struct_sheet

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• Previous message: Dale Tronrud: "RE: Definition of Pseudorotation Angles"

There is an inconsistency between the examples and the
struct_sheet_hbond definitions.  Look at Example 1, the simple
beta barrel.  11 N is bonded to 30 O and 19 O is bonded to 40 N
in the diagram.  However in the mmCIF version of the example,
11 N is identified as range_1_beg and 30 O as range_2_beg, which
seems fine, until you read the text of the definitions, which
takes the range_1_beg items as "one partner of the first
hydrogen bond" and the range_2_beg items as "one partner of the
last hydrogen bond"  I would suggest changing the definitions
rather than the examples, as follows:

For the range_1_beg items:

     ... one partner of the first hydrogen bond ...

For the range_1_end items:

     ... one partner of the last hydrogen bond ...

For the range_2_beg items:

     ... one partner of the first hydrogen bond ...

For the range_2_end items:

    ... one partner of the last hydrogen bond ...

And add a general comment on the meaning of "first" and "last", which
is tricky but important.
  -- H. J. Bernstein

P.S.  Life is simpler if you follow the PDB approach of just giving
one representative hydrogen bond for registration, in which case
worrying about "first" and "last" is a non-problem.  This
simplification could be achieved by making the range_*_end items
implicit rather than mandatory, and allowing "first or representative"
for the range_*_beg items.  

• Previous message: Dale Tronrud: "RE: Definition of Pseudorotation Angles"