[Chimera-users] region bounds for pdb

Tom Goddard goddard at sonic.net
Wed Jun 14 12:19:58 PDT 2017


One more way to show just a slab of an atomic structure is to drag select (mouse ctrl-drag) a region — this selects all the atoms in the green rectangle you drag out.  Then you can invert the selection (menu Selection / Invert) and hide the atoms not in the box (menu Actions / Atoms / hide).

	Tom

> On Jun 14, 2017, at 11:30 AM, Elaine Meng  wrote:
> 
> Dear Eduardo,
> It isn’t exactly the same for atomic structures, but consider these approaches:
> 
> (1) You can specify exactly which atoms, residues, etc. to display using selections and the  Actions menu, or directly using commands.  If there is some central area of interest, the atom specification can include a zone operator.  For example, to show only residues within 4.5 Angstroms of residue HEM in chain A of 4hhb:
> 
> open 4hhb
> ~displayhttp://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
> display :hem.a z<4.5
> ~ribbon
> ribbon :hem.a z<4.5
> 
> See atom specifications, zones:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
> 
> (2) clipping.  You can adjust front-back clipping in the Side View or with commands, and per-model clipping (affects individual models, can be at any angle) with Per-Model Clipping or with commands. See this page and links within:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/clipping.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jun 14, 2017, at 3:06 AM, Edoardo D'Imprima <eddimpri at biophys.mpg.de> wrote:
>> 
>> Dear Chimera users,
>> I find very handy the function “Region bounds” to cut the EM maps in order to better visualise some part of the volume. I was wondering if there is an equivalent for PDBs. 
>> Many thanks in advance,
>> Edoardo
> 
> 
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