Hi Nick doesn’t look encouraging -
> ~/maxit/maxit-v8.120-prod-bin-linux/bin/maxit-v8.01-O -i 1A9W_A.pdb -o 1 > Initial filter libaray failed No need to worry - since the pdb2cif from the pdb-redo team works, and they’re the ones who produce AlphaFill, they can always help out if (when) things go wrong! best wishes and thanks again Harry > On 23 Feb 2024, at 14:00, Nicholas Clark > <0000b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote: > > 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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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%7C2f0b5620024b4430110208dc346f20b3%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442899115963225%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=MygtzZ%2F%2BjkYqxof8vjv2W%2BYyLWsfZLrMw%2FSjW6C1x40%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 > ######################################################################## 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/
