If you have not edited the file, the WebCSD file will contain the contents of the asymmetric unit of a small molecule structure, with reported geometry and esds, but no restraints, not least of all because small molecule refinements are (nearly always) unrestrained. This would be CIF format.
Coot is probably expecting mmCIF format, related but not the same thing (different dictionary/data items), which is consistent with the error messages. Phil Princeton ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Hu, Wenhao <wenhao.hu...@ucl.ac.uk> Sent: Thursday, August 15, 2024 11:08 AM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] CIF file Cannot Open by Coot Hi Paul, Thank you for your reply. I’ve attached screenshots that show the error message from Coot, along with the contents of the line that the message refers to. Since this CIF file contains experimental data and restrains that would be difficult to rebuild in other software, I’m seeking solutions to successfully import this file into Coot. Any help you can provide would be greatly appreciated. Best regards, Martin ________________________________ From: Paul Emsley <pems...@mrc-lmb.cam.ac.uk> Sent: Thursday, August 15, 2024 3:09 PM To: Hu, Wenhao <wenhao.hu...@ucl.ac.uk>; CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] CIF file Cannot Open by Coot ⚠ Caution: External sender On 8/15/24 14:44, Martin Hu wrote: > Dear [Recipient's Name], Dear [Correspondent's Name], > > I have downloaded a CIF file of a ligand of interest directly from WebCSD, > which was originally obtained from experimental crystallography research, and > attempted to import it into Coot. However, Coot indicates that it cannot read > the file for some reason. And what is that reason? > I've also tried opening the CIF file in JLigand, but encountered the same > issue, with the program stating that it cannot read the file. At a guess, I'd imagine that it is for the same reason. > > I have already checked the file and confirmed that it contains all necessary > descriptions about this ligand. Has anyone encountered a similar problem or > know how to resolve it? > It might be a matter of too much rather than too little. One wonders. Until you tell us what coot says in the console, we are a bit in the dark. Regards, Paul. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
