Core restraints dictionary v 0.0.3 for COMCIFS approval
Herbert J. Bernstein
yaya at bernstein-plus-sons.com
Tue Sep 21 13:56:51 BST 2010
Looks very useful. A few typos:
line 131: categroy_overview
should be category_overview
line 476: _enumeration)range
should be _enumeration_range
line 560: data_restr_distance_min_details
should be data_restr_distance_min_detail
line 1780: _units_details
should be _units_detail
line 2006: _example_details
should be _example_details
line 2030: ' _restr_rigid_body_id'
should be '_restr_rigid_body_id'
lines 2065:
data_restr_rigid_body_site_symmetry_label_
should be data_restr_rigid_body_site_symmetry
line 2353:
data_restr_U_isotropic_weight_param
should be data_restr_U_iso_weight_param
subject to those corrections, my vote is yes -- well done.
-- Herbert
At 10:14 PM +1000 9/21/10, James Hester wrote:
>Dear COMCIFS,
>
>Following this email is a new version of the restraints dictionary,
>which has been revised according to Herbert's suggestion and has now
>once again been submitted to COMCIFS for final approval. The
>dictionary will be considered approved once all voting members have
>voted to approve it, or else no objections have been received in the
>next 6 weeks, whichever occurs first.
>
>James.
>=======================================
>
>##############################################################################
># #
># CIF RESTRAINTS AND CONSTRAINTS DICTIONARY VERSION 0.03 #
># ------------------------------------------------------ #
># #
># Proposed dictionary code for reporting restraints and constraints in the #
># core CIF dictionary #
># #
># This dictionary contains the names and definitions proposed for reporting #
># restraints and constraints in the Core CIF dictionary #
># #
># 2010-09-15 #
># This dictionary has been approved by the core dictionary maintenance group #
># The items described below have been preseneted for final approvcal by #
># COMCIFS on behalf of the International Union of Crystallography #
># #
># Copyright 2010 International Union of Crystallography #
>##############################################################################
>
>##############################################################################
># #
># Some notes on the philosophy followed in this dictionary #
># -------------------------------------------------------- #
># A RESTRAINT is a condition used in the refinement of a crystal structure #
># that requires one or more of the parameters of the refinement to lie #
># within a certain range. #
># #
># A CONSTRAINT is a condition used in the refinement of a crystal structure #
># that requires one or more parameters of the refinement to have a #
># specific value or be exactly equal to another refined parameter. #
># #
># The range of values allowed in a restraint is given in this dictionary #
># by a target value and a weighting parameter, the latter being the #
># expectation value of the difference between the refined value and #
># the target. #
># Constraints are indicated by setting the weighting parameter to zero. #
># #
># Restraints and constraints are handled in many different ways in different #
># programs. The actual parameters restrained are determined by the way the #
># restraint is expressed within the program, and different programs #
># express the same restraint in different ways. In this dictionary the #
># restraints are expressed in a way that is most natural to the description #
># of the crystal structure which means that the parameters given here #
># may not correspond to the parameters that were actually restrained. #
># For example the rigid body constraint is expressed here by listing the #
># atoms in the rigid body. Distances and angles between them are constant. #
># For a rigid body the target parameters are the same as the refined #
># parameters, allowing the target geometry of the rigid body to be found #
># from the reported atomic coordinates. However, in order to apply #
># this constraint in a refinement, either the coordinates of the atoms #
># in some arbitrary coordinate system, or a sufficient number of geometric #
># parameters of the body, must be specified. Since all these methods #
># preserve the rigid body intact, it is only the result that needs #
># to be reported, not the details of the method used. #
># In this way the description of restraints and constraints has been #
># kept as simple as possible. #
># #
># The restraints and constraints used are many and varied, and not all #
># can be given in the forms listed in this dictionary. #
># For this reason a general item _restr_special_details has been #
># provided so that a text description can be given for #
># a restraint or constraint that cannot be reported in any other way. #
># #
># Attention is drawn to existing items in the core dictionary that flag #
># whether items have been restrained or constrained. #
># _atom_site_refinement_flags_adp #
># _atom_site_refinement_flags_occupation #
># _atom_site_refinement_flags_posn #
># _atom_site_restraints #
># #
>##############################################################################
>
>
>data_on_this_dictionary
> _dictionary_name cif_core_restraints.dic
> _dictionary_version 0.3
> _dictionary_update 2010-09-15
> _dictionary_history
>;
>2009-18-10 Following consultations between the user community
>and I.David Brown and
>Ilia Guzei IDB started preparing this dictionary using DDL1 by creating items
>required by distance and angle restraints.
>
>2009-12-09 IDB Completed first draft
>
>2010-01-13 IDB Corrected minor errors detected by IG prior to DMG reveiw
>
>2010-01-14 IDB: Run through vcif by Brian McMahon and corrections made.
>esd replaced by su in _type_conditions
>
>2010-06-03 IDB: U-ISO, U-SIMIILAR
>
>2010-10-15 IDB: The revised rigid body description is added.
>;
>
>#
># This dictionary describes 14 restraints some of which are also constraints.
>#
># 1. Other restraint or constraint
># 2. Angle
># 3. Distance
># 4. Minimum approach of two atoms
># 5. Angles restrained to be equal
># 6. Distances restrained to be equal
># 7. Torsion angles restrained to be equal
># 8. Restrained parameter
># 9. Rigid body
># 10. Atoms lie on a plane
># 11. Torsion angle
># 12. Isotropic atom
># 13. Rigid bond
># 14. Similar atomic displacement parameters
>
>#
>#-------------------------------------------------------------------
># RESTRAINT 1. GENERAL RESTRAINT
>#-------------------------------------------------------------------
># A general description of constraints and restraints not covered
># by other CIF items.
>#
>#
>######################
># #
># RESTR #
># #
>######################
>#
>data_restr_[]
> _name '_restr_[]'
> _category categroy_overview
> _type null
> _definition
>; This category is for describing restraints that cannot be
> described elsewhere.
>;
>
>data_restr_special_details
> _name '_restr_special_details'
> _category 'restr'
> _type char
> _definition
>; Text descring any restraint or constraint that cannot be
> described using any of the the other restraint items.
> See also _atom_site_restraints.
>;
>
>#
># ----------------------------------------------------------------------------
># RESTRAINT 2. AN ANGLE IS RESTRAINED TO A PREDETERMINED VALUE.
># ----------------------------------------------------------------------------
>#
>####################
># #
># RESTR_ANGLE #
># #
>####################
>
>data_restr_angle_[]
> _name '_restr_angle_[]'
> _category category_overview
> _type null
> _definition
>; Items in this category define angles that were restrained
>in the final
>refinement.
>;
> _example
>; loop_
>_restr_angle_atom_site_label_1
>_restr_angle_site_symmetry_1
>_restr_angle_atom_site_label_2
>_restr_angle_atom_site_label_3
>_restr_angle_site_symmetry_3
>_restr_angle_target
>_restr_angle_target_weight_param
>_restr_angle_diff
>_restr_angle_details
>C1 1_555 C2 C3 1_555 120 1 -0.3 'generated by JANA'
>C2 1_555 C3 C4 3_455 120 1.5 0.5 ?
>;
>
>data_restr_angle_atom_site_label_
> loop_ _name '_restr_angle_atom_site_label_1'
> '_restr_angle_atom_site_label_2'
> '_restr_angle_atom_site_label_3'
> _category 'restr_angle'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_atom_site_label'
> _definition
>; The _atom_site_labels used to define the angle. Atom 2 is at the apex of the
>angle.
>;
>
>data_restr_angle_details
> _name '_restr_angle_details'
> _category 'restr_angle'
> _type char
> _list yes
> _list_reference '_restr_angle_atom_site_label_'
> _definition
>; A free text description of the restraint.
>;
>data_restr_angle_diff
> _name '_restr_angle_diff'
> _category 'restr_angle'
> _type numb
> _type_conditions su
> _list yes
> _list_reference '_restr_angle_atom_site_label_'
> _units degrees
> _enumeration_range 0:
> _definition
>; The difference between the target and the refined angle
>;
>
>data_restr_angle_site_symmetry_
> loop_ _name '_restr_angle_site_symmetry_1'
> '_restr_angle_site_symmetry_2'
> '_restr_angle_site_symmetry_3'
> _category 'restr_angle'
> _type char
> _list yes
> _list_reference '_restr_angle_atom_site_label_'
> loop_ _example
> _example_detail . 'no symmetry or translation to site'
> 4 '4th symmetry operation applied'
> 7_645 '7th symm. posn.; +a on x; -b on y'
> _enumeration_default 1_555
> _definition
>; The symmetry transformation needed to generate the coordinates
> of the three atoms that define the angle.
>
> The symmetry code of each atom site as the symmetry-equivalent
> position number 'n' and the cell translation number 'klm'.
> These numbers are combined to form the code n_klm.
> The character string n_klm is composed as follows:
>
> n refers to the symmetry operation that is applied to the
> coordinates stored in _atom_site_fract_x, _atom_site_fract_y
> and _atom_site_fract_z. It should match a number given in
> _space_group_symop_id.
>
> k, l and m refer to the translations that are subsequently
> applied to the symmetry-transformed coordinates to generate
> the atom used in calculating the angle. These translations
> (x,y,z) are related to (k,l,m) by the relations
> k = 5 +
> l = 5 + y
> m = 5 + z
> By adding 5 to the translations, the use of negative numbers
> is avoided.
>;
>
>data_restr_angle_target
> _name '_restr_angle_target'
> _category 'restr_angle'
> _type numb
> _list yes
> _list_reference '_restr_angle_atom_site_label_'
> _units degrees
> _enumeration_range 0:180
> _definition
>; The expectation angle defined by the three atoms.
> This is the target angle for the restrained refinement.
>;
>
>data_restr_angle_target_weight_param
> _name '_restr_angle_target_weight_param'
> _category 'restr_angle'
> _type numb
> _list yes
> _list_reference '_restr_angle_atom_site_label_'
> _units degrees
> _enumeration_range 0:180
> _enumeration_default 0
> _definition
>; Weighting parameter = sqrt(1/weight).
> It is the expectation value of the difference between
> the refined value and the target.
