Hi Elaine, One additional question. I'm dealing with docking simulations. I have to open the ligand and receptor as separate models. Somehow I need to select both ligand and receptor before I use distance cutoff or Find Clashes/Contacts. Is there a way of doing this? Of course I could concatenate the receptor and ligand pdb files but this would be rather laborious. Many thanks in advance for your help George On Mar 5, 2011, at 9:54 PM, Elaine Meng wrote:
Hi George, You could either use a simple distance cutoff (zone around ligand), or use Find Clashes/Contacts to identify contacting residues, then display only those. There are several different ways to do either of these, including via menus/graphical interfaces or commands.
Commands are much more concise to explain, so I'll focus on those and briefly mention some of the other ways. Show command line by choosing it from the Favorites menu. Example with structure 2GBP, to display only residues within some distance of ligand:
open 2gbp ~disp disp ligand z<4.5
You would use whatever specifies your ligand, which depending on your structure could be "ligand" as in the example above, or a residue number or name preceded by colon, e.g. ":HEM". Here's the documentation for command-line zone specification: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones> Or, you could select the ligand residue, then use "Select... Zone" in the menu, then "Actions... Atoms/Bonds... show only". All of this takes care of atom/bond representations only. If you didn't want the ribbon you would also need to use "~ribb" (command) or hide ribbons using the Actions menu.
Here's an example for the findclash (contacts) approach, using recommended values for contacts:
~disp findclash ligand overlap -0.4 hb 0 select true sel up disp sel ~select ~findclash
...where the last command removes the lines showing the contacts. Again, as described above, you would use "ligand" or whatever indicates the ligand in your structure, and you would need to deal with ribbons separately. The Find Clashes/Contacts graphical interface could be used instead of the command "findclash". <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
The "Structure Analysis and Comparison" tutorial includes an example of using the Find Clashes/Contacts graphical interface. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
If you were only interested in H-bonds rather than all contacts, you could use FindHBond (or command findhbond) in a similar way. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 5, 2011, at 11:28 AM, George Tzotzos wrote:
Hi everybody, Any suggestions how to isolate & view binding site residues around a bound ligand? I have problems identifying the right topic in the manual. Many thanks in advance and best regards George