[Chimera-users] cavity cropped view

[Randy Heiland]

Is it possible that doing this "zone" specification would only crop out the
'surf' repr if I had a decent graphics card?  I *thought* I was able to do
this on my work linux box w/ an nividia card, but am unable to do it on my
wimpy Windows laptop or my wimpy Mac mini.

-Randy

> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
> Sent: Thursday, February 01, 2007 1:22 PM
> To: Randy Heiland
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] cavity cropped view
> 
> 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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