Hi Harry, Have you tried MAXIT from the PDB? It can be installed locally:
https://sw-tools.rcsb.org/apps/MAXIT/index.html 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 Fri, Feb 23, 2024 at 7:36 AM Harry Powell < 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi Martin, Marcin, Arturo, Avinash > > First off, I’m **NOT** saying that there’s anything wrong with the CIF > files produced by these routes - just that AlphaFill doesn’t like them (it > *does* like CIFs from AlphaFold - > > > alphafill process alphafold.cif filled.cif > > 1DKE > =========----------------------------------------------- 14% > > But (while Alphafold models are wonderful, have put us all out of jobs, > etc, etc) they are just a starting point for my project and, for this > purpose, no good in themselves. > > Martin, Marcin - gemmi would be a good way to go, but - > > > >>> import gemmi > > >>> structure = gemmi.read_structure('old.pdb') > > >>> structure.make_mmcif_document().write_file('new.cif') > > > > alphafill process new.cif filled.cif > > Structure file does not seem to contain polymers, perhaps > pdbx_poly_seq_scheme is missing? > > > gemmi convert old.pdb gemmi.cif > > alphafill process gemmi.cif filled.cif > > Structure file does not seem to contain polymers, perhaps > pdbx_poly_seq_scheme is missing? > > :-( > > Arturo - I’ve never scripted PyMol, but saving as CIF from the graphics > interface - > > > alphafill process pymol.cif filled.cif > > Structure file does not seem to contain polymers, perhaps > pdbx_poly_seq_scheme is missing? > > > Avinash - Maxit *might* work, but I fell at the first hurdle - although > the help page says > > > Note: It is highly recommended to utilize binary distribution, > > it’s not obvious where to get this. So I download and try to build from > source, and get (after unpacking and setting ENVs) - > > > make > > Warning: this seems to be an unsupported operating system. > > > > Supported systems are: > > SunOS ...... version 4.1.x and 5.2 or higher > > Linux ...... any version > > SGI IRIX ... version 5.3-6.4 > > make: *** [Makefile:32: compile] Error 1 > > which is odd, because this is a new Linux system installed this week > > > [hpowell@ld-mjeste3 maxit-v11.100-prod-src]$ more /etc/redhat-release > > Rocky Linux release 9.3 (Blue Onyx) > > best wishes all > > Harry > > > > > > > On 23 Feb 2024, at 11:55, Martin Malý <martin.maly...@email.cz> wrote: > > > > Dear Harry, > > > > You can try to read your PDB file and save it as mmCIF using gemmi: > > > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgemmi.readthedocs.io%2Fen%2Flatest%2Fmol.html%23reading&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885643631876%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=kPhUsO0dv9gty%2F08hhxQw5IlXdJGu%2BkXlxyLUKYNLm4%3D&reserved=0 > > > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgemmi.readthedocs.io%2Fen%2Flatest%2Fmol.html%23id3&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885648007195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=hWTaO6gd4gJkDaPGMB5e5cx5mCPaqpVKnrrNKcngeN4%3D&reserved=0 > > > > Best wishes, > > Martin > > > > > >> Hi folks > >> > >> I am in the situation of having coordinates of apoproteins (i.e. > polypeptide chains without prosthetic groups) in PDB format - but I need > them in mmCIF format so I can run them through a locally built copy of > AlphaFill. > >> > >> I need something I can install locally, so web services are a no-no. > >> > >> I’ve tried obabel and Coot to convert the PDB to mmCIF, but AlphaFill > doesn’t like the files produced. Before I spend time searching through > available options on the interweb, does anyone know of a utility that can > provide me with suitable mmCIFs? Note that I *only* have the coordinates > because they come from modelling. > >> > >> I’m assuming that I’ve run obabel and Coot correctly! > >> > >> obabel: > >> > >>> alphafill process protein_obabel.cif filled.cif > >>> Structure file does not seem to contain polymers, perhaps > pdbx_poly_seq_scheme is missing? > >> > >> Coot: > >> > >>> alphafill process protein_A-coot-0.cif filled.cif > >>> Error reading file ‘protein_A-coot-0.cif' > >>> >> parse error at line 2: This file does not seem to be an mmCIF file > >> > >> 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%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885648007195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=72t1COllpj79MnYmV3BUMjwIS7q12xAPl7OKUNDVy14%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%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885648007195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=csv1ds9sfVVrJv9OCqm6lHkqAuFngq7eHM%2FXw5eoODA%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%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885648007195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Yf3llnjNm5uRr3hlsFspxpbOopP8IztJSjcsg67Q9tg%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%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885648007195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Z7u1zg6Jj%2FPjv%2BPWV6C1%2BGXKkf4JfZ02jF9meMdYob8%3D&reserved=0 > > > > ######################################################################## > > 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%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885648007195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=72t1COllpj79MnYmV3BUMjwIS7q12xAPl7OKUNDVy14%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%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885648007195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=csv1ds9sfVVrJv9OCqm6lHkqAuFngq7eHM%2FXw5eoODA%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%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885648007195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Yf3llnjNm5uRr3hlsFspxpbOopP8IztJSjcsg67Q9tg%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%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885648007195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Z7u1zg6Jj%2FPjv%2BPWV6C1%2BGXKkf4JfZ02jF9meMdYob8%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/
