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cif_rstr.examples
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################################################################################
# #
# CIF RESTRAINTS AND CONSTRAINTS DICTIONARY VERSION #
# ------------------------------------------------- #
# #
# This dictionary contains the names and definitions proposed for reporting #
# restraints and constraints in the Core CIF dictionary #
# #
# Converted from a DDL1 dictionary to DDLM 29 June 2014 #
# #
################################################################################
#
# ----------------------------------------------------------------------------
# RESTRAINT 1. GENERAL RESTRAINT
# ----------------------------------------------------------------------------
# A general description of constraints and restraints not covered
# by other CIF items.
#
######################
# #
# RESTR #
# #
######################
#
# ----------------------------------------------------------------------------
# RESTRAINT 2. AN ANGLE IS RESTRAINED TO A PREDETERMINED VALUE.
# ----------------------------------------------------------------------------
#
####################
# #
# RESTR_ANGLE #
# #
####################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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 ?
;
;
Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_restr_angle.id
_restr_angle.target
_restr_angle.target_weight_param
_restr_angle.diff
_restr_angle.details
[[C1,1_555],[C2,1_555],[C3,1_555]] 120 1 -0.3 'generated by JANA'
[[C2,1_555],[C3,1_555],[C4,3_455]] 120 1.5 0.5 ?
;
;
Example 1.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
# ----------------------------------------------------------------------------
# RESTRAINT 3. A DISTANCE IS RESTRAINED TO A PREDETERMINED VALUE.
# ----------------------------------------------------------------------------
#
#####################
# #
# RESTR_DISTANCE #
# #
#####################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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 ?
;
;Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
# ----------------------------------------------------------------------------
# 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 #
# #
###########################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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'
;
;Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
# ----------------------------------------------------------------------------
# RESTRAINT 5. SEVERAL ANGLES ARE RESTRAINED TO BE EQUAL.
# ----------------------------------------------------------------------------
# This restraint contains two categories.
# The first defines the angles restrained and assigns
# them to different classes that are restrained independently.
# The second category defines the properties of each class.
#
##########################
# #
# RESTR_EQUAL_ANGLE #
# #
##########################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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_detail
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 ?
;
;Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
###################################
# #
# RESTR_EQUAL_ANGLE_CLASS #
# #
###################################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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_detail
1 0.50 123.52 0.32 0.62 ?
2 0.50 118.23 0.52 1.43 ?
;
;Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
# ----------------------------------------------------------------------------
# RESTRAINT 6. SEVERAL DISTANCES ARE RESTRAINED TO BE EQUAL.
# ----------------------------------------------------------------------------
# This restraint contains two categories.
# The first defines the distances restrained and assigns
# them to different classes that are restrained independently.
# The second category defines the properties of each class.
#
#############################
# #
# RESTR_EQUAL_DISTANCE #
# #
#############################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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 ?
;
;Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
###################################
# #
# RESTR_EQUAL_DISTANCE_CLASS #
# #
###################################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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 ?
;
;Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
# ----------------------------------------------------------------------------
# RESTRAINT 7. SEVERAL TORSION ANGLES ARE RESTRAINED TO BE EQUAL.
# ----------------------------------------------------------------------------
# This restraint contains two categories.
# The first defines the torsion angles restrained and assigns
# them to different classes that are restrained independently.
# The second category defines the properties of each class.
#
############################
# #
# RESTR_EQUAL_TORSION #
# #
############################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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 ?
;
;Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
###################################
# #
# RESTR_EQUAL_TORSION_CLASS #
# #
###################################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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 ?
;
;Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
# ----------------------------------------------------------------------------
# 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 #
# #
########################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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 category restr_parameter_class.
Example 1. 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
;
;
Example 2.
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
;
;
Example 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
;
;
Example 4.
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
;
;
Example 5.
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].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
###################################
# #
# RESTR_PARAMETER_CLASS #
# #
###################################
- - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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 1.
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_coefficient 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.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
# ----------------------------------------------------------------------------
# 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 #
# #
######################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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) ?
;
;Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
############################
# #
# RESTR_PLANE_CLASS #
# #
############################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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
_restr_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'
;
; Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
# ----------------------------------------------------------------------------
# RESTRAINT 10. ATOMS ARE DEFINED AS BELONGING TO RIGID BODIES.
# ----------------------------------------------------------------------------
#
#############################
# #
# RESTR_RIGID_BODY #
# #
#############################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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 ?
;
; Example 1.
The first rigid body contains C1, C2, C3 and C4, the second rigid body
contains C3, C4, C5 and C6. The bond between C3 and C4 is common to both
rigid bodies.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
###################################
# #
# RESTR_RIGID_BODY_CLASS #
# #
###################################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_restr_rigid_body_class_class_id
_restr_rigid_body_class_details
1 'Phenyl ring'
2 'methyl group'
;
; Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# ----------------------------------------------------------------------------
# RESTRAINT 11. A TORSION ANGLE IS CONSTRAINED TO A PREDETERMINED VALUE
# ----------------------------------------------------------------------------
#
######################
# #
# RESTR_TORSION #
# #
######################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_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_target
_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 ?
;
; Example 1.
An example of a torsion angle restrained to 90+/-1 degree with a refined
difference of 0.97 degrees.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
# ----------------------------------------------------------------------------
# RESTRAINT 12: THE ATOMIC DISPLACEMENT PARAMETER IS RESTRAINED TO BE
# ISOTROPIC.
# ----------------------------------------------------------------------------
#
#####################
# #
# RESTR_U_ISO #
# #
#####################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_restr_U_iso_atom_site_label
_restr_U_iso_weight_param
Na1 0.003
O3 0.008
O8 0.008
;
; Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
# ----------------------------------------------------------------------------
# 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 #
# #
######################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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'
;
; Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
# ----------------------------------------------------------------------------
# RESTRAINT 14. TWO ATOMS ARE RESTRAINED TO HAVE THE SAME ADPs.
# ----------------------------------------------------------------------------
#
#####################
# #
# RESTR_U_SIMILAR #
# #
#####################
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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
;
; Example 1.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# -------------- End of restraint and constraint dictionary -------------