> If this parameter is set to zero, the angle will be constrained
> to refine to the target value.
> If this item is absent, its value will be taken as zero
> and the distance will be constrained
>;
>
>#
># ----------------------------------------------------------------------------
># RESTRAINT 3. A DISTANCE IS RESTRAINED TO A PREDETERMINED VALUE.
># ----------------------------------------------------------------------------
>#
>#####################
># #
># RESTR_DISTANCE #
># #
>#####################
>
>data_restr_distance_[]
> _name '_restr_distance_[]'
> _category category_overview
> _type null
> _definition
>; Category of items that describes restraints applied to distances
>during the final refinement.
>;
> _example
># - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>- - - - - -
>;
>loop_
> _restr_distance_atom_site_label_1
> _restr_distance_atom_site_label_2
> _restr_distance_site_symmetry_2
> _restr_distance_target
> _restr_distance_target_weight_param
> _restr_distance_diff
> _restr_distance_details
> C1 C2 1_555 1.524 0.04 -0.032 'generated by SHELX DFIX'
> C2 C3 1_555 1.340 0.04 0.051 'generated by SHELX DFIX'
> Na1 Ca1 1_555 0.0 0.0 0.0 'Na1 is constrained to occupy Ca site'
> Fe1 Ca1 1_555 0.0 0.0 0.0 ?
> Al1 Ca1 1_555 0.0 0.0 0.0 ?
>;
>
>data_restr_distance_atom_site_label_
> loop_ _name '_restr_distance_atom_site_label_1'
> '_restr_distance_atom_site_label_2'
> _category 'restr_distance'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_atom_site_label_'
> _definition
>; The _atom_site_labels of the two atoms defining the distance to be
>restrained
>;
>
>data_restr_distance_details
> _name '_restr_distance_details'
> _category 'restr_distance'
> _type char
> _list yes
> _list_reference '_restr_distance_atom_site_label_'
> _definition
>; A free text description of the restraint.
>;
>
>data_restr_distance_diff
> _name '_restr_distance_diff'
> _category 'restr_distance'
> _type numb
> _list yes
> _list_reference '_restr_distance_atom_site_label_'
> _type_conditions su
> _units A
> _units_detail Angstrom
> _definition
>; The difference between the target and the refined distance
>;
>
>data_restr_distance_site_symmetry_
> loop_ _name '_restr_distance_site_symmetry_1'
> '_restr_distance_site_symmetry_2'
> _category 'restr_distance'
> _type char
> _list yes
> _list_reference '_restr_distance_atom_site_label_'
> loop_ _example
> _example_detail . 'no symmetry or translation to site'
> 4 '4th symmetry operation applied'
> 7_645 '7th symm. posn.; +a on x; -b on y'
> _enumeration_default 1_555
> _definition
>; The symmetry transformation needed to generate the coordinates
> of the two atoms that define the distance.
>
> The symmetry code of each atom site as the symmetry-equivalent
> position number 'n' and the cell translation number 'klm'.
> These numbers are combined to form the code n_klm.
> The character string n_klm is composed as follows:
>
> n refers to a symmetry operation that is applied to the
> coordinates stored in _atom_site_fract_x, _atom_site_fract_y
> and _atom_site_fract_z. It should match a number given in
> _space_group_symop_id (formerly _symmetry_equiv_pos_site_id).
>
> k, l and m refer to the translations that are subsequently
> applied to the symmetry-transformed coordinates to generate
> the atom used in calculating the distance. These translations
> (x,y,z) are related to (k,l,m) by the relations
> k = 5 + x
> l = 5 + y
> m = 5 + z
> By adding 5 to the translations, the use of negative numbers
> is avoided.
>;
>
>data_restr_distance_target
> _name '_restr_distance_target'
> _category 'restr_distance'
> _type numb
> _list yes
> _list_reference '_restr_distance_atom_site_label_'
> _units A
> _units_detail Angstrom
> _definition
>; The expectation distance between the two atoms.
> This is the target distance for the restrained refinement.
>;
>
>data_restr_distance_target_weight_param
> _name '_restr_distance_target_weight_param'
> _category 'restr_distance'
> _type numb
> _list yes
> _list_reference '_restr_distance_atom_site_label_'
> _units A
> _units_detail Angstrom
> _enumeration_default 0
> _definition
>; Weighting parameter = sqrt(1/weight).
> It is the expectation value of the difference between
> the refined value and the target.
> If this parameter is set to zero, the distance will be constrained
> to refine to the target value.
> If this item is absent, its value will be taken as zero
> and the distance will be constrained
>;
>
>#
># ----------------------------------------------------------------------------
># RESTRAINT 4. ATOMS CANNOT OCCUPY THE SAME POSITION
># ----------------------------------------------------------------------------
># The "anti-bumping" restraint prevents two atoms from occupying the
>same site.
># It would normally be reported only for those distances
># in which this restraint was invoked.
>#
>###########################
># #
># RESTR_DISTANCE_MIN #
># #
>###########################
>
>data_restr_distance_min_[]
> _name '_restr_distance_min_[]'
> _category category_overview
> _type null
> _definition
>; Items in this category offer power law and exponential expressions for
> a function designed to prevent two atoms occupying the same location.
>;
> _example
>;
> loop_
> _restr_distance_min_atom_site_label_1
> _restr_distance_min_site_symmetry_1
> _restr_distance_min_atom_site_label_2
> _restr_distance_min_site_symmetry_2
> _restr_distance_min_A
> _restr_distance_min_B
> _restr_distance_min_C
> _restr_distance_min_E
> _restr_distance_min_F
> _restr_distance_min_G
> _restr_distance_min_distance
> _restr_distance_min_details
> O1 1_555 O2 1_555 0 . . 1 2.8 0.3 2.75(1) 'using the exponential restraint'
> O2 1_555 O3 2_455 0 0 0 1 2.8 0 2.83(1) 'using the hard sphere model'
>;
>
>data_restr_distance_min_A
> _name '_restr_distance_min_A'
> _category 'restr_distance_min'
> _type numb
> _list yes
> _list_reference 'restr_distance_min_atomi_site_label_'
> _enumeration)range 0:
> _enumeration_default 0
> _definition
>; The weight associated with the difference between the refined
>distance D and
> the prescribed minimum distance (B or F) is given by the expression:
>
> w = A*(B/D)^C + E*exp((D-F)/G)
>
> A and E are dimensionless weighting parameters.
> Either function could be used alone by setting A or E to zero.
> The default values of A and E are zero.
>
> If A=0, B and C are undefined, if E=0, F and G are undefined
>
> A hard sphere contact can be generated by setting E=1,
> F=prescribed minimum distance and G=0. In this case G (combined
> with a non zero E) should be treated as a flag indicating a hard sphere
> interaction with a target distance of F so as to avoid division by zero.
>;
>
>data_restr_distance_min_atom_site_label_
> loop_ _name '_restr_distance_min_atom_site_label_1'
> '_restr_distance_min_atom_site_label_2'
> _category 'restr_distance_min'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_atom_site_label'
> _definition
>; _atom_site_labels for the two atoms that are to be kept apart.
>;
>
>data_restr_distance_min_B
> _name '_restr_distance_min_B'
> _category 'restr_distance_min'
> _type numb
> _list yes
> _list_reference 'restr_distance_min_atomi_site_label_'
> _units A
> _units_detail Angstrom
> _enumeration_range 0:
> _enumeration_default 0
> _definition
>; The weight associated with the difference between the refined
>distance D and
> the prescribed minimum distance (B or F) is given by the expression:
>
> w = A*(B/D)^C + E*exp((D-F)/G)
>
> A and E are dimensionless weighting parameters.
> Either function could be used alone by setting A or E to zero.
> The default values of A and E are zero.
>
> If A=0, B and C are undefined, if E=0, F and G are undefined
>
> A hard sphere contact can be generated by setting E=1,
> F=prescribed minimum distance and G=0. In this case G (combined
> with a non zero E) should be treated as a flag indicating a hard sphere
> interaction with a target distance of F so as to avoid division by zero.
>;
>
>data_restr_distance_min_C
> _name '_restr_distance_min_C'
> _category 'restr_distance_min'
> _type numb
> _list yes
> _list_reference 'restr_distance_min_atomi_site_label_'
> _definition
>; The weight associated with the difference between the refined
>distance D and
> the prescribed minimum distance (B or F) is given by the expression:
>
> w = A*(B/D)^C + E*exp((D-F)/G)
>
> A and E are dimensionless weighting parameters.
> Either function could be used alone by setting A or E to zero.
> The default values of A and E are zero.
>
> If A=0, B and C are undefined, if E=0, F and G are undefined
>
> A hard sphere contact can be generated by setting E=1,
> F=prescribed minimum distance and G=0. In this case G (combined
> with a non zero E) should be treated as a flag indicating a hard sphere
> interaction with a target distance of F so as to avoid division by zero.
>;
>
>data_restr_distance_min_details
> _name '_restr_distance_min_detail'
> _category 'restr_distance_min'
> _type char
> _list yes
> _list_reference 'restr_distance_min_atomi_site_label_'
> _definition
>; A text description of the restraint giving details not
> given elsewhere.
>;
>
>data_restr_distance_min_difference
> _name '_restr_distance_min_difference'
> _category 'restr_distance_min'
> _type numb
> _list yes
> _list_reference 'restr_distance_min_atomi_site_label_'
> _units A
> _units_detail Angstrom
> _definition
>; The difference in Angstroms between the refined distance of approach
> of the two atoms and the target distance B or F:
>
> difference = D - B or D - F
>;
>
>data_restr_distance_min_distance
> _name '_restr_distance_min_distance'
> _category 'restr_distance_min'
> _type numb
> _list yes
> _list_reference 'restr_distance_min_atomi_site_label_'
> _units A
> _units_detail Angstrom
> _enumeration_range 0:
> _definition
>; The refined distance, D, between the two atoms.
>;
>
>data_restr_distance_min_E
> _name '_restr_distance_min_E'
> _category 'restr_distance_min'
> _type numb
> _list yes
> _list_reference 'restr_distance_min_atomi_site_label_'
> _enumeration_default 0
> _definition
>; The weight associated with the difference between the refined
>distance D and
> the prescribed minimum distance (B or F) is given by the expression:
>
> w = A*(B/D)^C + E*exp((D-F)/G)
>
> A and E are dimensionless weighting parameters.
