Hi Kate, The Find Clashes/Contacts tool will report all atoms near your ligand and the corresponding distances. However, it does not work with a single strict cutoff, but instead uses the atoms' VDW radii. For example, if you used a cutoff of 0.0 overlap, that would find all atoms with VDW surfaces either intersecting or just touching. It finds all the atoms meeting your specified cutoff criteria, so you would still need to look at the list of results to see which atom is the closest from each residue. There are two cutoff parameters, the amount of VDW overlap and the extra closeness allowed for H-bonding pairs. As mentioned in the manual page, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ findclash.html the suggested values for these two parameters are: 0.4-1.0 and 0.2-0.6, respectively, if you only want to detect "clashes" (unfavorably close contacts) -0.4-1.0 (negative values) and 0.0, respectively, to detect contacts in general It sounds like you want the latter. Select your ligand (for example by Ctrl-click on one atom and then hitting the keyboard up arrow), open the tool (Tools... Structure Analysis... Find Clashes/Contacts), click "Designate" to specify you want to find contacts of the selected atoms (the ligand) versus all other atoms. Set the parameters to -0.5 and 0.0. In the bottom section check "Write information to reply log" and uncheck the other options. Open the reply log (it's in the Favorites menu). Click Apply and the list of results will be written in the Reply Log window. You could play around with the VDW overlap parameter and when you think you have what you want, you could use the "Write information to file" instead of the reply log. As I mentioned above, you would still have to look through the results to see the closest atom from each residue. The more negative the parameter, the more atoms will be found (including those which are further away from the ligand). There is also a command version of this tool, http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html If you really care that you include all residues with any atom within 5 angstroms, you could do an additional step first: select the ligand, then Select... Zone using 5 angstroms, then use Actions... Write List to save the names of the "selected residues" to a file. You can compare this list to the more detailed results from Find Clashes/Contacts to find the closest atom from each of the residues. I hope this helps, Elaine p.s. I'm sending this to chimera-users too because that is more for user questions, while chimera-dev is more for developer/programmer questions ----- 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 May 20, 2007, at 10:12 PM, khar6039@mail.usyd.edu.au wrote:
Hi all, I'm new to chimera and would like a simple way to zone 5 Angstroms around a ligand and then have chimera tell me what the shortest distances are between these residues and the ligand. Is this possible? Cheers, Kate