Individual atom sites
Fitzgerald, P. M. D.,
Westbrook, J. D.,
Bourne, P. E.,
McMahon, B.,
Watenpaugh, K. D. and
Berman, H. M.,
International Tables for Crystallography
(2006).
Vol. G,
Section 3.6.7.1.1,
p.
[ doi:10.1107/97809553602060000738 ]
position.
The relationships between categories describing atom sites are shown in Fig.
3.6.7.1 .
Figure
3.6.7.1
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The family of categories used to describe atom sites. Boxes surround categories ...
Collections of atom sites
Fitzgerald, P. M. D.,
Westbrook, J. D.,
Bourne, P. E.,
McMahon, B.,
Watenpaugh, K. D. and
Berman, H. M.,
International Tables for Crystallography
(2006).
Vol. G,
Section 3.6.7.1.2,
p.
[ doi:10.1107/97809553602060000738 ]
the electron density is very weak, or atoms for which static disorder has been modelled. Example
3.6.7.2 shows how an author has used these data items to describe alternative orientations in part of a structure. However, the very large number of data names ...
Secondary structure
Fitzgerald, P. M. D.,
Westbrook, J. D.,
Bourne, P. E.,
McMahon, B.,
Watenpaugh, K. D. and
Berman, H. M.,
International Tables for Crystallography
(2006).
Vol. G,
Section 3.6.7.5.2,
p.
[ doi:10.1107/97809553602060000738 ]
version of the mmCIF dictionary.
The relationships between categories used to describe secondary structure are shown in Fig.
3.6.7.9 .
Figure
3.6.7.9
| top | pdf |
The family of categories used to describe ...
Bond-valence information
Fitzgerald, P. M. D.,
Westbrook, J. D.,
Bourne, P. E.,
McMahon, B.,
Watenpaugh, K. D. and
Berman, H. M.,
International Tables for Crystallography
(2006).
Vol. G,
Section 3.6.7.7,
p.
[ doi:10.1107/97809553602060000738 ]
...
Distinct chemical species
Fitzgerald, P. M. D.,
Westbrook, J. D.,
Bourne, P. E.,
McMahon, B.,
Watenpaugh, K. D. and
Berman, H. M.,
International Tables for Crystallography
(2006).
Vol. G,
Section 3.6.7.3,
p.
[ doi:10.1107/97809553602060000738 ]
of the asymmetric unit.
The following discussion treats the data items used for entities in general (Section
3.6.7.3.1) and those used more specifically to describe polymeric entities (Section
3.6.7.3.2) separately.
3.6.7.3.1. Description ...
Molecular structure
Fitzgerald, P. M. D.,
Westbrook, J. D.,
Bourne, P. E.,
McMahon, B.,
Watenpaugh, K. D. and
Berman, H. M.,
International Tables for Crystallography
(2006).
Vol. G,
Section 3.6.7.5,
p.
[ doi:10.1107/97809553602060000738 ]
Structural interactions (§
3.6.7.5.3)
STRUCT_CONN
STRUCT_CONN_TYPE
Structural features of monomers (§
3.6.7.5.4)
STRUCT_MON_DETAILS
STRUCT_MON_NUCL
STRUCT_MON_PROT ...
Atom types
Fitzgerald, P. M. D.,
Westbrook, J. D.,
Bourne, P. E.,
McMahon, B.,
Watenpaugh, K. D. and
Berman, H. M.,
International Tables for Crystallography
(2006).
Vol. G,
Section 3.6.7.1.3,
p.
[ doi:10.1107/97809553602060000738 ]
...
External databases
Fitzgerald, P. M. D.,
Westbrook, J. D.,
Bourne, P. E.,
McMahon, B.,
Watenpaugh, K. D. and
Berman, H. M.,
International Tables for Crystallography
(2006).
Vol. G,
Section 3.6.7.5.6,
p.
[ doi:10.1107/97809553602060000738 ]
(or regions) of the alignment may be identified using data items in the STRUCT_REF_SEQ category. Comments on the alignment may be given in _struct_ref_seq.details (Example
3.6.7.13).
Example
3.6.7.13. The relationship ...
β-sheets
Fitzgerald, P. M. D.,
Westbrook, J. D.,
Bourne, P. E.,
McMahon, B.,
Watenpaugh, K. D. and
Berman, H. M.,
International Tables for Crystallography
(2006).
Vol. G,
Section 3.6.7.5.7,
p.
[ doi:10.1107/97809553602060000738 ]
in the STRUCT_SHEET_ORDER category specify the relative pairwise orientation of strands and data items in the STRUCT_SHEET_HBOND category provide details of specific hydrogen-bonding interactions between strands (see Fig.
3.6.7.15 and Example
3.6.7.14). Note ...
Chemical links
Fitzgerald, P. M. D.,
Westbrook, J. D.,
Bourne, P. E.,
McMahon, B.,
Watenpaugh, K. D. and
Berman, H. M.,
International Tables for Crystallography
(2006).
Vol. G,
Section 3.6.7.2.3,
p.
[ doi:10.1107/97809553602060000738 ]
in Fig.
3.6.7.4, which also shows how information about the links is passed to the CHEM_COMP and CHEM_LINK categories. For simplicity, the categories CHEM_COMP_PLANE, CHEM_COMP_PLANE_ATOM, CHEM_COMP_CHIR ...