Nick, What files do you mean when call them CCP4 formatted? Coordinates are accepted only in mmCIF. Experimental data in mtz. What else?
Thank you. Vaheh From: CCP4 bulletin board <[email protected]> On Behalf Of Nicholas Clark Sent: Wednesday, January 31, 2024 3:49 PM To: [email protected] Subject: Re: [ccp4bb] Error in "Prepare and validate files for deposition" task" Maria, Apologies for the second email. I forgot that "Prepare files for deposition" also merges the CCP4 formatted files into an MTZ. If I recall correctly, I used "CONVERT2MTZ" in the command line to complete the merging of the CCP4 files to generate the necessary MTZ for deposition. Instructions can be found here: https://www.ccp4.ac.uk/html/convert2mtz.html<https://www.ccp4.ac.uk/html/convert2mtz.html>. Best regards, Nick Clark On Tue, Jan 30, 2024 at 12:47 PM mdimarog <[email protected]<mailto:[email protected]>> wrote: Dear all, I am trying to deposit 2 structures to the PDBe, solved and refined in CCP4 (version 7), and checked in PRIVATEER as they have a lot of sugars in. To this end, I used "Prepare and validate files for deposition" task, as I had previously (and succesfully) done. However, and in spite of switching to the latest CCP4 version (8.0.017), I keep getting this error message "adding_stats_to_mmcif_i2_gui:Error in wrapper Failed to add 204". I am using macOS Monterey, version 12.6.5. Does anybody have an idea what is going wrong? If not, does anybody know a different way to submit the reflection data to the PDBe? For example, would this be somehow possible just using the output from Refmac and AIMLESS? I wouldn't want to repeat the scaling/MR/refinement procedure because there are a lot of sugars there, quite difficult to built. Many thanks in advance for your help! Kind regards, Maria -- Maria Dimarogona Assistant Professor Department of Chemical Engineering University of Patras Greece ######################################################################## To unsubscribe from the CCP4BB list, click the following link: 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%7C02%7Cndclark2%40g-mail.buffalo.edu%7C545ac7ba998f4ce2969808dc21bb8142%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638422336438814400%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=YKfa3h9sRJj6cbgJFBxpBi5EVoqQzgQ2WhR3emet%2FpA%3D&reserved=0<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%7C02%7Cndclark2%40g-mail.buffalo.edu%7C545ac7ba998f4ce2969808dc21bb8142%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638422336438814400%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=YKfa3h9sRJj6cbgJFBxpBi5EVoqQzgQ2WhR3emet%2FpA%3D&reserved=0> This message was issued to members of https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C545ac7ba998f4ce2969808dc21bb8142%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638422336438814400%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=vX9RTJ76l5tJcyJ34%2BS9%2BN8s3h7NJzDaAaicXIkXsS0%3D&reserved=0<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C545ac7ba998f4ce2969808dc21bb8142%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638422336438814400%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=vX9RTJ76l5tJcyJ34%2BS9%2BN8s3h7NJzDaAaicXIkXsS0%3D&reserved=0>, a mailing list hosted by https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C545ac7ba998f4ce2969808dc21bb8142%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638422336438814400%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=j1PiKnOm5Kl9o52iCrPFKB2yn1G0NEE8LSN6NWYKMMY%3D&reserved=0<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C545ac7ba998f4ce2969808dc21bb8142%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638422336438814400%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=j1PiKnOm5Kl9o52iCrPFKB2yn1G0NEE8LSN6NWYKMMY%3D&reserved=0>, terms & conditions are available at https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C545ac7ba998f4ce2969808dc21bb8142%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638422336438814400%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=u5gtFHV93OQIdSkO0ILxTtANE%2BAppKE4sWQgXMQieeA%3D&reserved=0<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C545ac7ba998f4ce2969808dc21bb8142%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638422336438814400%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=u5gtFHV93OQIdSkO0ILxTtANE%2BAppKE4sWQgXMQieeA%3D&reserved=0> -- Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Sciences 955 Main Street, RM 5130 Buffalo, NY 14203 Cell: 716-830-1908 ________________________________ 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://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/
