[Chimera-users] cavity cropped view

Eric Pettersen pett at cgl.ucsf.edu
Wed Feb 14 13:19:34 PST 2007

So does "unable to do it" mean that the command never finishes, or  
that it does finish but somehow doesn't produce the right result?


On Feb 13, 2007, at 6:12 PM, Randy Heiland wrote:

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