> Either function could be used alone by setting A or E to zero.
> The default values of A and E are zero.
>
> If A=0, B and C are undefined, if E=0, F and G are undefined
>
> A hard sphere contact can be generated by setting E=1,
> F=prescribed minimum distance and G=0. In this case G (combined
> with a non zero E) should be treated as a flag indicating a hard sphere
> interaction with a target distance of F so as to avoid division by zero.
>;
>
>data_restr_distance_min_F
> _name '_restr_distance_min_F'
> _category 'restr_distance_min'
> _type numb
> _list yes
> _list_reference 'restr_distance_min_atomi_site_label_'
> _units A
> _units_detail Angstrom
> _enumeration_range 0:
> _definition
>; The weight associated with the difference between the refined
>distance D and
> the prescribed minimum distance (B or F) is given by the expression:
>
> w = A*(B/D)^C + E*exp((D-F)/G)
>
> A and E are dimensionless weighting parameters.
> Either function could be used alone by setting A or E to zero.
> The default values of A and E are zero.
>
> If A=0, B and C are undefined, if E=0, F and G are undefined
>
> A hard sphere contact can be generated by setting E=1,
> F=prescribed minimum distance and G=0. In this case G (combined
> with a non zero E) should be treated as a flag indicating a hard sphere
> interaction with a target distance of F so as to avoid division by zero.
>;
>
>data_restr_distance_min_G
> _name '_restr_distance_min_G'
> _category 'restr_distance_min'
> _type numb
> _list yes
> _list_reference 'restr_distance_min_atomi_site_label_'
> _units A
> _units_detail Angstrom
> _definition
>; The weight associated with the difference between the refined
>distance D and
> the prescribed minimum distance (B or F) is given by the expression:
>
> w = A*(B/D)^C + E*exp((D-F)/G)
>
> A and E are dimensionless weighting parameters.
> Either function could be used alone by setting A or E to zero.
> The default values of A and E are zero.
>
> If A=0, B and C are undefined, if E=0, F and G are undefined
>
> A hard sphere contact can be generated by setting E=1,
> F=prescribed minimum distance and G=0. In this case G (combined
> with a non zero E) should be treated as a flag indicating a hard sphere
> interaction with a target distance of F so as to avoid division by zero.
>;
>
>data_restr_distance_min_site_symmetry_
> loop_ _name '_restr_distance_min_site_symmetry_1'
> '_restr_distance_min_site_symmetry_2'
> _category 'restr_distance_min'
> _type char
> _list yes
> _list_reference 'restr_distance_min_atomi_site_label_'
> _definition
>; The site symmetries of the two atoms to be kept apart.
>
> The symmetry code of each atom site as the symmetry-equivalent
> position number 'n' and the cell translation number 'klm'.
> These numbers are combined to form the code n_klm.
> The character string n_klm is composed as follows:
>
> n refers to the symmetry operation that is applied to the
> coordinates stored in _atom_site_fract_x, _atom_site_fract_y
> and _atom_site_fract_z. It should match a number given in
> _space_group_symop_id.
>
> k, l and m refer to the translations that are subsequently
> applied to the symmetry-transformed coordinates to generate
> the atom that are to be kept apart. These translations
> (x,y,z) are related to (k,l,m) by the relations
> k = 5 + x
> l = 5 + y
> m = 5 + z
> By adding 5 to the translations, the use of negative numbers
> is avoided.
>;
>
>
>#
># ----------------------------------------------------------------------------
># RESTRAINT 5. SEVERAL ANGLES ARE RESTRAINED TO BE EQUAL.
># ----------------------------------------------------------------------------
># This restraint contains two categories.
># The first defines the angles to be restrained and assigns
># them to different classes that are restrained independently.
># The second category defines the properties of each class.
>#
>#
>##########################
># #
># RESTR_EQUAL_ANGLE #
># #
>##########################
>
>data_restr_equal_angle_[]
> _name '_restr_equal_angle_[]'
> _category category_overview
> _type null
> _definition
>; Items in this category list the atoms defining the angles
> that are restrained to be equal in the final refinement.
>;
> _example
>;
>loop_
>_restr_equal_angle_atom_site_label_1
>_restr_equal_angle_site_symmetry_1
>_restr_equal_angle_atom_site_label_2 # Atom 2 is at the apex of the angle
>_restr_equal_angle_site_symmetry_2
>_restr_equal_angle_atom_site_label_3
>_restr_equal_angle_site_symmetry_3
>_restr_equal_angle_class_id
>_restr_equal_angle_details
>C1 1_555 C2 1_555 C3 1_555 1 'Benzene ring with mirror symmetry'
>C2 1_555 C3 1_555 C4 2_655 2 ?
>C4 1_555 C5 1_555 C6 1_555 2 ?
>C5 1_555 C6 1_555 C1 1_555 1 ?
>;
>
>
>data_restr_equal_angle_atom_site_label_
> loop_ _name '_restr_equal_angle_atom_site_label_1'
> '_restr_equal_angle_atom_site_label_2'
> '_restr_equal_angle_atom_site_label_3'
> _category 'restr_equal_angle'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_atom_site_label'
> _definition
>; The _atom_site_labels of the three atoms that define one of the
> angles to be restrained to be equal to other angles in
> the same class.
>;
>
>data_restr_equal_angle_class_id
> _name '_restr_equal_angle_class_id'
> _category 'restr_equal_angle'
> _type char
> _list yes
> _list_reference '_restr_equal_angle_atom_site_label_'
> _enumeration_default 1
> _definition
>; A character string identifying the class of equal angles
> to which this angle belongs.
>;
>
>data_restr_equal_angle_details
> _name '_restr_equal_angle_details'
> _category 'restr_equal_angle'
> _type char
> _list yes
> _list_reference '_restr_equal_angle_atom_site_label_'
> _definition
>; A text description giving details of an angle in
> a class of angles that are restrained to be equal.
>;
>
>data_restr_equal_angle_site_symmetry_label_
> loop_ _name '_restr_equal_angle_site_symmetry_label_1'
> '_restr_equal_angle_site_symmetry_label_2'
> '_restr_equal_angle_site_symmetry_label_3'
> _category 'restr_equal_angle'
> _type char
> _list yes
> _list_reference '_restr_equal_angle_atom_site_label_'
> _definition
>; The site symmetries of the three atoms that define an angle
> to be restrained to be equal to other angles in the same class.
>
> The symmetry code of each atom site as the symmetry-equivalent
> position number 'n' and the cell translation number 'klm'.
> These numbers are combined to form the code n_klm.
> The character string n_klm is composed as follows:
>
> n refers to the symmetry operation that is applied to the
> coordinates stored in _atom_site_fract_x, _atom_site_fract_y
> and _atom_site_fract_z. It should match a number given in
> _space_group_symop_id.
>
> k, l and m refer to the translations that are subsequently
> applied to the symmetry-transformed coordinates to generate
> the atom used in calculating the angle. These translations
> (x,y,z) are related to (k,l,m) by the relations
> k = 5 + x
> l = 5 + y
> m = 5 + z
> By adding 5 to the translations, the use of negative numbers
> is avoided.
>;
> loop_ _example
> _example_detail . 'no symmetry or translation to site'
> 4 '4th symmetry operation applied'
> 7_645 '7th symm. posn.; +a on x; -b on y'
> _enumeration_default 1_555
>
>
>
>###################################
># #
># RESTR_EQUAL_ANGLE_CLASS #
># #
>###################################
>#
>#
>data_restr_equal_angle_class_[]
> _name '_restr_equal_angle_class_[]'
> _category category_overview
> _type null
> _definition
>; Items in this category give details of the target angles
> for each class of angles that are restrained to be equal
> in the final refinement.
>;
> _example
>;
>loop_
>_restr_equal_angle_class_class_id
>_restr_equal_angle_class_target_weight_param
>_restr_equal_angle_class_average
>_restr_equal_angle_class_esd
>_restr_equal_angle_class_diff_max
>_restr_equal_angle_class_details
>1 0.50 123.52 0.32 0.62 ?
>2 0.50 118.23 0.52 1.43 ?
>;
>
>data_restr_equal_angle_class_average
> _name '_restr_equal_angle_class_average'
> _category 'restr_equal_angle_class'
> _type numb
> _list yes
> _units degrees
> _enumeration_range 0:
> _definition
>; The average angle in the class of angles restrained to
> be the same after refinement.
>;
>
>data_restr_equal_angle_class_class_id
> _name '_restr_equal_angle_class_class_id'
> _category 'restr_equal_angle_class'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_restr_equal_angle_class_id'
> _enumeration_default 1
> _definition
>; A character string that identifies the class of angles
> whose properties are described.
>;
>
> data_restr_equal_angle_class_details
> _name '_restr_equal_angle_class_details'
> _category 'restr_equal_angle_class'
> _type char
> _list yes
> _definition
>; A text description giving details of the class of angles that
> are restrained to be equal.
>;
>
> data_restr_equal_angle_class_diff_max
> _name '_restr_equal_angle_class_diff_max'
> _category 'restr_equal_angle_class'
> _type numb
> _type_conditions su
> _list yes
> _units degrees
> _enumeration_range 0:
> _definition
>; The maximum deviation of an angle in the class from the
> class average after refinement.
>;
>
>data_restr_equal_angle_class_esd
> _name '_restr_equal_angle_class_esd'
> _category 'restr_equal_angle_class'
> _type numb
> _list yes
> _units degrees
> _enumeration_range 0:
> _definition
>; The actual estimated standard deviation of the angles in the
> class from their average after refinement.
> This number is expected to be similar to the value set for
> _restr_equal_angle_class_target_weight_param
>;
>
>data_restr_equal_angle_class_target_weight_param
> _name '_restr_equal_angle_class_target_weight_param'
> _category 'restr_equal_angle_class'
> _type numb
> _list yes
> _units degrees
> _enumeration_range 0:
> _enumeration_default 0
> _definition
>; The weighting parameter = sqrt(1/weight).
