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Re: CoreCIFchem Discussion #6

Season's Greetings

HDF's comment concerning coreCIFchem#6

I think #6 is a vast improvement over the previous draft. Apart from as detailed below I accept all of its proposals and suggestions.
I also studied PMR1 sent 5th Oct 14h35 by IDB. I found Peter's comments very helpful indeed.



For knowing where we are 
#6L1>                DISCUSSION PAPER #6
is line 1 which makes the last line 
L1972># End of sample CIFs



#6L43> HDF on tecton v molecular unit

   I would be even happier using PMR's suggestion of 'atomSet' rather than 'tecton'. I like 'fragment' just about as much as 'tecton'.



#6L83>CIF.  Every list (i.e., loop) in a CIF must have a list-reference

   I think that is not correct. For proof, from #6
L1844>loop_
L1845> _geom_bond_atom_site_label_1
L1846> _geom_bond_atom_site_label_2
L1847> _geom_bond_distance
L1848> _geom_bond_site_symmetry_1
L1849> _geom_bond_site_symmetry_2
    and the current cif_core.dic version 2.3, and many cif's on journals.iucr.org concur. This means that the following data items and the corresponding data values are NOT required as they serve no purpose.
  _tecton_conformer_id
  _tecton_geom_dist_id
  _tecton_geom_angle_id
  _tecton_geom_torsion_id
  _map_tecton_atom_map_id
  _map_tecton2crystal_atom_id
  _map_tecton2crystal_bond_id

  _tecton_topology_bond_id is NOT required in the TNT example but IS required in the CaCrF5 example. I hope my list is complete and correct.



#6L98>The implications of these two views are brought out clearly in the examples we
This paragraph reads like just one more battle in the war of crystallographers versus 
IT specialists. Essentially what is designed to be easy to programme is difficult to use for the crystallographer and what is designed to be easy to use by the crystallographer is difficult to programme. Certainly we have to find a middle implementable ground.



#6L215>HDF comment on dangling bonds

   It seemed like a good idea but the complexity it involves is just not worth the bother. It was kind of David to give it a try but honestly I think it should be dropped right now. Sorry for the extra work. I'm convinced by PMR's recommendation
PMR>One of the most important contributions would be to require that EVERY atom is reported.
 is a good one to follow. It's good for INChI and it's good for validation.



#6L289>(N.B.
>isomers differ at the topological level, conformers have the same topology but
>differ at the geometry level).
also 
#6L375>The topological description does not include any information on the geometry
>of the tecton but it does distinguish between isomers. 

   Here and in quite a few other places in the text we have mention of molecules, isomers and conformers. This is due to the nature of the TNT example. However one needs also to be precise on where and how the following sub-categories of molecules fit in:
    (1) enantiomers (coming orginally from 'enantiomorphous isomer') including enantiomers of known absolute configuration, enantiomers of unknown or relative configuration and racemates.
    (2) diastereoisomers
    (1) and (2) above have the same topology but are not considered as being conformers.

   The question arises as to the best place and method to specify the chirality of the molecules. I recommend that we do it the way that things are set up in the IUPAC dictionnary of stereochemistry. Chiral molecules of unknown or relative configuration and racemates are treated as an extension of the nomenclature of enantiopure compounds.
   A very common case is of chiral molecules containing chiral centres. Clearly the best place to include the specification of the chirality of these atom-based centres is either in _tecton_topology_atom_chirality or in the _tecton_geom_atom_ loop as a data value with name _tecton_geom_atom_chirality taking a value from one of the following taken from the IUPAC dictionnary: R or S for an enantiopure enantiomer of known absolute configuration, R* or S*  for an enantiopure enantiomer of unknown or relative absolute configuration, RS or SR for a racemate. What should one do if an atom is not a chiral centre i.e. it is achiral? Clearly one needs a data value meaning 'this atom is not a chiral centre'. This value does not mean the same as 'chirality unknown'.
  Another very common case occurs where a single symbol is used to indicate the chirality of a molecule with or without chiral centres. The ones one sees all the time are D or L for carbohydrates and amino acids. There are others as well. [HDF should make a list of possible values]. These indications of chirality go naturally in _tecton_chirality and _tecton_conformer_chirality as values D, L, DL, rac, rel, {traditionalists might like to add +, - and +or- which personally I detest totally}, and maybe some others for values like 'enantiopure', 'unknown' [HDF needs to think more about this].
  The information that is currently coded in _chemical_absolute_configuration needs to be included in the _tecton_* and _tecton_conformer _loop_s. _chemical_absolute_configuration needs to be deprecated.
  [Need to think more about the racemate because this may still be a problem because the IUPAC stereochemistry dictionnary insists on having R as the first CIP symbol. The crystallographer may not have chosen the opposite enantiomer in the asymmetric unit. Also the chemical diagram needs carefull attention. I think there are specific ways of drawing a chemical diagram to indicate a racemate rather than just one of its enantiopure components.]

