On Wed, Oct 29, 2014 at 8:53 PM, luzuok <[email protected]> wrote: > I think it is better for COOT to solve this issue. >
Coot already can be used to solve this issue - I think the automation is somewhat lacking, but it's vastly preferable to anything involving a text editor or shell commands. 1. Load molecule and electron density maps in Coot 2. From the "Validate" menu, select "Check/Delete waters..." 3. Just select for waters with very close distances, for example 0.2Å; I've attached a screenshot of what it should look like. 4. This will give you a list of overlapping waters - then you just need to delete one of each pair. (It doesn't matter which one - the waters will be renumbered later anyway.) Alternately, you can set "Action" to "Delete", which is much less effort, but that will delete both copies. If you are just going to run a program (or Coot function) to place more waters automatically (my preference), this won't matter, but if they're atoms you really care about, you should delete them manually. -Nat [image: Inline image 1]