> The expectation value of the estimated standard deviation of the
> angles in the class from their average after refinement.
> This value determines the weight assigned to the restraint.
> If it is zero the angles are constrained to be equal.
> The default value is zero.
>;
>
>#
># ----------------------------------------------------------------------------
># RESTRAINT 6. SEVERAL DISTANCES ARE RESTRAINED TO BE EQUAL.
># ----------------------------------------------------------------------------
># This restraint contains two categories.
># The first defines the distances to be restrained and assigns
># them to different classes that are restrained independently.
># The second category defines the properties of each class.
>#
>#############################
># #
># RESTR_EQUAL_DISTANCE #
># #
>#############################
>
>data_restr_equal_distance_[]
> _name '_restr_equal_distance_[]'
> _category category_overview
> _type null
> _definition
>; Items in this category list the atoms defining the distances
> that are restrained to be equal in the final refinement.
>;
> _example
>;
>loop_
> _restr_equal_distance_atom_site_label_1
> _restr_equal_distance_site_symmetry_1
> _restr_equal_distance_atom_site_label_2
> _restr_equal_distance_site_symmetry_2
> _restr_equal_distance_class_id
> _restr_equal_distance_details
> C1 1_555 C2 1_555 1 'C1-C2 and C3-C4 are restrained to be equal'
> C2 1_555 C3 1_555 2 'C2-C3, C4-C5 and C5-C6 are restrained to be equal'
> C3 1_555 C4 2_655 1 ?
> C4 1_555 C5 1_555 2 ?
> C5 1_555 C6 1_555 2 ?
>;
>
>
>data_restr_equal_distance_atom_site_label_
> loop_ _name '_restr_equal_distance_atom_site_label_1'
> '_restr_equal_distance_atom_site_label_2'
> _category 'restr_equal_distance'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_atom_site_label'
> _definition
>; The _atom_site_labels of the two atoms that define one of the
> distances to be restrained to be equal to other distances in
> the same class.
>;
>
>data_restr_equal_distance_class_id
> _name '_restr_equal_distance_class_id'
> _category 'restr_equal_distance'
> _type char
> _list yes
> _list_reference '_restr_equal_distance_atom_site_label_'
> _enumeration_default 1
> _definition
>; A character string identifying the class of equal distances
> to which this distance belongs.
>;
>
>data_restr_equal_distance_details
> _name '_restr_equal_distance_details'
> _category 'restr_equal_distance'
> _type char
> _list yes
> _list_reference '_restr_equal_distance_atom_site_label_'
> _definition
>; A text description giving details of a distance in
> a class of distances that are restrained to be equal.
>;
>
>data_restr_equal_distance_site_symmetry_label_
> loop_ _name '_restr_equal_distance_site_symmetry_label_1'
> '_restr_equal_distance_site_symmetry_label_2'
> _category 'restr_equal_distance'
> _type char
> _list yes
> _list_reference '_restr_equal_distance_atom_site_label_'
> _definition
>; The site symmetries of the two atoms that define a distance
> to be restrained to be equal to other distances in the same class.
>
> The symmetry code of each atom site as the symmetry-equivalent
> position number 'n' and the cell translation number 'klm'.
> These numbers are combined to form the code n_klm.
> The character string n_klm is composed as follows:
>
> n refers to the symmetry operation that is applied to the
> coordinates stored in _atom_site_fract_x, _atom_site_fract_y
> and _atom_site_fract_z. It must should a number given in
> _space_group_symop_id.
>
> k, l and m refer to the translations that are subsequently
> applied to the symmetry-transformed coordinates to generate
> the atom used in calculating the distance. These translations
> (x,y,z) are related to (k,l,m) by the relations
> k = 5 + x
> l = 5 + y
> m = 5 + z
> By adding 5 to the translations, the use of negative numbers
> is avoided.
>;
> loop_ _example
> _example_detail . 'no symmetry or translation to site'
> 4 '4th symmetry operation applied'
> 7_645 '7th symm. posn.; +a on x; -b on y'
> _enumeration_default 1_555
>
>
>
>###################################
># #
># RESTR_EQUAL_DISTANCE_CLASS #
># #
>###################################
>#
>#
>data_restr_equal_distance_class_[]
> _name '_restr_equal_distance_class_[]'
> _category category_overview
> _type null
> _definition
>; Items in this category give details of the target distances
> for each class of distances that are restrained to be equal
> in the final refinement.
>;
> _example
>;
> loop_
> _restr_equal_distance_class_class_id
> _restr_equal_distance_class_target_weight_param
> _restr_equal_distance_class_average
> _restr_equal_distance_class_esd
> _restr_equal_distance_class_diff_max
> _restr_equal_distance_class_details
> 1 0.04 1.534 0.032 0.053 ?
> 2 0.04 1.338 0.052 0.103 ?
>;
>
> data_restr_equal_distance_class_average
> _name '_restr_equal_distance_class_average'
> _category 'restr_equal_distance_class'
> _type numb
> _list yes
> _units A
> _units_detail Angstrom
> _enumeration_range 0:
> _definition
>; The average distance in the class of distances restrained to
> be the same after refinement.
>;
> data_restr_equal_distance_class_class_id
> _name '_restr_equal_distance_class_class_id'
> _category 'restr_equal_distance_class'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_restr_equal_distance_class_id'
> _enumeration_default 1
> _definition
>; A character string that identifies the class of distances
> whose properties are described.
>;
>
> data_restr_equal_distance_class_details
> _name '_restr_equal_distance_class_details'
> _category 'restr_equal_distance_class'
> _type char
> _list yes
> _definition
>; A text description giving details of the class of distances that
> are restrained to be equal.
>;
>
> data_restr_equal_distance_class_diff_max
> _name '_restr_equal_distance_class_diff_max'
> _category 'restr_equal_distance_class'
> _type numb
> _type_conditions su
> _list yes
> _units A
> _units_detail Angstrom
> _enumeration_range 0:
> _definition
>; The maximum deviation of a distance in the class from the
> class average after refinement.
>;
>
> data_restr_equal_distance_class_esd
> _name '_restr_equal_distance_class_esd'
> _category 'restr_equal_distance_class'
> _type numb
> _list yes
> _units Angstrom
> _enumeration_range 0:
> _definition
>; The actual estimated standard deviation of the distances in the
> class from their average after refinement.
> This number is expected to be similar to the value set for
> _restr_equal_distance_class_target_weight_param
>;
> data_restr_equal_distance_class_target_weight_param
> _name '_restr_equal_distance_class_target_weight_param'
> _category 'restr_equal_distance_class'
> _type numb
> _list yes
> _units A
> _units_detail Angstrom
> _enumeration_range 0:
> _enumeration_default 0
> _definition
>; The weighting parameter = sqrt(1/weight).
> The expectation value of the estimated standard deviation of the
> distances in the class from their average after refinement.
> This value determines the weight assigned to the restraint.
> If it is zero the distances are constrained to be equal.
> The default value is zero.
>;
>
>#
># ----------------------------------------------------------------------------
># RESTRAINT 7. SEVERAL TORSION ANGLES ARE RESTRAINED TO BE EQUAL.
># ----------------------------------------------------------------------------
># This restraint contains two categories.
># The first defines the torsion angles to be restrained and assigns
># them to different classes that are restrained independently.
># The second category defines the properties of each class.
>#
>############################
># #
># RESTR_EQUAL_TORSION #
># #
>############################
>#
>
>data_restr_equal_torsion_[]
> _name '_restr_equal_torsion_[]'
> _category category_overview
> _type null
> _definition
>; Items in this category list the atoms defining the torsion angles
> that are restrained to be equal in the final refinement.
>;
> _example
>;
>loop_
>_restr_equal_torsion_atom_site_label_1
>_restr_equal_torsion_site_symmetry_1
>_restr_equal_torsion_atom_site_label_2
>_restr_equal_torsion_site_symmetry_2
>_restr_equal_torsion_atom_site_label_3
>_restr_equal_torsion_site_symmetry_3
>_restr_equal_torsion_atom_site_label_4
>_restr_equal_torsion_site_symmetry_4
>_restr_equal_torsion_class_id
>_restr_equal_torsion_details
>C1 1_555 C2 1_555 C3 1_555 C4 1_555 1 ?
>C5 1_555 C6 1_555 C1 1_555 C2 1_555 1 ?
>;
>
>
>data_restr_equal_torsion_atom_site_label_
> loop_ _name '_restr_equal_torsion_atom_site_label_1'
> '_restr_equal_torsion_atom_site_label_2'
> '_restr_equal_torsion_atom_site_label_3'
> '_restr_equal_torsion_atom_site_label_4'
> _category 'restr_equal_torsion'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_atom_site_label'
> _definition
>; The _atom_site_labels of the four atoms that define one of the
> torsion angles to be restrained to be equal to other torsion
> angles in the same class. The torsion angle is the dihedral angle
> between the plane defined by atoms 1, 2 and 3, and the plane defined
> atoms 2, 3 and 4.
>;
>
>data_restr_equal_torsion_class_id
> _name '_restr_equal_torsion_class_id'
> _category 'restr_equal_torsion'
> _type char
> _list yes
> _list_reference '_restr_equal_torsion_atom_site_label_'
> _enumeration_default 1
> _definition
>; A character string identifying the class of equal torsion
> angles to which this torsion angle belongs.
>;
>
>data_restr_equal_torsion_details
> _name '_restr_equal_torsion_details'
> _category 'restr_equal_torsion'
> _type char
> _list yes
> _list_reference '_restr_equal_torsion_atom_site_label_'
> _definition
>; A text description giving details of a torsion angle in
> a class of torsion angles that are restrained to be equal.
>;
>
>data_restr_equal_torsion_site_symmetry_label_
> loop_ _name '_restr_equal_torsion_site_symmetry_label_1'
> '_restr_equal_torsion_site_symmetry_label_2'
> '_restr_equal_torsion_site_symmetry_label_3'
> '_restr_equal_torsion_site_symmetry_label_4'
> _category 'restr_equal_torsion'
> _type char
> _list yes
> _list_reference '_restr_equal_torsion_atom_site_label_'
> _enumeration_default 1_555
> _definition
>; The site symmetries of the four atoms that define a torsion angle
> to be restrained to be equal to other torsion angles in the
> same class.
