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 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 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
https://datascience.unm.edu/tomcat/biocomp/convert
Sometimes the conversion doesn't take place and I have no idea why.
HTH,
Fred.
On 5/19/23 11:28, 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?
OpenBabel apparently does not.
I thought the PDB processing tools would, but my collaborator
couldn't find them.
Any pointers welcome. (To save us time.)
Thanks!
Frank
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