[Chimera-users] cavity cropped view

[Elaine Meng]

Hi Randy,
This does not sound like a graphics hardware issue.  All I can say is  
make sure you start with the surface hidden, and then just show  
surface for the zone.  Displaying surface for a zone does not in  
itself hide the surface outside the zone.  If you used a command,  
check that the command is typed correctly and that the atom  
specification really specifies what you wanted.  You could  
alternatively accomplish the same task with the menu: hide all  
surface first, select the atoms used to define the zone, Select...  
Zone... and enter the desired cutoff, then show the surface for that  
zone.
Best,
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 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
>
>