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
