Re: [ccp4bb] PDB validation - oligosacchides
Hi Natalie, comp_id needs to be a valid CCD ID, in this case 'GLC'. Not sure why/how the invalid value 'GLC-b-D' was generated. Let us know if you need further assistance, Deborah On 03/05/2024 22:25, Natalie Losada wrote: I am validating a structure with two sucrose molecules. I am getting the following error when uploading the file: ERROR: In 'data_comp_GLC' block: In 'chem_comp_atom' category: The 'comp_id' field value 'GLC-b-D' is not same as 'GLC' defined in data block name. I have copied sucrose directly from 5d3g.cif in Coot, and refined in phenix. I have also made the sucrose manually and acquired the cif from another website, followed by placement in Coot and refinement with phenix. Any thoughts how to save the file in a way that PDB will accept? Natalie To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- --- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK http://www.PDBe.org --- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] PDB validation - oligosacchides
Natalie If you send me the model file off-list I can help. BTW, there is a Phenix specific BB that can help with all things Phenix. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web : CCI.LBL.gov ORCID : orcid.org/-0001-8857-9464 On Fri, May 3, 2024 at 2:36 PM Natalie Losada < cf601a9f7333-dmarc-requ...@jiscmail.ac.uk> wrote: > I am validating a structure with two sucrose molecules. I am getting the > following error when uploading the file: > > ERROR: In 'data_comp_GLC' block: > > In 'chem_comp_atom' category: > The 'comp_id' field value 'GLC-b-D' is not same as 'GLC' defined in data > block name. > > I have copied sucrose directly from 5d3g.cif in Coot, and refined in > phenix. I have also made the sucrose manually and acquired the cif from > another website, followed by placement in Coot and refinement with phenix. > > Any thoughts how to save the file in a way that PDB will accept? > > Natalie > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] PDB validation - oligosacchides
I am validating a structure with two sucrose molecules. I am getting the following error when uploading the file: ERROR: In 'data_comp_GLC' block: In 'chem_comp_atom' category: The 'comp_id' field value 'GLC-b-D' is not same as 'GLC' defined in data block name. I have copied sucrose directly from 5d3g.cif in Coot, and refined in phenix. I have also made the sucrose manually and acquired the cif from another website, followed by placement in Coot and refinement with phenix. Any thoughts how to save the file in a way that PDB will accept? Natalie To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
