Dear Ning, their is some confusion. When a small molecule crystal structure is determined, the coordinates and data are usually submitted to the CCDC or the COD (crystallographic open database). The structure receives a checkcif report which, as Phil has pointed out, is specific to small molecule structures. As you submitted a macromolecular structure to the PDB, the PDB code replaces the CCDC ID during the submission process.
Best wishes, Tim On Thu, 20 Apr 2023 16:34:18 -0400 Ning Li <lining...@gmail.com> wrote: > Hi Phil, > > Thank you for the clarification, I didn't realize the CheckCIF is for > small molecules. We tried to submit the manuscript to a chemical > magazine and found "CheckCIF reports must be submitted to the > Cambridge Crystallographic Data Centre (CCDC) *prior to manuscript > submission". In fact I have had the validation for protein structure > as I submitted the structure to PDB library. I'll ask our > collaborator whether they really need it for protein structure.* > > *Thanks* > > *Ning* > > On Thu, Apr 20, 2023 at 4:19 PM Phil Jeffrey <pjeff...@princeton.edu> > wrote: > > > Hello Ning > > > > CheckCIF checks small molecule crystallographic cif files - the > > dictionaries and expectations on the contents are not the same as > > for mmcif, although the underlying syntax is the same. > > > > I'm unaware of anything that does the equivalent of CheckCIF for > > macromolecular cif files. > > > > Phil Jeffrey > > Princeton > > > > > > On 4/20/23 4:02 PM, Ning Li wrote: > > > Hi all, > > > > > > Does anybody know why I got this error message: > > > > > > /Checking for embedded fcf data in CIF .../ > > > /No extractable fcf data in found in CIF/ > > > > > > as I uploaded the CIF file to https://checkcif.iucr.org/ > > > < > > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcheckcif.iucr.org%2F&data=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=AGJyz7EJ7Isif6JDsBSfsrr8lg%2BgFsp4gjjA2pOTld0%3D&reserved=0> > > for structure validation? The CIF file was directly from > > phenix.refine during structure refinement. > > > > > > Appreciate your help > > > > > > Ning > > > > > > > > > ------------------------------------------------------------------------ > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > < > > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lPCCK274is8BSjU5Hl5qTY6wODAdprb5VepQ%2F%2FLJTUA%3D&reserved=0 > > > > > > > > > > > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
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