Hi John, You could select them with Ctrl-click or Ctrl-drag in the graphics window, but that can be somewhat tedious. I usually just use commands with some kind of distance criterion. For example, if the protein chains that form the dimer are A and B, I might use commands: sel :.a-b z>5 delete sel You could do it in a single command and not bother selecting, but with the above you can verify what is selected before nuking it! Also, there are many possible variations, such as different distances, or only residues with a particular name, and referring to the dimer as "protein" (assuming you don't have other proteins around). If the bleomycins were named BLE (I'm just making this up), additional possibilities would be something like sel :ble & :.a-b z>4.5 delete sel -- OR -- sel :ble & protein z>3.8 delete sel All the distance calculations in the zone spec can make command execution a little slow. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 16, 2009, at 1:43 PM, John Lowenstein wrote:
Dear Folks, In PDB 1ewj the structure comes up as an octamer. The physiological entity, in which I am interested, is a dimer. I can eliminate three of the for dimers, but I have not found a way to eliminate the six extra ligands (bleomycin) associated with the three eliminated dimers. (I want the dimer with two ligands.) Any suggestions? Thanks.
Sincerely, John Lowenstein