Dear Steve Please can you communicate with the wwPDB curation team through the OneDep system and we can look into specific issues with your deposition.
We report all issues back to the developers (CCP4/Refmac/Phenix/Buster and OneDep) and they have all been very quick at fixing any problems. Please ensure that you are running the latest version of CCP4 as this contains the latest updates which are required to ensure that deposition goes smoothly. Hope this helps John PDBe -----Original Message----- From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of stephen.c...@rc-harwell.ac.uk Sent: 25 September 2019 15:49 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Errors reading mmcif files when trying to deposit coordinates to pdb Dear Roberto, I am using ccp4i at the moment, but am trying i2 to see if this corrects the problem. I have also tried pdb-extract as suggested by Isobel, but am still awaiting the results. Thanks fir the suggestions so far, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 ________________________________ From: Steiner, Roberto <roberto.stei...@kcl.ac.uk> Sent: 25 September 2019 15:08:11 To: Carr, Stephen (MRC,RAL,RCAH) Cc: ccp4bb Subject: Re: [ccp4bb] Errors reading mmcif files when trying to deposit coordinates to pdb I assume you're using ccp4i and not i2. If you use the latter the mmcif coords file produced should be ok. I have had the same problem a few days ago. Best wishes Roberto On 25 Sep 2019, at 15:00, stephen.c...@rc-harwell.ac.uk<mailto:stephen.c...@rc-harwell.ac.uk> <stephen.c...@rc-harwell.ac.uk<mailto:stephen.c...@rc-harwell.ac.uk>> wrote: Dear ccp4ers, I have refined several structures using refmac5 within ccp4i and tried to upload the output mmcif files to the pdb in order to deposit the coordinates/structure factors. However, during the initial upload process when the files are scanned I get the following errors: ERROR - Read file 'input_file_1' failed: syntax error at line 30421 ERROR - syntax error at line 30426 Warning - Duplicate category name chem_comp_atom at line 30428 Warning - Duplicate category name chem_comp_bond at line 30446 Warning - Duplicate category name chem_comp_angle at line 30467 ERROR - syntax error at line 30581 ERROR - syntax error at line 30585 These all lie after the coordinates in the dictionary part of the file. When I have investigated this I cannot see any duplicated category names that would result in the above warnings and the syntax errors are not a result of anything obvious. I have checked for hidden characters, found none, and can see nothing else wrong. Finally, line 30585 does not exist, the file stops at 30584. Has anyone had similar problems or any suggestions that might solve this? Thanks, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk<mailto:stephen.c...@rc-harwell.ac.uk> tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. 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