Hi Harry, Unfortunately, I did not see that the latest binary update was from 2008. I do not have access to any newer binaries for Linux, as I'm on MacOS.
Maybe you can use the MineProt software from the quote I mentioned previously to (in a roundabout way) accomplish the CIF file generation? "“Huiwenke: MineProt (https://github.com/huiwenke/MineProt) can be used to curate AlphaFold predictions, where PDBs are converted into CIFs using MAXIT ( https://sw-tools.rcsb.org/apps/MAXIT/index.html). The generated CIF files support Mol* visualization and downstream analysis such as AlphaFill ( https://github.com/PDB-REDO/alphafill). Another possible option is to use MAXIT directly, while it needs several additional steps to make generated CIF files support older versions of Mol*. Please refer to https://github.com/huiwenke/MineProt/blob/master/web/api/pdb2alphacif/index.php .”" Best, Nick ---------- Forwarded message --------- From: Nicholas Clark <ndcla...@buffalo.edu> Date: Fri, Feb 23, 2024 at 8:03 AM Subject: Re: [ccp4bb] mmCIF files from PDB format for AlphaFill To: Harry Powell <hrp-ccp...@virginmedia.com> Cc: Harry Powell <hrp-ccp...@virginmedia.com> Hi Harry, MAXIT binaries are located here: https://sw-tools.rcsb.org/apps/MAXIT/binary.html Best, Nick 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 7:58 AM Harry Powell <hrp-ccp...@virginmedia.com> wrote: > Hi Nick > > Thanks for responding, but see my earlier reply to Avinash - the build > doesn’t like my brand-new, hot off the production line Linux and the > location of pre-built exes is not obvious. > > best wishes > > Harry > > > On 23 Feb 2024, at 12:43, Nicholas Clark < > 0000b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote: > > > > Hi Harry, > > > > Have you tried MAXIT from the PDB? It can be installed locally: > > > > > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsw-tools.rcsb.org%2Fapps%2FMAXIT%2Findex.html&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C2f0b5620024b4430110208dc346f20b3%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442899115806976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=W3%2BzEKkB1%2BpJznVNIUjTDqMcww3v3YxylxULJCOLgf4%3D&reserved=0 > > > > 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%7C2f0b5620024b4430110208dc346f20b3%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442899115806976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=PtxZi0pOsgMF41SmBxeT1dGJRMGICHGYG4XagRvE3%2BI%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%7C2f0b5620024b4430110208dc346f20b3%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442899115806976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=bLo6wRZWM6%2BvkYC%2FziTZTS%2FvbtrzErNrdY7iA1mqmUM%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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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 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/
