Many thanks to all that replied. Ida’s suggestion of pdb2cif from the PDB-REDO people is the only one that’s worked to date (“worked” in this context means produces a CIF that AlphaFill accepts without complaining - can’t imagine why).
Now off to play with my voids… As they say, standards are wonderful - that’s why there are so many of them. Have a great weekend Harry > On 23 Feb 2024, at 12:46, Ida de Vries <i.d.vr...@nki.nl> wrote: > > Dear Harry, > > You could also try to use pdb2cif from the cif-tools: > https://github.com/PDB-REDO/cif-tools. The only strict requirement for a PDB > formatted file is that it has a HEADER at the first line. After installation, > running from the command line is as simple as: pdb2cif file.pdb . > > Best regards, > > Ida > > On 23-02-2024 13:43, Nicholas Clark wrote: >> 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: >> >> 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