secondary structure

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• Previous message: Peter Keller: "Re: TER suggestion"

    I have questions about the mmCIF list of allowed values for
_struct_conf.conf_type_id and how to fit existing PDB information
into these categories.

    For helices, a number of classes are defined in mmCIF and there is a
class HELX-OTHR 'helix other (protein)'.  However, some PBD entries have
HELIX records that are classified as alpha with notes such as kinked,
bent, alpha but 3/10 in part, etc.  Should such helices fall into the
category HELX-RHAL 'right-handed alpha helix (protein)' or HELX-OTHR?

    For turns there are several types given in mmCIF and there is TURN-OTHR
'turn other (protein)'.  Most turns in PDB entries are not classified.
It does not seem appropriate to list these turns as TURN-OTHR; is it
expected that the type will be computed from the coordinates?

    I suppose that one could make the general comment here that the
geometry of secondary structures is not always as regular as people who
want to classify it would like it to be.

    A general question which arises is whether categories should be added
for 'unspecified' or 'unknown' which clearly have a different meaning than
'other'.

                                    Frances C. Bernstein

• Previous message: Peter Keller: "Re: TER suggestion"