Hi Francesco, Zone selection does not require separate models. You can use any specifiers to indicate the atoms in the zone, for example open 1zik select solvent & protein z<4 (depending on what the waters are named you could use :wat or :.water instead of "solvent" and it sounds like you want to specify your lipids instead of protein... :popc or whatever those residues were named) Then you can "delete sel" or use Actions... Delete to delete the selection (warning: there is no undo except by reopening the starting structure). Find Clashes/Contacts could also be used to select the atoms, but remember it looks at "amount of VDW overlap" rather than "distance between atom centers" and there are more steps than the simple zone approach above. One of the options in Find Clashes/Contacts is to select the pairs of atoms. That would give water atom + lipid atom pairs in your case. Then subtract from the selection the lipid atoms. That would leave just selected water atoms. If you have hydrogens on the waters, promote the selection to the whole water residues. Then proceed as before to delete the selection. Here is a findclash example pretending I want to delete waters with 0.1 A VDW overlap with the protein in 1zik. open 1zik addh findclash solvent overlap .1 hbond 0 makePseudobonds false select true [that preceding findclash command is all one line!] ~sel ~ solvent sel up del sel You could do the same thing with the GUI and menus instead of commands. Best, 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 Dec 2, 2007, at 1:27 AM, Francesco Pietra wrote:
I would like to delete all water residues that are in steric clash with lipid residues. What I have is a single pdb file that includes both types of residues. Can't have the two as different models.
Therefore I can't apply the zone tool that I know how to manage for two different models.
The only alternative I can figure out is through the "Find Clashes,Contacts", writing a file for all WAT at a specified distance from the lipid residues and then manually deleting, or inventing a script for that (at <=0.6A there are 386 clashes).
Hope to have missed an automatic tool from Chimera. If not, I suggest that as a most useful additional tool for cleaning systems. I dropped into the problem when at the first minimization, in view of MD, the system met segmentation fault after a few steps, with gradient decreasing by eight orders of magnitude along those few steps. Then I recognized not to have been careful enough before making the coordinate files for the MD suite. I should have not relied too much in the membrane builder and I had better spent time in checking for steric clashes.
Thanks francesco pietra