> On 13/09/14 19:06, Oliver Smart wrote: >> On Sat, 13 Sep 2014, Shane Caldwell wrote: >> >>> >>> Hi Helena, >>> >>> I'm not sure if this is the same issue, but I've run into a problem where >>> there is a mismatch between atom names and restraints >>> files where some programs use 'primes' and others use asterisks (I assume >>> this is part of ongoing standardization?). The ribose >>> ring goofs it up. Keeping the restraints and coordinates from the same >>> program (I have been using GRADE) through all refinement >>> has kept this from being an issue anymore for me. You just need to load >>> your own .cif file when you open the coordinates as well. >>> >>> Cheers, >>> Shane Caldwell >>> McGill University >>> >>> > On Sep 12, 2014 8:36 AM, "Helena Taberman" <[email protected]> wrote: >>> >> >>> >> Hi, >>> >> >>> >> I am using the coot 0.8-pre (revision 5201) version and having problems >>> >> with my ligand cif files. My ligand is just a common >>> NADP and the atom names at the PDB file match the atom names at the cif >>> file, but for some reason I am not able to do any real >>> space refinement ect. at coot for it since the coot fails to match (to the >>> dictionary) the following model atom names and it >>> would cause exploding atoms. I have tried to change my NADP to different >>> molecules downloaded form PDB or just searching with the >>> three letter code from the dictionary of coot, but having trouble with any >>> molecule used. There’s also this persistent clash in >>> the middle of the NADP molecule on both sides of the phosphorous next to >>> the ribose ring. >>> >> >>> >> I’m getting despered. Would you have any ideas? >>> >> >>> >> Best regards, >>> >> Helena >>> >>> >> Helena, >> >> Shane is completely correct. You have almost certainly hit >> a problem that your PDB file is using old v2 atom names whereas >> you recent coot/ccp4 is using the "new" (5 years ago?) atom names. > > I am unconvinced. Helena says that her Coot is recent and therefore the > dictionary against which Helena compared the atoms is recent too. There > haven't been asterisks in Coot for (as you say) about 5 years. > > Helena, please try this: > > File -> Get Monomer -> NAP > then > Regularize Zone on the imported NAP. > > It should just work. > > For the refinement to work on your NAP the atom names should match both the > dictionary and the imported NAP. > >> p.s. you could try a grade dictionary from http://grade.globalphasing.org/ >> (thanks Shane) but I shouldn't abuse the coot list :-; > > Grade-chat not unwelcome here :-) > > Paul.
Hi all, Thanks for your help! It was the freaking asterisks. So even though my cif and PDB-file matched, coot was not able to understand my NADP with the asterisks. Not even when I tried to change the molecule for a dictionary one, since coot was connected to phenix where I still had the old cif. -Helena
