Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Draft CIF dictionary for rgid body description

  • To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group <coredmg@iucr.org>
  • Subject: Draft CIF dictionary for rgid body description
  • From: David Brown <idbrown@mcmaster.ca>
  • Date: Wed, 11 Aug 2010 11:07:37 -0400
Title:
Dear Colleagues,

In January I circulated to you, the coreCIF Dictionary Maintenance Group, the draft of a CIF dictionary containing items for reporting the restraints and constraints that were applied during the final round of refinement.  This was approved by this group after a six week consultaion period and passed on to COMCIFS for final approval.  During this stage an objection was raised that under the proposal it was not possible for an atom to belong to more than one rigid body, because the rigid bodies were defined by a flag in the atom_site list which identified which rigid body a partcular atom belonged to. 

In order to address this weakness, Ilia Guzei and I have proposed an amendment to the earlier draft.  This is more flexible in that it defines each rigid body in terms of any atom in the atom_site list together with a symmetry operation.  This places no restriction on the number of rigid bodies an atom can belong to.  I am circulating this amendment in the attached ASCII file which contains the amended dictionary text.

Can you please check this and respond to this Discussion List with your approval or reservation before September 10 (2010-09-10).  If there are no unresolved issues at that time, I will incorporate this amendment into the original restraint dictionary and pass it back to COMCIFS for final approval.

I am looking forward to heariing from you

David Brown
Chair CoreCIF DMG

# 2010-08-11
# Addendum to the proposed addition of restraint and constraint descriptors 
# circulated 2010-01-13
#
#--------------------------------------------------------------
# Constraint   Rigid Body
#--------------------------------------------------------------

#
# The category restr_rigid_body is used to list the atoms that define one or more
# rigid bodies.  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_body, permits a description 
# of each rigid body to be given in a *_special_details item.  
# 
#############################
#                           #
#  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 bodies
          that are constrained to be rigid in the final refinement.
;
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. 
;

################# End of dictionary text ##################
begin:vcard
fn:I.David Brown
n:Brown;I.David
org:McMaster University;Brockhouse Institute for Materials Research
adr:;;King St. W;Hamilton;Ontario;L8S 4M1;Canada
email;internet:idbrown@mcmaster.ca
title:Professor Emeritus
tel;work:+905 525 9140 x 24710
tel;fax:+905 521 2773
version:2.1
end:vcard

_______________________________________________
coreDMG mailing list
coreDMG@iucr.org
http://scripts.iucr.org/mailman/listinfo/coredmg

[Send comment to list secretary]
[Reply to list (subscribers only)]