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

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)

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

Hi Huw, When I was at the workshop, I have to admit that after ccp4i2 refused to do it I switched to Phenix and used phenix.reflection_file_converter! It would be better if i2’s reindex or change spacegroup task didn’t refuse, and I guess this might improve after the overly-zealous consistency

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

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?

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

Hi Randy, > On 23 Feb 2024, at 11:49, Randy John Read wrote: > > Why would we want to impose an arbitrary restriction on users for this > relatively common scenario. If the user has the unmerged data this can be imported into CCP4i2 via the data reduction task and merged in P1. How would you

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

On Fri, Feb 23, 2024 at 9:58 AM Winter, Graeme (DLSLtd,RAL,LSCI) < 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > While I get where you are coming from, it is still from a mathematical > standpoint correct to consider e.g. a tetragonal crystal as monoclinic - > P21 is a subgroup of

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

Hi Harry, I remember the C222/P622 confusion from some of Phil's old slides, and I thought that was an impressive case! It probably appears in a few places on the internet, but one I found just now is slide 15 of this presentation:

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

Hi Huw, This is tricky because in certain situations the cell parameter esds can get lost. For example if best_unit_cell= has been passed during scaling or merging with DIALS. Or, if cell parameter refinement was done using the LFBGS engine, in which case the esds are not calculated. Cheers

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] i2 won't accept 90 degree angles in moniclinic

In the recent crystallography workshop in Thailand, we had at least 3 cases brought by participants where we had reason to suspect that the data had been over-merged because of undetected twinning. Often there is more than one possible twinning operator and (as potentially in one of the cases

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

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Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

> On 23 Feb 2024, at 09:58, Winter, Graeme (DLSLtd,RAL,LSCI) > <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > > so strictly it is possible and correct - if experimentally unlikely - to > have the situation we are discussing here occur. I believe this is only technically possible

Re: [ccp4bb] problem transferring ccp4i2 projects from one computer to another

Dear Stuart Thank you for your reply Yes, you are right. The reports are not displayed for any project (not just the imported ones). What should I look at to solve the problem ? Stefano - Mail original - > De: "Stuart McNicholas" > À: "Stefano Trapani" > Cc: CCP4BB@jiscmail.ac.uk >

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

Hi Graeme (I may well have mentioned this when we shared an office) et al I’ll add something from my small-molecule crystallography days, when we used point detectors - so this would be pre-1996 which was the last time I used one of these machines. I don’t remember which structure it was (feel

Re: [ccp4bb] problem transferring ccp4i2 projects from one computer to another

Dear Stefano, I wonder if the problem is simply displaying any ccp4i2 reports on the new computer, rather than just the imported ones. Have you tried creating a completely new project and seeing if anything works in that? There are some potential things to think about in the log file. Best

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

Hi Huw (first: thank to Phil for picking this up; it caused much confusion) While I get where you are coming from, it is still from a mathematical standpoint correct to consider e.g. a tetragonal crystal as monoclinic - P21 is a subgroup of P43212 (say) so strictly it is possible and correct -

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

Hi Graeme, > On 21 Feb 2024, at 16:52, Winter, Graeme (DLSLtd,RAL,LSCI) > <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > > Processing a data set in lower than necessary symmetry e.g. tetragonal as > monoclinic you _cannot_ import the merged MTZ file into i2 because it is >