[Chimera-users] cavity cropped view

[Randy Heiland]

Thanks very much, Elaine.  Your 2nd approach did indeed produce the desired
result for my case.  (I should have mentioned that I was not using the 1yc1
protein from the PDB, which has a bound ligand, but rather was displaying 2
separate molecules from a local DB.  Therefore I just substituted 'ligand'
with 'sel' after I selected the ligand molecule).

Aside:  why doesn't the 'delete' cmd also delete the MSMS surface?  It
remains displayed, remains in the Model Panel, however I cannot graphically
select it (in order to try to delete it).
 

> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
> Sent: Thursday, February 15, 2007 11:58 AM
> To: Randy Heiland
> Cc: Chimera BB
> Subject: Re: [Chimera-users] cavity cropped view
> 
> 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
> -----
> 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 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