For reference, the CCP4 tool is called 'pdb2to3' -- David
On 14 January 2014 18:32, Almudena Ponce Salvatierra <maps.fa...@gmail.com>wrote: > Thank you all very much for your very helpful advices! I managed to solve > my problem! :-) > > Best, > > Almudena. > > > 2014/1/14 Ashley Pike <ashley.p...@sgc.ox.ac.uk> > >> Hi Almudena - I came across this issue recently as well with an old pdb >> file. As Paul says you need to convert from v2.3 to v3.2 pdb formats. In >> addition to the link he gave, you can also accomplish this using the iotbx >> toolbox that comes with phenix. >> >> iotbx.pdb_remediator file_name=in.pdb output_file=out.pdb >> >> >> >> will rename * atom names to ' (eg O4* to O4') which can then be >> regularised in coot. >> >> >> >> Ashley >> >> >> >> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of >> *Almudena Ponce Salvatierra >> *Sent:* 14 January 2014 15:52 >> *To:* CCP4BB@JISCMAIL.AC.UK >> *Subject:* [ccp4bb] refining nucleic acids with Coot >> >> >> >> Dear all, >> >> I am trying to refine an oligonucleotide chain in Coot and I get the >> following message when I try: >> >> "Fail to match (to the dictionary) the following model atom names: >> >> G >> >> O5* C5* O4* etc.... >> >> That would cause exploding atoms so the refinement did not start" >> >> Does anyone know how to solve this? >> >> Best wishes, >> >> Almudena. >> >> >> -- >> >> Almudena Ponce-Salvatierra >> >> Macromolecular crystallography and Nucleic acid chemistry >> >> Max Planck Institute for Biophysical Chemistry >> >> Am Fassberg 11 37077 Göttingen >> >> Germany >> >> >> > > > > -- > Almudena Ponce-Salvatierra > Macromolecular crystallography and Nucleic acid chemistry > Max Planck Institute for Biophysical Chemistry > Am Fassberg 11 37077 Göttingen > Germany > >