>
> The symmetry code of each atom site as the symmetry-equivalent
> position number 'n' and the cell translation number 'klm'.
> These numbers are combined to form the code n_klm.
> The character string n_klm is composed as follows:
>
> n refers to the symmetry operation that is applied to the
> coordinates stored in _atom_site_fract_x, _atom_site_fract_y
> and _atom_site_fract_z. It should match a number given in
> _space_group_symop_id.
>
> k, l and m refer to the translations that are subsequently
> applied to the symmetry-transformed coordinates to generate
> the atom used in calculating the torsion angle.
> These translations (x,y,z) are related to (k,l,m)
> by the relations
> k = 5 + x
> l = 5 + y
> m = 5 + z
> By adding 5 to the translations, the use of negative numbers
> is avoided.
>;
> loop_ _example
> _example_detail . 'no symmetry or translation to site'
> 4 '4th symmetry operation applied'
> 7_645 '7th symm. posn.; +a on x; -b on y'
>
>
>
>###################################
># #
># RESTR_EQUAL_TORSION_CLASS #
># #
>###################################
>#
>#
>data_restr_equal_torsion_class_[]
> _name '_restr_equal_torsion_class_[]'
> _category category_overview
> _type null
> _definition
>; Items in this category give details of the target torsion
> nagles for each class of torsion angles that are restrained
> to be equal in the final refinement.
>;
> _example
>;
> loop_
> _restr_equal_torsion_class_class_id
> _restr_equal_torsion_class_target_weight_param
> _restr_equal_torsion_class_average
> _restr_equal_torsion_class_esd
> _restr_equal_torsion_class_diff_max
> _restr_equal_torsion_class_details
>
> 1 0.50 123.52 0.32 0.62 ?
>;
>
>data_restr_equal_torsion_class_average
> _name '_restr_equal_torsion_class_average'
> _category 'restr_equal_torsion_class'
> _type numb
> _list yes
> _units degrees
> _enumeration_range 0:
> _definition
>; The average torsion angle in the class of torsion angles
> restrained to be the same after refinement.
>;
>
>data_restr_equal_torsion_class_class_id
> _name '_restr_equal_torsion_class_class_id'
> _category 'restr_equal_torsion_class'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_restr_equal_torsion_class_id'
> _enumeration_default 1
> _definition
>; A character string that identifies the class of torsion
> angles whose properties are described.
>;
>
>data_restr_equal_torsion_class_details
> _name '_restr_equal_torsion_class_details'
> _category 'restr_equal_torsion_class'
> _type char
> _list yes
> _definition
>; A text description giving details of the class of torsion
> angles that are restrained to be equal.
>;
>
>data_restr_equal_torsion_class_diff_max
> _name '_restr_equal_torsion_class_diff_max'
> _category 'restr_equal_torsion_class'
> _type numb
> _type_conditions su
> _list yes
> _units degrees
> _enumeration_range 0:
> _definition
>; The maximum deviation of a torsion angle in the class from the
> class average after refinement.
>;
>
>data_restr_equal_torsion_class_esd
> _name '_restr_equal_torsion_class_esd'
> _category 'restr_equal_torsion_class'
> _type numb
> _list yes
> _units degrees
> _enumeration_range 0:
> _definition
>; The actual estimated standard deviation of the torsion
> angles in the class from their average after refinement.
> This number is expected to be similar to the value set for
> _restr_equal_torsion_class_target_weight_param
>;
>
>data_restr_equal_torsion_class_target_weight_param
> _name '_restr_equal_torsion_class_target_weight_param'
> _category 'restr_equal_torsion_class'
> _type numb
> _list yes
> _units degrees
> _enumeration_range 0:
> _enumeration_default 0
> _definition
>; The weighting parameter = sqrt(1/weight).
> This is the expectation value of the estimated
> standard deviation (given in _restr_equal_torsion_class_esd)
> of the torsion angles in the class from their
> average after refinement.
> This value determines the weight assigned to the target.
> If it is zero the torsion angles are constrained to be equal.
> The default value is zero.
>;
>
>
>
>#
># ----------------------------------------------------------------------------
># RESTRAINT 8. THE SUM OF A GIVEN PARAMETER OF THE SPECIFIED ATOMS IS
># RESTRAINED
># ----------------------------------------------------------------------------
># This restraint, which will normally be used to restrain the total
># occupancy of an atom site, can be used to restrain the value of
># SUM(over the specified atoms){PARAMETER*COEFFICIENT}
># where PARAMETER will usually be the occupancy
># (but other allowed quantities such as x, y and z will be specified
># in the enumeration list) and COEFFICIENT is a user defined
># number with a default value of 1.0.
># Two loops are needed to describe this restraint.
>#
>########################
># #
># RESTR_PARAMETER #
># #
>########################
>#
>
>data_restr_parameter_[]
> _name '_restr_parameter_[]'
> _category category_overview
> _type null
> _definition
>; This restraint, which will normally be used to restrain the total
> occupancy of an atom site, can be used to restrain the value of
> SUM(over the specified atoms){PARAMETER*COEFFICIENT}
> where PARAMETER will usually be the value of the occupancy
> (but other allowed quantities such as x, y and z can be specified
> in the enumeration) and COEFFICIENT is a user defined
> number with a default value of 1.0.
> The restraint requires two loops, the first defines the atoms in
> each sum (class) and the second describes the properties of the class.
>;
> loop_ _example
> _example_detail
>#---------------------------------------------------------
>; loop_
> _restr_parameter_id
> _restr_parameter_class_id
> _restr_parameter_atom_site_label
> _restr_parameter_atom_coefficient
>1 1 O1 1
>2 1 O1a 1
>3 1 O1b 1
>;
>; These examples should be read in conjunction with the examples
> given for the loop restr_parameter_class.
>
> In Class 1 the sites O1, O1a and O1b refer to separate sites
> over which oxygen is disordered, but which in total contain
> 0.8 oxygen atoms (as defined by _restr_parameter_class_target).
>;
>#-----------------------------------------------------------
>; loop_
> _restr_parameter_id
> _restr_parameter_class_id
> _restr_parameter_atom_site_label
> _restr_parameter_atom_coefficient
>a 2 Na1 1
>b 2 K1 1
>c 2 Ca1 1
>d 2 Al1 1
>;
>;
> Class 2 consists of a mixture of Na, K, Ca and Al atoms on the same
> site with the total occupancy set to 1.0 as defined in
> _restr_parameter_class_target.
>;
>#------------------------------------------------------------
>; loop_
> _restr_parameter_id
> _restr_parameter_class_id
> _restr_parameter_atom_site_label
> _restr_parameter_atom_coefficient
>1 3 Na1 1
>2 3 K1 1
>3 3 Ca1 2
>4 3 Al1 3
>;
>;
> Class 3 consists of the same atoms as Class 2, but by using coefficients
> equal to the ionic charge, the total charge on the site is
> restrained to 2.0.
> Note that the parameter restrained is still the occupancy
> but the use of coefficients transforms the restraint from
> occupancy to formal charge.
>;
>#---------------------------------------------------------------
>; loop_
> _restr_parameter_id
> _restr_parameter_class_id
> _restr_parameter_atom_site_label
> _restr_parameter_atom_coefficient
>1 4 O2 1
>;
>; In Class 4 the y coordinate of O2 is restrained to be close to a
> pseudo-mirror plane at y = 0.5 (see _restr_parameter_class_target).
> This example may not have much practical use, but is included
> to show what can be done with this definition.
>;
>#----------------------------------------------------------------
>; loop_
> _restr_parameter_id
> _restr_parameter_class_id
> _restr_parameter_atom_site_label
> _restr_parameter_atom_coefficient
>1 5 O3 1
>2 5 O4 1
>;
>;
> In Class 5 the positions of O3 and O4 are correlated in such a way that
> these atoms are displaced equal distances from the plane x = 0
> (i.e., x(O3)+x(O4) = 0)
>;
># ---------------------------- end of examples -------------------
>
>data_restr_parameter_atom_coefficient
> _name '_restr_parameter_atom_coefficient'
> _category 'restr_parameter'
> _type numb
> _list yes
> _list_reference '_restr_parameter_id'
> _enumeration_default 1
> _definition
>; A parameter that scales the qantity being restrained.
> It can be used to convert a constraint on occupance to
> a constraint on ionic charge.
>;
>
>data_restr_parameter_atom_site_label
> _name '_restr_parameter_atom_site_label'
> _category 'restr_parameter'
> _type char
> _list yes
> _list_reference '_restr_parameter_id'
> _list_link_parent '_atom_site_label'
> _definition
>; The _atom_site_label for an atom in this class.
>;
>
>data_restr_parameter_class_id
> _name '_restr_parameter_class_id'
> _category 'restr_parameter'
> _type char
> _list yes
> _list_reference '_restr_parameter_id'
> _enumeration_default '1'
> _definition
>; The identifier of the class of restraint applied to the atoms
>;
>
>data_restr_parameter_id
> _name '_restr_parameter_id'
> _category 'restr_parameter'
> _type char
> _list yes
> _list_mandatory yes
> _definition
>; A unique identifier for each line in a loop
>;
>
>#
>###################################
># #
># RESTR_PARAMETER_CLASS #
># #
>###################################
>#
>
>data_restr_parameter_class_[]
> _name '_restr_parameter_class_[]'
> _category category_overview
> _type null
> _list_reference '_restr_parameter_class_class_id'
> _definition
>; This restraint, which will normally be used to restrain the total
> occupancy of an atom site, can be used to restrain the value of
> SUM(over the specified atoms){PARAMETER*COEFFICIENT}
> where PARAMETER will usually be the value of the occupancy
> (but other allowed quantities such as x, y and z can be specified
> in the enumeration) and COEFFICIENT is a user defined
> number with a default value of 1.0.
> The restraint requires two loops, the first defines the atoms in
> each sum (class) and the second describes the properties of the class.
