[Chimera-users] Remove steric clashes

Elaine Meng meng at cgl.ucsf.edu
Sun Dec 2 08:30:56 PST 2007

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 

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
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.

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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

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