Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

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

Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

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

Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

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

Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

Nick > > > > -- Forwarded message ----- > From: Nicholas Clark > Date: Fri, Feb 23, 2024 at 8:03 AM > Subject: Re: [ccp4bb] mmCIF files from PDB format for AlphaFill > To: Harry Powell > Cc: Harry Powell > > > Hi Harry, > > MAXIT binar

[ccp4bb] Fwd: [ccp4bb] mmCIF files from PDB format for AlphaFill

uot; Best, Nick -- Forwarded message - From: Nicholas Clark Date: Fri, Feb 23, 2024 at 8:03 AM Subject: Re: [ccp4bb] mmCIF files from PDB format for AlphaFill To: Harry Powell Cc: Harry Powell Hi Harry, MAXIT binaries are located here: https://sw-tools.rcsb.org/apps/MAXIT/b

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

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

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

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 .

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

Harry, After a little digging, it seems this was previously reported as an issue to AlphaFold… see: https://github.com/google-deepmind/alphafold/issues/252 There are a few options others recommended or got to work in the comments. Notably, MAXIT was used: “Huiwenke: MineProt

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

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

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

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

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

Thanks Martin for writing about gemmi. It also has a command-line program: gemmi convert input.pdb input.cif https://gemmi.readthedocs.io/en/latest/utils.html#convert On Fri, Feb 23, 2024 at 12:44 PM Martin Malý wrote: > > Dear Harry, > > You can try to read your PDB file and save it as mmCIF

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

Hi Harry, You can do this using the MAXIT tool [https://sw-tools.rcsb.org/apps/MAXIT/index.html] which can be installed locally. Best wishes, Avinash To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

Hi Harry Thank you for the information on how hard it is to work locally. I wish you all the best! Marta El 2024-02-23 12:48, Harry Powell escribió: Hi Marta Thanks for this. Unfortunately, I can't use a web resource for this - I have to do it locally (partly because I'm providing a

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

Hi Marta Thanks for this. Unfortunately, I can’t use a web resource for this - I have to do it locally (partly because I’m providing a web service, and it’s better not to blame other providers when my service fails). I’d be likely to be doing this > 1000 times a day (every day from now until

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

Dear Harry, You can try to read your PDB file and save it as mmCIF using gemmi: https://gemmi.readthedocs.io/en/latest/mol.html#reading https://gemmi.readthedocs.io/en/latest/mol.html#id3 Best wishes, Martin On Fri, 2024-02-23 at 11:32 +, Harry Powell wrote: > Hi folks > > I am in the

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

Hi Harry I use this link: https://mmcif.pdbj.org/converter/ to convert pdb to mmCIF . Hope, it was usuful for your modelled coodinates. Regards Marta El 2024-02-23 12:32, Harry Powell escribió: Hi folks I am in the situation of having coordinates of apoproteins (i.e. polypeptide

[ccp4bb] mmCIF files from PDB format for AlphaFill

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