Actually, that was the issue. I manually reset the occupancies of the problematic atoms in the PDB to unity. This solved my problem.
Thanks to Nat and Tom. Best, Chris On 4/21/14, tom.p...@csiro.au <tom.p...@csiro.au> wrote: > Hello Chris, > > This probably isn't your problem, but I once put some atoms into difference > density (in Coot) and for some reason the occupancy was set to zero, so > although everything was refined, the density was the same as before (massive > difference density). You might want to just check. > cheers, tom > > Tom Peat > Biophysics Group > CSIRO, CMSE > 343 Royal Parade > Parkville, VIC, 3052 > +613 9662 7304 > +614 57 539 419 > tom.p...@csiro.au > ________________________________ > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Chris Fage > [cdf...@gmail.com] > Sent: Tuesday, April 22, 2014 8:21 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Trouble Refining Ligand in Phenix > > Hi Everyone, > > I am trying to refine a structure with a phosphorylated amino acid. After > refining in Phenix, the Fo-Fc density (green) overlaps the 2Fo-Fc density > for all atoms of the derivatized amino acid in Coot, almost as if I had not > built in the residue. I am loading a .cif for the derivative when I run > phenix.refine. I have also tried ReadySet, but when I click the "Run in > phenix.refine" button, I see the message > > Error interpreting command line argument as parameter definition: > "refine_65-coot-2.metal.edits" > RuntimeError: Unexpected end of output. > > Am I just seeing noise, or is Phenix not actually refining this portion of > the model? I would appreciate any suggestions. > > Best, > Chris >
