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 .
Best regards,
Ida
On 23-02-2024 13:43, Nicholas Clark wrote:
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 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:
>
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> 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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