+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ DICTIONARY +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ What follows are definitions, extracted from the mmCIF dictionary, for the data items used in the above examples and for a few closely related data names. There are of course many other data items in this dictionary, but this subset should handle all of the various information that is deposited with PDB structure factor files. CIF data items are organized into categories, so in each case the defintion of the category is given preceding the definitions of the individual data items. All data items are presented in alphabetical order. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ################ ## DATABASE_2 ## ################ ; Data items in the DATABASE_2 category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a data block if they originate from that source. The somewhat clunky name of this category (DATABASE_2) is a consequence of the name DATABASE having been already used in the CIF core, but used in a manner different than the usage in mmCIF. Since CIF data names, once adopted, cannot be changed, a new category was created. ; _database_new.database_id ; An abbreviation that identifies the database. ; _database_new.database_code ; The code assigned to the data block by the database identified in _database_new.database_id. ; ##################### ## PHASING_MIR_DER ## ##################### ; Data items in the PHASING_MIR_DER category record details about individual derivatives used in the phasing of the structure when methods involving isomorphous replacement are involved. ; _phasing_MIR_der.details ; A description of special aspects of this derivative, its data, its solution, or its use in phasing. ; _phasing_MIR_der.id ; The value of _phasing_MIR_der.id must uniquely identify a record in the PHASING_MIR_DER list. Note that this item need not be a number; it can be any unique identifier. ; ####################### ## PHASING_MIR_REFLN ## ####################### ; Data items in the PHASING_MIR_REFLN category record details about the reflection data used in an MIR experiment. This category of data items is provided so that derivative intensity and phase information can be stored in the same data block as the native information. However, no provision is made for the storage of all of the details of obtaining those data; to store such detailed information a separate data block should be used for each derivative. ; _phasing_MIR_refln.der_id ; This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category. ; _phasing_MIR_refln.F_calc ; The calculated value of the structure factor for this derivative, in electrons. ; _phasing_MIR_refln.F_calc_au ; The calculated value of the structure factor for this derivative, in arbitrary units. ; _phasing_MIR_refln.F_meas ; The measured value of the structure factor for this derivative, in electrons. ; _phasing_MIR_refln.F_meas_au ; The measured value of the structure factor for this derivative, in arbitrary units. ; _phasing_MIR_refln.F_meas_sigma ; The estimated standard deviation of _phasing_MIR_refln.F_meas, in electrons. ; _phasing_MIR_refln.F_meas_sigma_au ; The estimated standard deviation of _phasing_MIR_refln.F_meas, in arbitrary units. ; _phasing_MIR_refln.index_h ; Miller index h of the reflection. ; _phasing_MIR_refln.index_k ; Miller index k of the reflection. ; _phasing_MIR_refln.index_l ; Miller index l of the reflection. ; _phasing_MIR_refln.phase_calc ; The calculated value of the structure-factor phase, based on the heavy atom model, for this derivative, in degrees. ; ########### ## REFLN ## ########### ; Data items in the REFLN category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in loop lists. ; _refln.A_calc ; The calculated value of structure-factor component A, in electrons. A = |F|cos(phase) ; _refln.A_calc_au ; The calculated value of structure-factor component A, in arbitrary units. A = |F|cos(phase) ; _refln.B_calc ; The calculated value of structure-factor component B, in electrons. B = |F|sin(phase) ; _refln.B_calc_au ; The calculated value of structure-factor component B, in arbitrary units. B = |F|sin(phase) ; _refln.F_calc ; The calculated value of the structure factor, in electrons. ; _refln.F_calc_au ; The calculated value of the structure factor, in arbitrary units. ; _refln.F_meas ; The measured value of the structure factor, in electrons. ; _refln.F_meas_au ; The measured value of the structure factor, in arbitrary units. ; _refln.F_meas_sigma ; The estimated standard deviation of _refln.F_meas, in electrons. ; _refln.F_meas_sigma_au ; The estimated standard deviation of _refln.F_meas, in arbitrary units. ; _refln.index_h ; Miller index h of the reflection. ; _refln.index_k ; Miller index k of the reflection. ; __refln.index_l ; Miller index l of the reflection. ; _refln.status ; Classification of a reflection so at to indicate its status with respect to inclusion in refinement and calculation of R-factors. ; _refln.phase_calc ; The calculated value of the structure-factor phase, in degrees. ; ############ ## REFLNS ## ############ ; Data items in the REFLNS category record details about the reflection data used to determine the ATOM_SITE data items. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. ; _reflns.details ; A description of reflection data not covered by the other data names. It should include details of the Friedel reflection data. ; +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++