Why? Merging waters like that in coot is a user error, and it does not happen too often. I realize you are talking about changeable settings, but it would be really annoying if a refinement program kept removing water molecules that were placed manually because it does not fit some internal standard. Adding waters by default may obscure density that is due to other components.
I just feel one should be careful when changing chemical compositon of a model. That is something algorithms do not (yet) do well. Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: Pavel Afonine <[email protected]> </div><div>Date:10/30/2014 12:27 AM (GMT-05:00) </div><div>To: [email protected] </div><div>Subject: Re: [ccp4bb] water at the same exactly position </div><div> </div>This conversation makes me more and more certain that water update (add/remove/refine water) done as part of (a default) refinement run is a good idea -:) Pavel On Wed, Oct 29, 2014 at 5:08 AM, luzuok <[email protected]> wrote: Dear all, I found that there are some water molecules in my pdb that share the same position. This maybe cause by merging molecules in coot. It seems that I have mereged water molecules into my protein for more than one time. Does anyone tell me how to fix this problem? Best regards! Lu Zuokun -- 卢作焜 南开大学新生物站A202
