Hi Luzuok, Any validation program that detects clashes should hind these.
Cheers, Robbie Sent from my Windows Phone ________________________________ Van: luzuok Verzonden: 30-10-2014 10:58 Aan: [email protected] Onderwerp: Re: [ccp4bb] water at the same exactly position Dear Nat, But if there are other solvent molecules, such as Mg2+, SO4-,,,,,, in the same position. How can this problem be solved? Lu Zuokun -- 卢作焜 南开大学新生物站A202 在 2014-10-30 12:57:31，"Nat Echols" <[email protected]> 写道： 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