>;
> _example
># ------------------------------------------------------
>;
> loop_
> _restr_parameter_class_class_id
> _restr_parameter_class_parameter_type
> _restr_parameter_class_target
> _restr_parameter_class_target_weight_param
> _restr_parameter_class_details
> 1 occupancy 0.8 0.01 'total occupation is 0.8'
> 2 occupancy 1.0 0.001 'total occupation is 1.0'
> 3 occupancy 2.0 0.01 'total charge is 2.0'
> 4 position_y 0.5 0.002 'keep close to pseudo-mirror plane'
> 5 position_x 0 0.01 'correlate position of O3 and O4'
>;
>
> _example_detail
>
>; This example gives the properties of the five classes given as examples in
> restr_parameter.
>
> The _*_class_id is the _list_reference and is the same as _*_class_id
> in the restr_parameter loop
>
> The _*_parameter_type indicates the atomic parameter that is restrained.
>
> _*_target is the target value for the sum of the product of
> _restr_parameter_atom_coeffcient and the value of the _*_parameter_type
> for the atom.
>
> _*_target_weight_sum gives the expectation value of the difference
> between the target and the refined value of sum(coefficient*parameter)
>
> _*_details gives a description of the restraint applied
>;
># --------------------------------------------------------------
>
>data_restr_parameter_class_class_id
> _name '_restr_parameter_class_class_id'
> _category 'restr_parameter_class'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_restr_parameter_class_id'
> _enumeration_default '1'
> _definition
>; The class id of the restraint described in this category
>;
>
>data_restr_parameter_class_details
> _name '_restr_parameter_class_details'
> _category 'restr_parameter_class'
> _type char
> _list yes
> _list_reference '_restr_parameter_class_class_id'
> _definition
>; A text description of the restraint.
>;
>
>data_restr_parameter_class_parameter_type
> _name '_restr_parameter_class_parameter_type'
> _category 'restr_parameter_class'
> _type char
> _list yes
> _list_reference '_restr_parameter_class_class_id'
> loop_
> _enumeration _enumeration_detail
> #------------ -------------------
> 'occupancy' '_atom_site_occupancy'
> 'position_x' '_atom_site_fract_x'
> 'position_y' '_atom_site_fract_y'
> 'position_z' '_atom_site_fract_z'
> _definition
>; A flag that indicates the nature of the value
> that is being restrained.
>;
>
>data_restr_parameter_class_target
> _name '_restr_parameter_class_target'
> _category 'restr_parameter_class'
> _type numb
> _list yes
> _list_reference '_restr_parameter_class_class_id'
> _definition
>; The target value for the sum of values of the appropriate
> parameter type multiplied by the _*_target_weight_param.
>;
>
>data_restr_parameter_class_target_weight_param
> _name '_restr_parameter_class_target_weight_param'
> _category 'restr_parameter_class'
> _type numb
> _list yes
> _list_reference '_restr_parameter_class_class_id'
> _enumeration_default 0
> _definition
>; Weighting parameter = sqrt(1/weight).
> It is the expectation value of the difference between
> the refined value of the sum(parameter*coefficient)
> and the _*_target.
> If this parameter is set to zero, the sum will be constrained
> to refine to the target value.
> If this item is absent, its value will be taken and zero
> and the distance will be constrained
>;
>
>#
># ----------------------------------------------------------------------------
># RESTRAINT 9. A GROUP OF ATOMS IS RESTRAINED TO LIE ON A PLANE.
># ----------------------------------------------------------------------------
># This restraint contains two categories.
># The first lists the atoms that define each plane, each plane being
># composed of atoms from the same class.
># The second category describes the properties of each plane (class).
>#
>######################
># #
># RESTR_PLANE #
># #
>######################
>#
>
>data_restr_plane_[]
> _name '_restr_plane_[]'
> _category category_Overview
> _type null
> _definition
>; Items in this category define the atoms that make up each class of plane.
>;
> _example
>;
> loop_
> _restr_plane_id
> _restr_plane_atom_site_label
> _restr_plane_site_symmetry
> _restr_plane_class_id
> _restr_plane_target_weight_param
> _restr_plane_displacement
> _restr_plane_details
>1 c1 1_555 1 0.02 0.002(1) 'c1 to c4 lie on one plane'
>2 c2 1_555 1 0.02 -0.003(2) ?
>3 c3 1_555 1 0.02 -0.002(1) ?
>4 c4 1_555 1 0.02 0.002(2) ?
>5 c1 2_655 2 0.003 0.004(1) 'c1, c5, c6 and c7 lie on one plane'
>6 c5 1_555 2 0.003 -0.002(2) ?
>7 c6 1_555 2 0.003 0.002(3) ?
>8 c7 1_555 2 0.003 -0.002(2) ?
>;
>
>data_restr_plane_atom_site_label
> _name '_restr_plane_atom_site_label'
> _category 'restr_plane'
> _type char
> _list yes
> _list_reference ?
> _list_mandatory yes
> _list_link_parent '_atom_site_label'
> _definition
>; An _atom_site_label of one of the atoms that form the plane
>;
>
>data_restr_plane_class_id
> _name '_restr_plane_class_id'
> _category 'restr_plane'
> _type char
> _list yes
> _list_reference ?
> _list_mandatory yes
> _enumeration_default 1
> _definition
>; A character string that identifies the plane
> to which this atom is constrained.
>;
>
>data_restr_plane_details
> _name '_restr_plane_details'
> _category 'restr_plane'
> _type char
> _list yes
> _list_reference ?
> _definition
>; A text string giving details not described elsewhere.
>;
>
>data_restr_plane_displacement
> _name '_restr_plane_displacement'
> _category 'restr_plane'
> _type numb
> _type_conditions su
> _list yes
> _list_reference ?
> _units A
> _units_details Angstrom
> _enumeration_range 0:
> _definition
>; The distance between this atom and the best plane through
> all the atoms.
>;
>
>data_restr_plane_id
> _name '_restr_plane_id'
> _category 'restr_plane'
> _type char
> _list yes
> _list_mandatory yes
> _enumeration_default '1'
> _definition
>; A unique identifier for each line in the list.
>;
>
>data_restr_plane_site_symmetry
> _name '_restr_plane_site_symmetry'
> _category 'restr_plane'
> _type char
> _list yes
> _list_reference ?
> _list_mandatory yes
> _enumeration_default '1_555'
> _definition
>; The site symmetries of the atom that helps to define the plane
> to which it to be restrained.
>
> The symmetry code of each atom site as the symmetry-equivalent
> position number 'n' and the cell translation number 'klm'.
> These numbers are combined to form the code n_klm.
> The character string n_klm is composed as follows:
>
> n refers to the symmetry operation that is applied to the
> coordinates stored in _atom_site_fract_x, _atom_site_fract_y
> and _atom_site_fract_z. It should match a number given in
> _space_group_symop_id.
>
> k, l and m refer to the translations that are subsequently
> applied to the symmetry-transformed coordinates to generate
> the atom used in calculating the plane. These translations
> (x,y,z) are related to (k,l,m) by the relations
> k = 5 + x
> l = 5 + y
> m = 5 + z
> By adding 5 to the translations, the use of negative numbers
> is avoided.
>;
> loop_ _example
> _example_detail . 'no symmetry or translation to site'
> 4 '4th symmetry operation applied'
> 7_645 '7th symm. posn.; +a on x; -b on y'
>
>data_restr_plane_target_weight_param
> _name '_restr_plane_target_weight_param'
> _category 'restr_plane'
> _type numb
> _list yes
> _units A
> _units_detail Angstrom
> _enumeration_range 0:
> _enumeration_default 0.
> _definition
>; The weighting parameter = sqrt(1/weight).
> The expectation value of the distance in Angstroms between this atom
> and the best plane through all the atoms of the class.
>;
>
>#
>############################
># #
># RESTR_PLANE_CLASS #
># #
>############################
>#
>
>data_restr_plane_class_[]
> _name '_restr_plane_class_[]'
> _category category_overview
> _type null
> _definition
>; Items in thiscategory describe the properties of
> the different groups of atoms that are restrained
> to form a plain.
>;
> _example
>;
> loop_
> _restr_plane_class_class_id
> _restr_plane_class_displacement_esd
> _restr_plane_class_displacement_max_atom_site_label
> _restr_plane_class_displacement_max_site_symmetry
> _restr_plane_class_displacement_max
> _resrt_plane_class_details
>
> 1 0.032 c2 1_555 0.094 'displacements for plane 1'
> 2 0.0021 c1 2_655 0.010 'displacements for plane 2'
>;
>
>data_restr_plane_class_class_id
> _name '_restr_plane_class_class_id'
> _category 'restr_plane_class'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_restr_plane_class_id'
> _enumeration_default 1
> _definition
>; The class identifier for the plane whose properties are described
>;
>
>data_restr_plane_class_details
> _name '_restr_plane_class_details'
> _category 'restr_plane_class'
> _type char
> _list yes
> _list_reference '_restr_plane_class_class_id'
> _definition
>; Text describing any special features of the restraint.
>;
>
>data_restr_plane_class_displacement_esd
> _name '_restr_plane_class_displacement_esd'
> _category 'restr_plane_class'
> _type char
> _list yes
> _list_reference '_restr_plane_class_class_id'
> _units A
> _units_detail Angstrom
> _enumeration_range 0:
> _definition
>; The observed estimated standard deviation of the atoms from this plane.
>;
>
>data_restr_plane_class_displacement_max
> _name '_restr_plane_class_displacement_max'
> _category 'restr_plane_class'
> _type numb
> _type_conditions su
> _list yes
> _list_reference '_restr_plane_class_class_id'
> _units A
> _units_detail Angstrom
> _enumeration_range 0:
> _definition
>; The distance in Angstrom from the plane to the atom furthest
> removed from the plane.
>;
>
>data_restr_plane_class_displacement_max_atom_site_label
> _name '_restr_plane_class_displacement_max_atom_site_label'
> _category 'restr_plane_class'
> _type char
> _list yes
> _list_reference '_restr_plane_class_class_id'
> _list_link_parent '_atom_site_label'
> _definition
>; The _atom_site_label of the atom that lies furthest
> from the plane defined by this class
>;
>
>data_restr_plane_class_displacement_max_site_symmetry
> _name '_restr_plane_class_displacement_max_site_symmetry'
> _category 'restr_plane_class'
> _type char
> _list yes
> _list_reference '_restr_plane_class_class_id'
> _enumeration_default '1_555'
> _definition
>; The site symmetries of the atom that helps to define the plane
> to which it to be restrained.
