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@cgl.ucsf.edu] Sent: Thursday, February 01, 2007 1:22 PM To: Randy Heiland Cc: chimera-users@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@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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