Dear all,
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 ;-)
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
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?
Cheers
Clemens
[1]
http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/chem_comp_chir.html
[2] http://www.ccp4.ac.uk/html/mon_lib.html
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*--------------------------------------------------------------
* 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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