>
> The symmetry code of each atom site as the symmetry-equivalent
> position number 'n' and the cell translation number 'klm'.
> These numbers are combined to form the code n_klm.
> The character string n_klm is composed as follows:
>
> n refers to the symmetry operation that is applied to the
> coordinates stored in _atom_site_fract_x, _atom_site_fract_y
> and _atom_site_fract_z. It should match a number given in
> _space_group_symop_id.
>
> k, l and m refer to the translations that are subsequently
> applied to the symmetry-transformed coordinates to generate
> the atom furthest from the plane. These translations
> (x,y,z) are related to (k,l,m) by the relations
> k = 5 + x
> l = 5 + y
> m = 5 + z
> By adding 5 to the translations, the use of negative numbers
> is avoided.
>;
> loop_ _example
> _example_detail . 'no symmetry or translation to site'
> 4 '4th symmetry operation applied'
> 7_645 '7th symm. posn.; +a on x; -b on y'
>
>#
>#--------------------------------------------------------------
># RESTRAINT 10. ATOMS ARE DEFINED AS BELONGING TO RIGID BODIES
>#--------------------------------------------------------------
>#
>#############################
># #
># RESTR_RIGID_BODY #
># #
>#############################
>
>data_restr_rigid_body_[]
> _name '_restr_rigid_body_[]'
> _category category_overview
> _type null
> _definition
>; Items in this category list the atoms defining the one or
> more bodies that are constrained to be rigid in the final
> refinement. This is done by listing the atom_site_label
> and symop for each atom in each rigid body.
>
> Since rigid bodies are only constrained, not restrained,
> the rigid body is adequately defined by the refined coordinate
> in the atom_site list. A second category,
> restr_rigid_body_class, permits a description
> of each rigid body to be given in a *_details item.
>;
>loop_ _example _example_details
>;
>loop_
> _restr_rigid_body_id
> _restr_rigid_body_atom_site_label
> _restr_rigid_body_site_symmetry
> _restr_rigid_body_class_id
> _restr_rigid_body_details
>1 C1 1_555 1 ?
>2 C2 1_555 1 ?
>3 C3 1_555 1 'C3 is a hinge atom'
>4 C4 1_555 1 'C4 is a hinge atom'
>5 C3 1_555 2 ?
>6 C4 1_555 2 ?
>7 C5 2_555 2 ?
>8 C6 1_555 2 ?
>;
>; The first rigid body contains C1, C2, C3 and C4, the second rigid body
> contains C3, C4, C5 and C6. The boond beteeen C3 and C4 is common to both
> rigid bodies
>;
>
>data_restr_rigid_body_id
> _name ' _restr_rigid_body_id'
> _category 'restr_rigid_body'
> _type char
> _list yes
> _list_mandatory yes
> _definition
>; A unique identifier for each atom in the list of atoms in the
> restr_rigid_body category
>;
> _example ?
> _example_detail ?
>
>
>data_restr_rigid_body_class_id
> _name '_restr_rigid_body_class_id'
> _category 'restr_rigid_body'
> _type char
> _list yes
> _list_reference '_restr_rigid_body_id'
> _enumeration_default 1
> _definition
>; A character string identifying a rigid body.
>;
>
>data_restr_rigid_body_atom_site_label
> _name '_restr_rigid_body_atom_site_label'
> _category 'restr_rigid_body'
> _type char
> _list yes
> _list_reference '_restr_rigid_body_id'
> _list_link_parent '_atom_site_label'
> _definition
>; The _atom_site_labels of an atom in a rigid body.
>;
>
>data_restr_rigid_body_site_symmetry_label_
> _name '_restr_rigid_body_site_symmetry'
> _category 'restr_rigid_body'
> _type char
> _list yes
> _list_reference '_restr_rigid_body_id'
> _definition
>; The site symmetry of an atom in a rigid body
>
> The symmetry code of each atom site as the symmetry-equivalent
> position number 'n' and the cell translation number 'klm'.
> These numbers are combined to form the code n_klm.
> The character string n_klm is composed as follows:
>
> n refers to the symmetry operation that is applied to the
> coordinates stored in _atom_site_fract_x, _atom_site_fract_y
> and _atom_site_fract_z. It should the number given in
> _space_group_symop_id.
>
> k, l and m refer to the translations that are subsequently
> applied to the symmetry-transformed coordinates to generate
> the atom used in calculating the distance. These translations
> (x,y,z) are related to (k,l,m) by the relations
> k = 5 + x
> l = 5 + y
> m = 5 + z
> By adding 5 to the translations, the use of negative numbers
> is avoided.
>;
> loop_ _example
> _example_detail . 'no symmetry or translation applied'
> 4 '4th symmetry operation applied'
> 7_645 '7th symm. posn.; +1 on x; -1 on y'
> _enumeration_default 1_555
>
>data_restr_rigid_body_details
> _name '_restr_rigid_body_details'
> _category 'restr_rigid_body'
> _type char
> _list yes
> _list_reference '_restr_rigid_body_id'
> _definition
>; A text description giving details of a distance in
> a class of distances that are constrained to be equal.
>;
>
>
>###################################
># #
># RESTR_RIGID_BODY_CLASS #
># #
>###################################
>#
>
>data_restr_rigid_body_class_[]
> _name '_restr_rigid_body_class_[]'
> _category category_overview
> _type null
> _definition
>; Items in this category give details of the dfferent rigid
> bodies as defined by _restr_rigid_body_class_id
>;
> _example
>;
> loop_
> _restr_rigid_body_class_class_id
> _restr_rigid_body_class_details
> 1 'Phenyl ring'
> 2 'methyl group'
>;
>
>
> data_restr_rigid_body_class_class_id
> _name '_restr_rigid_body_class_class_id'
> _category 'restr_rigid_body_class'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_restr_rigid_body_class_id'
> _enumeration_default 1
> _definition
>; A character string that identifies the rigid body.
> It must match one of the values of _restr_rigid_body_class_id
>;
>
> data_restr_rigid_body_class_details
> _name '_restr_rigid_body_class_details'
> _category 'restr_rigid_body_class'
> _type char
> _list yes
> _list_reference '_restr_rigid_body_class_class_id'
> _definition
>; A text description giving details of a rigid body.
>;
>
># ----------------------------------------------------------------------------
># RESTRAINT 11. A TORSION ANGLE IS CONSTRAINED TO A PREDETERMINED VALUE
># ----------------------------------------------------------------------------
>#
>######################
># #
># RESTR_TORSION #
># #
>######################
>
>data_restr_torsion_[]
> _name '_restr_torsion_[]'
> _category category_overview
> _type null
> _definition
>; Items in this category define torsion angles that were restrained
> in the final refinement.
>;
>loop_ _example
> _example_detail
>; _restr_torsion_atom_site_label_1
> _restr_torsion_site_symmetry_1
> _restr_torsion_atom_site_label_2
> _restr_torsion_site_symmetry_2
> _restr_torsion_atom_site_label_3
> _restr_torsion_site_symmetry_3
> _restr_torsion_atom_site_label_4
> _restr_torsion_site_symmetry_4
> _restr_torsion_angle
> _restr_torsion_weight_param
> _restr_torsion_diff
> _restr_torsion_details
> Na1 1_555 Na1 2_555 O1 2_555 H101 1_555 90 1 0.97 ?
>;
>; An example of a torsion angle restrained to 90+/-1 degree with a refined
> difference of 0.97 degrees.
>;
>
>data_restr_torsion_angle_target
> _name '_restr_torsion_angle_target'
> _category 'restr_torsion'
> _type numb
> _list yes
> _list_reference '_restr_torsion_atom_site_label_'
> _units degree
> _enumeration_range -180:180
> _definition
>; The angle in degrees to which the torsion angle is restrained.
> The torsion angle is the dihedral angle between the plane defined
> by atoms 1, 2 and 3, and the plane defined by atoms 2, 3 and 4.
>;
>
>data_restr_torsion_atom_site_label_
> loop_ _name '_restr_torsion_atom_site_label_1'
> '_restr_torsion_atom_site_label_2'
> '_restr_torsion_atom_site_label_3'
> '_restr_torsion_atom_site_label_4'
> _category 'restr_torsion'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_atom_site_label_'
> _definition
>; The _atom_site_labels of the atoms in the sequence in
>which they are
> linked by the bonds whose torsion angle is to be restrained.
>;
>
>data_restr_torsion_details
> _name '_restr_torsion_details'
> _category 'restr_torsion'
> _type numb
> _list yes
> _list_reference '_restr_torsion_atom_site_label_'
> _units degree
> _definition
>; A free text description of the restraint.
>;
>
> data_restr_torsion_diff
> _name '_restr_torsion_diff'
> _category 'restr_torsion'
> _type numb
> _type_conditions su
> _list yes
> _list_reference '_restr_torsion_atom_site_label_'
> _units degree
> _definition
>; The difference between the target and the refined torsion angle.
>;
>
>data_restr_torsion_site_symmetry_
> loop_ _name '_restr_torsion_site_symmetry_1'
> '_restr_torsion_site_symmetry_2'
> '_restr_torsion_site_symmetry_3'
> '_restr_torsion_site_symmetry_4'
> _category 'restr_torsion'
> _type char
> _list yes
> _list_reference '_restr_torsion_atom_site_label_'
> _enumeration_default '1_555'
> loop_ _example
> _example_detail . 'no symmetry or translation to site'
> '4' '4th symmetry operation applied'
> '7_645' '7th symm. posn.; +a on x; -b on y'
> _definition
>; The symmetry transformation needed to generate the coordinates
> of the four atoms that define the torsion angle.
>
> The symmetry code of each atom site as the symmetry-equivalent
> position number 'n' and the cell translation number 'klm'.
> These numbers are combined to form the code n_klm.
> The character string n_klm is composed as follows:
>
> n refers to the symmetry operation that is applied to the
> coordinates stored in _atom_site_fract_x, _atom_site_fract_y
> and _atom_site_fract_z. It should match a number given in
> _space_group_symop_id.
