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Re: Core restraints dictionary v 0.0.3 for COMCIFS approval
- To: "Discussion list of the IUCr Committee for the Maintenance of the CIFStandard (COMCIFS)" <comcifs@iucr.org>
- Subject: Re: Core restraints dictionary v 0.0.3 for COMCIFS approval
- From: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
- Date: Tue, 21 Sep 2010 08:56:51 -0400
- In-Reply-To: <AANLkTi=hBfxX11vbuspJT3tor82=fqMO-foTSUA9RhO4@mail.gmail.com>
- References: <AANLkTi=hBfxX11vbuspJT3tor82=fqMO-foTSUA9RhO4@mail.gmail.com>
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 >_______________________________________________ >comcifs mailing list >comcifs@iucr.org >http://scripts.iucr.org/mailman/listinfo/comcifs -- ===================================================== 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@dowling.edu =====================================================
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