Zones" section of
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ 
frameatom_spec.html

The mostly-menu approach has more steps:
- select the small molecule (for example by Ctrl-clicking one of its  
atoms and then pressing the up arrow key)
- use the command
         ~display
to undisplay everything (if you use the Actions menu, it would just  
undisplay the current selection)
- select a zone defined by the current selection (Select... Zone)  
with specified cutoff and whether you want it to be atom-based or  
residue-based
- display that selection (for example, with Actions... Atoms/Bonds...  
show)

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Feb 1, 2007, at 10:01 AM, Randy Heiland wrote:

> What options exist in Chimera for letting me show only that portion  
> of a
> protein that is "near" another smaller molecule?  Specifically, I  
> have a
> ligand in a cavity of a large protein and would like to eliminate the
> "clutter" of the protein away from the cavity of interest.
>
> Thanks, Randy
>
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