Hi Clemens,
> On Wed, Jun 03, 2020 at 04:39:06PM +0000, Robbie Joosten wrote:
> > The restraint file for DGL in the dictionary was wrong and the
> > chirality of the CA was not forced into the D-chirality.
>
> Yes, having
>
> loop_
> _chem_comp_chir.comp_id
> _chem_comp_chir.id
> _chem_comp_chir.atom_id_centre
> _chem_comp_chir.atom_id_1
> _chem_comp_chir.atom_id_2
> _chem_comp_chir.atom_id_3
> _chem_comp_chir.volume_sign
> DGL chir_1 CA N C CB both
> ^^^^
>
> to distinguish a D-amino acid from its L form is not ideal. But then, the CIF
> file defines it only as a "peptide" (as opposed to the "L-peptide" of GLU) in
> _check_comp.group ;-)
That wouldn't matter as the handedness would have to be explicit anyway;
handedness of internal chiral centres is not stored anywhere else. Besides,
_chem_comp.group doesn't even exist in the mmCIF dictionary. It is an internal
reference that is used (mostly) to define linkages at a compound group level
not an individual compound level, for instance TRANS peptide bonds. As TRANS
linkages are defined exactly the same for D- and L-peptides (and compounds
marked by the PDB as "L-peptide linking") it would be a useless duplication to
define all the separate categories. This is also the reason why proline-like
and N-methylated amino acids do have their own categories as the definition of
TRANS linkages does not fit.
> Out of interest: is there an advantage of having
>
> DGL chir_1 CA N CB C positiv
>
> versus
>
> DGL chir_1 CA N C CB negative
>
> which would be more similar to
>
> GLU chir_1 CA N C CB positive
Yes, it matches my copy of GLU.cif 😉
> Those atom_id_{1,2,3} and volume_sign are not part of the PDBx/mmCIF
> dictionary [1] as of now and [2] seems to be slightly behind current usage as
> well (it doesn't seem to allow "both").
>
> Does it matter? Am I missing something?
The restraint files used by CCP4 (and Phenix) are not mmCIF compliant. This has
become a serious issue as refinement programs now integrate the restraint files
(including the non-supported records) into the coordinate files.
The mmCIF dictionary could indeed use some updates here as well because the
_chec_comp_chir category alone is not very useful for defining chirality
restraints. Obviously the documentation at ccp4.ac.uk is outdated.
Cheers,
Robbie
>
> Cheers
>
> Clemens
>
>
> [1]
> http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/che
> m_comp_chir.html
> [2] http://www.ccp4.ac.uk/html/mon_lib.html
>
> --
>
> *--------------------------------------------------------------
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK www.globalphasing.com
> *--------------------------------------------------------------
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