[Chimera-users] cavity cropped view

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 15 08:58:06 PST 2007

Hi Randy,
Here is the process you tried:
# Here is what I attempted: display a protein (1yc1)
# display a ligand (in purple)
# 'surf' on the protein
# select the ligand
# '~display' --> removes the selected ligand
# 'show sel zr<5' --> shows ligand + cropped stick repr of protein,  
but doesn't crop the surf

The "show" command only acts on atoms/bonds (not ribbon, not  
surface ...).  You have to use surf/~surf (or the menu) to show and  
hide surface.

Here are two different approaches that will work.  The first displays  
only the surface that you want.  The second displays the whole  
surface and then undisplays the part outside the zone.

command: open 1yc1
command: sel ligand zr<5
command: surf sel & main

(the "& main" part says not to surface the ligand itself)
-- OR --

command: open 1yc1
command: surf
command: ~surf ligand zr>5

I hope this helps,
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

On Feb 15, 2007, at 7:12 AM, Randy Heiland wrote:

> 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

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