Hi Simon,
This is related to the naming system it is selecting for interpreting the
atom names in the coordinate file - for CNS that would be XPLOR and that
naming system is not available for non-standard amino acids.
When matching resonances to a molecular system (with the linkResonances
code) it can now handle things on a per-chemComp basis, so it would select
a different naming system for the non-standard amino acid, but that is not
the case for coordinates (yet).
Bye,
Wim
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