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 <[email protected]> wrote:
>
> 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
>
>
>> 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
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