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