Hi Nick I noticed this today when I was researching the differences between mmCIF and modelCIF - but thanks anyway.
I haven't tried running it yet, but the important thing for me is to be able to convert my bare-bones PDB format files to something that AlphaFill will accept - and as the PDB-REDO team's pdb2cif does the job, I think my search is over. In fact, better than that - it seems that the latest version of AlphaFill reads "my" PDB files correctly, so I should be able to avoid the conversion step. Harry -- Dr Harry Powell > On 26 Feb 2024, at 17:54, Nicholas Clark > <0000b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi Harry, > > I did stumble upon this python mmCIF handler for modelCIF: > > https://github.com/ihmwg/python-modelcif/blob/main/examples/README.md > > > Maybe this will have something of use to your efforts? > > Best, > > Nick Clark > > 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 > > >> On Mon, Feb 26, 2024 at 7:16 AM Harry Powell >> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> Hi folks >> >> I’ve made considerable progress in getting to the bottom of this problem. >> From what I can gather, AlphaFold writes “modelCIF”, which is not quite the >> same as “mmCIF”, and just saying “CIF” is not unambiguous. So I guess I >> should have been more aware of this when posting my original question. >> >> With regard to the programs mentioned (note these are not all my analyses, >> so please don’t shoot the messenger!) - >> >> * Pymol produces a file which is some way from “standard” and would need >> work to make it usable (so something for Schroedinger to work on, perhaps). >> >> * Coot *almost* produces a file that can be used (authors aware). >> >> * Gemmi is also close, but no cigar (authors aware). >> >> * I’d guess that Maxit was last revised many years before modelCIF was >> introduced so I don’t think this would be a fruitful path to follow (the >> build failed on my newly installed Linux because it was an unrecognised >> system, and the most recent binary was built in 2008). >> >> Many thanks to everyone who took the time to read and answer my question! >> >> Harry >> >> ######################################################################## >> >> 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%7C4b61569c771540b3e08b08dc36c4b41b%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638445465773022347%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=xYMS5WSaukIQH01xhrcT49KB%2Fk2n0%2FgBxj%2BmhVV8%2F48%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%7C4b61569c771540b3e08b08dc36c4b41b%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638445465773022347%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=LycsBxH4qFwd5BLg8%2BKWR264yylOYJkO4J2fH9atfU4%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%7C4b61569c771540b3e08b08dc36c4b41b%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638445465773022347%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=GOMHrLwX%2B5G8cvye1qGGdmpMATWZxFVn7IKISNvv3t0%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%7C4b61569c771540b3e08b08dc36c4b41b%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638445465773022347%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=x1FsTM0njQwvNEHdpb%2B3xbiRtnFwixCshZG9mHrjqco%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 ######################################################################## 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/
