The PDB format does not encode the bond orders (single, double, triple,
aromatic bond) that are required to produce the correct format of input
(SMILES / MOL / SDF / MOL2 / mmCIF) to Grade. This is particularly
important if some or all H atoms are absent and/or the PDB co-ordinates
have not been
Hi Frank,
in line with Paul's comment, what is so apparent about openbabel not
doing the job? I use it frequently to generate the input from PDB to the
Grade-Server.
Cheers,
Tim
On Fri, 19 May 2023 10:28:32 +0100 Frank von Delft
wrote:
> OpenBabel apparently does not.
--
--
Tim Gruene
Head
On 19/05/2023 10:28, Frank von Delft wrote:
Hello - as in the subject line, does anybody know of, or have, code
that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the
restraints CIF file used in refinement, and generate a .mol (or .sdf)
file?
Isn't this a bit of strange
apologies for a brief note:
mmCIF is the default for structural biology data and the ways to avoid
its use are just improvisations leading to more improvisations.
Bohdan, bs.structbio.org
On 2023-05-19 11:48, Frank von Delft wrote:
Really, no CIF needed?
As far as I know, it's only in the
Really, no CIF needed?
As far as I know, it's only in the CIF file that the precise atom
identities can be found. You can infer them from the PDB lines, but
that rather misses the point.
Frank
On 19/05/2023 10:42, Fred Vellieux wrote:
Hello Frank,
We have to convert betwen file formats
Hello Frank,
We have to convert betwen file formats very frequently (usually several
times daily) and:
1) we didn't need any restraints CIF file for that;
2) the tools we are using are
http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html
Hello - as in the subject line, does anybody know of, or have, code that
will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the
restraints CIF file used in refinement, and generate a .mol (or .sdf) file?
OpenBabel apparently does not.
I thought the PDB processing tools would, but my
