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

Hi George, I'm pretty sure there is no need to select both. For example, you would select the ligand only and then use "Select... Zone" to get the residues around it. Or, if you are using Find Clashes/Contacts you would select the ligand only and designate checking it against all other atoms. Or if you have a bunch of models (not just ligand and receptor) and you want the other ones to be ignored, you would select and designate the ligand as first set, then select and designate the receptor as the second set. They would not be selected at the same time. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...

If you are using commands it is not necessary to do any selection beforehand, as in my example commands in the previous message. The findclash example performed the selection itself when finding the contacting residues, you did not have to select anything before that. Also, the zone specifier can be used to find atoms in a different model than the ligand. For example, if the ligand is all of model #1.1 and receptor is model #0,

~disp disp #1.1 disp #0 & #1.1 z<4.5

Of course, you can select atoms from multiple models at once, and there are several ways. For example, command

select #0,1

or

select #0:1-25#1:his

or you could open the Model Panel (from Favorites menu), choose both models on the left side, and then click the "select" button on the right side. With commands you can specify only certain atoms from the multiple models. However, I very rarely make such selections and am not sure why you would need them; I just use the specification directly in the command (for coloring, displaying or whatever).

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 Mar 6, 2011, at 5:06 AM, George Tzotzos wrote:

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

Hi Huy,

There is no Chimera command for color zone, but there should be one. It is possible to make a Python script that does this and you could run that script with the Chimera runScript command. I put a Python script czone.py that does this on the Chimera Python scripts page

http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts

I also added a feature request for a color zone command.

http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests

Is the reason you want this command because you are writing some script, or you just prefer to use commands when looking at the data interactively?

Tom

Bui Khanh Huy wrote:

I have a density map and 3 marker sets for coloring my density map. Is this possible to select the 3 marker sets and color my density map with a selected radius (Color Zone tool) by command line?