[Chimera-users] Remove steric clashes

Francesco Pietra chiendarret at yahoo.com
Sun Dec 2 01:27:16 PST 2007

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

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

francesco pietra

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