[Chimera-users] cavity cropped view

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 1 10:22:04 PST 2007

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
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

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
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  
- display that selection (for example, with Actions... Atoms/Bonds...  

I hope this helps,
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

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
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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