I guess that if one adds an EDO or GOL to a water position, and does not delete the water, Coots wonderful real space refinement might place some atoms right on top of each other. My advice would be to first delete the water, before adding something else to the blob.
Best, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Paul Emsley Gesendet: Dienstag, 3. Januar 2017 15:30 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] error in phenix refinement On 03/01/2017 14:10, Vikram Dalal wrote: > Hi all, > > > I have added the water, EDO and GOL in coot in a protein structure. I > got this error message (Fig 1) after running the phenix refinement. > > Hello Vikram, A flicker of confusion crosses my brow as I contemplate the on-going thought process that occurred as you considered asking for advice for a problem of communication between Coot and PHENIX, and it was the CCP4BB to which you turned for advice... (we live in different worlds, it seems). At a guess you have put one atom on top of another. If I were to guess again, it would be a water and your EDO and GOL are not involved in this problem. Paul.
