If you open the original file with a text editor, you can see that it was slightly damaged. I opened the file you posted with a text editor, and the problems were easy to find, as they are at the top (and bottom) of the file. To be sure, I downloaded the file directly from CCDC. There are two differences.
This stuff was added by the CCP4BB software to the posted file, and people downloading it need to remove it for the file to conform to cif format. < ######################################################################## < < To unsubscribe from the CCP4BB list, click the following link: < https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64urwj9C80Q$<https://urldefense.com/v3/__https:/www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64urwj9C80Q$> < < This message was issued to members of https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64upQezFTrQ$<https://urldefense.com/v3/__http:/www.jiscmail.ac.uk/CCP4BB__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64upQezFTrQ$> , a mailing list hosted by https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64uqmy9_dAA$<https://urldefense.com/v3/__http:/www.jiscmail.ac.uk__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64uqmy9_dAA$> , terms & conditions are available at https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64upKZjvhxw$<https://urldefense.com/v3/__https:/www.jiscmail.ac.uk/policyandsecurity/__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64upKZjvhxw$> The original problem seems to be # guidelines are available at http://www.ccdc.cam.ac.uk/access/V1 was substituted with # guidelines are available at https://urldefense.com/v3/__http://www.ccdc.cam.ac.uk/access/V1__;!!Mak6IKo! OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64urJe0f3Kw$<https://urldefense.com/v3/__http:/www.ccdc.cam.ac.uk/access/V1__;!!Mak6IKo!%0bOV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64urJe0f3Kw$> This caused OV_3… to appear on a new line without a comment. If you put a “#” character in front of the OV_3, or delete the entire line starting with OV_3 (and get rid of the footer tacked on by CCP4BB) the file loads into pymol and coot just fine. Craig From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Martin Hu <wenhao.hu...@ucl.ac.uk> Date: Monday, August 19, 2024 at 6:43 AM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] CIF file Cannot Open by Coot Dear All, Thank you all for your help. I’ve tried several approaches to input this file, including changing the format to mmCIF, importing it as coordinates, and checking the restraints in the file. However, I am still unable to install the experimental ligand structure into the protein. It seems that COOT or JLigand cannot read the restraints from the CIF file. I’m wondering if anyone has faced a similar problem before, and if there is a way to input the experimental structure and save its restraints so that it can be refined with the overall protein structure in Refmac? I’ve attached the original CIF file here for your reference (in .txt format). Sincerely, Martin ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64urwj9C80Q$<https://urldefense.com/v3/__https:/www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64urwj9C80Q$> This message was issued to members of https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64upQezFTrQ$<https://urldefense.com/v3/__http:/www.jiscmail.ac.uk/CCP4BB__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64upQezFTrQ$> , a mailing list hosted by https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64uqmy9_dAA$<https://urldefense.com/v3/__http:/www.jiscmail.ac.uk__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64uqmy9_dAA$> , terms & conditions are available at https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64upKZjvhxw$<https://urldefense.com/v3/__https:/www.jiscmail.ac.uk/policyandsecurity/__;!!Mak6IKo!OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64upKZjvhxw$> ######################################################################## 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/
