[Cod-bugs] bond assignment by cod-tools vs approach by Jmol

Norwid Behrnd nbehrnd at yahoo.com
Sun Nov 14 12:39:51 EET 2021

Dear maintainers of COD,

on occasion, codtools used to rewrite content of .cif as a .sdf file
may assign a bond between cations and anions, e.g., between Ca^{2+}
and hydrogenphosphate in entry #2106184.

Of course, this may be adjusted by an manual edit of the .sdf file
written.  Andrius Merkus equally told me you already were working on
this, too.  Thus, the following only intends to indicate to you
about two threads in the Jmol user list of the previous week which
might be relevant / potentially interesting for you:

+ «Covalent bond cutoff distances?» initiated by Eric Martz on
  November 11th

+ «DOCUMENTATION autobonding», initiated by Eric Martz on November


With best regards,

Norwid Behrnd
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