[Chimera-users] cavity cropped view

[Randy Heiland]

The latter.  I'm sure I'm simply doing something incorrect.  BTW, I'm back
on my Linux box and still can't get it work.  I've tried to document what
I'm attempting at:
http://poincare.uits.iupui.edu/~heiland/chimera  and hope someone can tell
me what I'm doing wrong.

Thanks, Randy


> -----Original Message-----
> From: Eric Pettersen [mailto:pett at cgl.ucsf.edu]
> Sent: Wednesday, February 14, 2007 4:20 PM
> To: Randy Heiland
> Cc: 'Elaine Meng'; chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] cavity cropped view
> 
> 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?
> 
> --Eric
> 
> 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
> >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users