>
> k, l and m refer to the translations that are subsequently
> applied to the symmetry-transformed coordinates to generate
> the atom used in calculating the torsion angle. These
> translations (x,y,z) are related to (k,l,m) by the relations
> k = 5 + x
> l = 5 + y
> m = 5 + z
> By adding 5 to the translations, the use of negative numbers
> is avoided.
>;
>
>data_restr_torsion_weight_param
> _name '_restr_torsion_weight_param'
> _category 'restr_torsion'
> _type numb
> _list yes
> _list_reference '_restr_torsion_atom_site_label_'
> _units degree
> _enumeration_range 0:
> _enumeration_default 0
> _definition
>; Weighting parameter = sqrt(1/weight).
> It is the expectation value of the difference between
> the refined value and the target.
> If this parameter is set to zero, the angle will be constrained
> to refine to the target value.
> If this item is absent, its value will be taken as zero
> and the distance will be constrained
>;
>
>
>
>#-------------------------------------------------------------------
># RESTRAINT 12: THE ATOMIC DISPLACEMENT PARAMETER IS RESTRAINED TO
>BE ISOTROPIC
>#-------------------------------------------------------------------
>#
>#####################
># #
># RESTR_U-ISO #
># #
>#####################
>
>data_restr-U-iso_[]
> _name '_restr-U-iso_[]'
> _category category_overview
> _type null
> _list_reference '_restr_U_iso_atom_site_label'
> _definition
>; This restraints attempts to make an anisotropic
> atomic displaecement isotropic within the range of the
> weighting parameter.
> It corresponds to SHELX ISO.
>;
>loop_
> _example
>;loop_
> _restr_U_iso_atom_site_label
> _restr_U_iso_weight_param
>Na1 0.003
>O3 0.008
>O8 0.008
>;
>
>data_restr_U_iso_atom_site_label
> _name '_restr_U_iso_atom_site_label'
> _category 'restr_U_iso'
> _type char
> _list yes
> _list_reference '_restr_U_iso_atom_site_label'
> _list_mandatory yes
> _list_link_parent '_atom_site_label'
> _definition
>; Label of the atom whose atomic displacement parameters are to be restrained.
>;
>
>data_restr_U_isotropic_weight_param
> _name '_restr_U_iso_weight_param'
> _category 'restr_U_iso'
> _type numb
> _list yes
> _list_reference '_restr_U_iso_atom_site_label'
> _units A^-2^
> _units_detail 'reciprocal Angstrom squared'
> _enumeration_range 0:
> _enumeration_default 0
> _definition
>; The expectation value of the difference between
> the refined and the isotropic equivalent of the
> anisotropic atomic displacement parameters.
> The default value of zero indicates a constraint.
>;
>
>#
># ----------------------------------------------------------------------------
># RESTRAINT 13. ADPs ARE RESTRAINED FOR A RIGID BOND.
># ----------------------------------------------------------------------------
># This "rigid bond" restraint restrains the anisotropic displacement
># parameters of two atoms so that they are equal within a certain
># _weight_param along the direction of the vector joining the atoms.
>#
>######################
># #
># RESTR_U_RIGID #
># #
>######################
>#
>
>data_restr_U_rigid_[]
> _name '_restr_U_rigid_[]'
> _category category_overview
> _type null
> _definition
>; The items in this category restrains the anisotropic displacement
> parameters of two atoms to be equal within a certain
> _weight_param along the direction of the vector joining the atoms.
>;
> _example
>;
>loop_
>_restr_U_rigid_atom_site_label_1
>_restr_U_rigid_site_symmetry_1
>_restr_U_rigid_atom_site_label_2
>_restr_U_rigid_site_symmetry_2
>_restr_U_rigid_target_weight_param
>_restr_U_rigid_U_parallel
>_restr_U_rigid_diff
>_restr_U_rigid_details
>C1 1_555 C2 2_655 0.001 0.0023(2) 0.0006 'C1-C2 is a rigid bond'
>;
>
>data_restr_U_rigid_atom_site_label_
> loop_ _name '_restr_U_rigid_atom_site_label_1'
> '_restr_U_rigid_atom_site_label_2'
> _category 'restr_U_rigid'
> _type char
> _list yes
> _list_mandatory yes
> _list_link_parent '_atom_site_label'
> _definition
>; The _atom_site_labels of the two atoms that define the rigid bond.
>;
>
>data_restr_U_rigid_details
> _name '_restr_U_rigid_details'
> _category 'restr_U_rigid'
> _type char
> _list yes
> _list_reference 'restr_U_rigid_atom_site_label_'
> _definition
>; Free text information about the rigid bond restraint.
>;
>
>data_restr_U_rigid_diff
> _name '_restr_U_rigid_diff'
> _category 'restr_U_rigid'
> _type numb
> _type_conditions su
> _list yes
> _list_reference 'restr_U_rigid_atom_site_label_'
> _units A^-2^
> _units_detail Angstrom^-2^
> _definition
>; The difference between the components along the bond direction
> of the atomic displacement parameters, U, of the two atoms.
>;
>
>data_restr_U_rigid_site_symmetry_
> loop_ _name '_restr_U_rigid_site_symmetry_1'
> '_restr_U_rigid_site_symmetry_2'
> _category 'restr_U_rigid'
> _type char
> _list yes
> _list_reference 'restr_U_rigid_atom_site_label_'
> _enumeration_default '1_555'
> _definition
>; The site symmetries of the two atoms that define the rigid bond.
>
> The symmetry code of each atom site as the symmetry-equivalent
> position number 'n' and the cell translation number 'klm'.
> These numbers are combined to form the code n_klm.
> The character string n_klm is composed as follows:
>
> n refers to the symmetry operation that is applied to the
> coordinates stored in _atom_site_fract_x, _atom_site_fract_y
> and _atom_site_fract_z. It should match a number given in
> _space_group_symop_id.
>
> k, l and m refer to the translations that are subsequently
> applied to the symmetry-transformed coordinates to generate
> the atom used in calculating the rigid bond.
> These translations (x,y,z) are related to (k,l,m)
> by the relations
> k = 5 + x
> l = 5 + y
> m = 5 + z
> By adding 5 to the translations, the use of negative numbers
> is avoided.
>;
> loop_ _example
> _example_detail . 'no symmetry or translation to site'
> 4 '4th symmetry operation applied'
> 7_645 '7th symm. posn.; +a on x; -b on y'
>
>data_restr_U_rigid_target_weight_param
> _name '_restr_U_rigid_target_weight_param'
> _category 'restr_U_rigid'
> _type numb
> _list yes
> _list_reference 'restr_U_rigid_atom_site_label_'
> _units A^-2^
> _units_detail Angstrom^-2^
> _enumeration_default 0
> _definition
>; The weighting parameter = sqrt(1/weight).
> The expectation value of the difference between the components
> of the atomic displacement parameter, U,
> along the bond direction of the two atoms that define the bond.
> This number is used to assign a weight during refinement.
> A value of zero causes the restraint to become a constraint.
> This item as a default value of zero.
>;
>
>data_restr_U_rigid_U_parallel
> _name '_restr_U_rigid_U_parallel'
> _category 'restr_U_rigid'
> _type numb
> _list yes
> _list_reference 'restr_U_rigid_atom_site_label_'
> _units A^-2^
> _units_detail Angstrom^-2^
> _enumeration_default 0
> _definition
>; The average value of the components parallel to the bond
> of the atomic displacement parameters of the two atoms
> that define the bond.
>;
>
>#
>#--------------------------------------------------------------------
># RESTRAINT 14. TWO ATOMS ARE RESRAINED TO HAVE THE SAME ADPs
>#--------------------------------------------------------------------
>#
>#####################
># #
># RESTR_U-SIMILAR #
># #
>#####################
>
>data_restr_U_similar_[]
> _name '_restr_U_similar_[]'
> _category category_overview
> _type null
> _definition
>; This category forces the atomic displacement ellipsoids
> of atom 2 to be equal to that of atom 1 within the range
> of the weighting parameter.
> This is the same as SHELX SIMU
>;
>loop_
>_example
>;loop_
> _restr_U_similar_atom_site_label_1
> _restr_U_similar_atom_site_label_2
> _restr_U_similar_weight_param
>C1 C2 0.08
>C2 C3 0.08
>;
>
>data_restr_U_similar_atom_site_label_1
> _name '_restr_U_similar_atom_site_label_1'
> _category 'restr_U_similar'
> _type char
> _list yes
> loop_
> _list_reference '_restr_U_similar_atom_site_label_1'
> '_restr_U_similar_atom_site_label_2'
> _list_mandatory yes
> _list_link_parent '_atom_site_label'
> _definition
>; Atom site label of first atom, the atom whose
> atomic displacement parameters are used as the target.
>;
>
>data_restr_U_similar_atom_site_label_2
> _name '_restr_U_similar_atom_site_label_2'
> _category 'restr_U_similar'
> _type char
> _list yes
> loop_
> _list_reference '_restr_U_similar_atom_site_label_1'
> '_restr_U_similar_atom_site_label_2'
> _list_mandatory yes
> _list_link_parent '_atom_site_label'
> _definition
>; Atom site label of second atom, the atom whose
> atomic displacement parameters are to be restrained
> to be the same at atom 1.
>;
>
>data_restr_U_similar_weight_param
> _name '_restr_U_similar_weight_param'
> _category 'restr_U_similar'
> _type numb
> _list yes
> loop_
> _list_reference '_restr_U_similar_atom_site_label_1'
> '_restr_U_similar_atom_site_label_2'
> _units A^-2^
> _units_detail 'reciprocal Angstrom squared'
> _enumeration_range 0:
> _enumeration_default 0
> _definition
>; The expectation value of the difference between the
> anisotropic atomic displacement parameters
> of the two atoms.
> The default value of zero represents a constraint.
>;
>
>##-------------End of Restraint and Constraint Dictionary ---------
>
>--
>T +61 (02) 9717 9907
>F +61 (02) 9717 3145
>M +61 (04) 0249 4148
>_______________________________________________
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--
=====================================================
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
yaya at dowling.edu
=====================================================
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