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@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@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