Re: [ccp4bb] refining nucleic acids with Coot
For reference, the CCP4 tool is called 'pdb2to3' -- David On 14 January 2014 18:32, Almudena Ponce Salvatierra maps.fa...@gmail.comwrote: 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
[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
Re: [ccp4bb] refining nucleic acids with Coot
On 14/01/14 15:51, Almudena Ponce Salvatierra wrote: 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? Hello Almudena, It seems that your model is inconsistent with the dictionary. I imagine that the dictionary has PDB v3 prime names but your model has star names. I don't know of a tool in ccp4 to do the conversion, but I think the remediator will do this. http://kinemage.biochem.duke.edu/software/remediator.php Paul.
Re: [ccp4bb] refining nucleic acids with Coot
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