[NB to PMR: As you are a member of the IUPAC stereochemistry committee, I'm depending on you informing us of any relevant proposed changes to the nomenclature.]



#6L355>and conformation of a the tectons to be specified
  and to:
       and conformation of the tectons to be specified



#6L467>illustration, the molecule contains a crystallographic mirror plane that
  should better be:
   illustration, the average disordered molecule contains a crystallographic mirror plane that



#6L471>numbers of 0.5.  Because of the disorder the crystallographic structure does
  should better be:
numbers of 0.5.  Because of the disorder the average crystallographic structure does



#6L483># The first set of loops define the topology of the TNT molecule
  should be:
# The first set of loops defines the topology of the TNT molecule



#6L488># If a crystal contained molecules of more than one compound, or more than one
># isomer of a compound, each would be described by a separate tecton. 
># If the crystal contained more than one copy of the same molecule in the
># asymmetric unit (Z'>1) the topology of the tecton would be given only once
># but it would be mapped onto all the crystallographically distinct copies.  
  should better be
# If a crystal contains different types of molecules (isomers or diastereoisomers or enantiomers other than the racemate)
# each would be described by a separate tecton. 
# If the crystal contained more than one copy of the same molecule in the
# asymmetric unit (Z'>1) the topology of the tecton would be given only once
# and then this single topology would be mapped onto all the crystallographically distinct copies.  



#6L511># together their properties.  We may wish to define other properties, such as
   should better be:
# together with their properties.  We may wish to define other properties, such as



#6L526># _tecton_chirality   # time-averaged if no geometry given
  ADD after this line
# _atomSet_absolute_configuration   # defined like current _chemical_absolute_configuration



#6L582># The CIF dictionary already contains instructions for drawing a 2-D molecular
># diagram in the group of chemical_conn categories.  Although the
># chemical_conn categories also describe the topology of a molecule they are

  Do I understand correctly that you are thinking of deprecating chemical_conn items?



#6L627># I have added an item _tecton_topology_atom_chirality which is not needed in
# this example, but is needed in chiral structures to identify any atom that
# serves as a chiral center.  Chirality is not captured by the topology, but
# it is, like topology, a feature of the structure that can only be changed by
# breaking and making bonds.  It is included here because it is more closely
# related to the topology than to the geometry which can be changed without
# breaking any bonds.  I will defer to others what values should be associated
# with this item - presumably some letter like R or S.

  I don't at all like this discussion about breaking bonds etc. The real reason for me that one needs _chirality here is for the case where there is only one 'conformer' and you don't want to give any geometry information. Thus it turns out to be convenient to give it here. If you have several 'conformers' you give the chirality information in _tecton_atom_chirality. The possible values are given above.



#6L714>loop_
_tecton_topology_bond_id
_tecton_topology_bond_atom1_id     # Child of _tecton_topology_atom_id
_tecton_topology_bond_atom2_id     # Child of _tecton_topology_atom_id
_tecton_topology_bond_type
1     T.C1   T.C2   arom      # TNT benzene ring
2     T.C2   T.C3   arom
3     T.C3   T.C4   arom
4     T.C4   T.C5   arom
5     T.C5   T.C6   arom
6     T.C6   T.C1   arom
7     T.C3   T.H3   sing
8     T.C5   T.H5   sing
 etc, etc

 should be:

loop_
_atomSet_topology_bond_atom1_id     # Child of _atomSet_topology_atom_id
_atomSet_topology_bond_atom2_id     # Child of _atomSet_topology_atom_id
_atomSet_topology_bond_type
T.C1   T.C2   arom      # TNT benzene ring
T.C2   T.C3   arom
T.C3   T.C4   arom
T.C4   T.C5   arom
T.C5   T.C6   arom
T.C6   T.C1   arom
T.C3   T.H3   sing
T.C5   T.H5   sing
 etc, etc
  as the _tecton_topology_bond_id serves no purpose.



#6L834>loop_
_tecton_conformer_id            # List-reference
_tecton_conformer_tecton_id     # Child of _tecton_topology_id
_tecton_conformer_point_group   # Schoenflies point group symbol of conformer
_tecton_conformer_chirality     # We need to define allowed symbols
_tecton_conformer_details

  should be

loop_
_atomSet_conformer_id            # List-reference
_atomSet_conformer_tecton_id     # Child of _tecton_topology_id
_atomSet_conformer_point_group   # Schoenflies point group symbol of conformer
_atomSet_conformer_chirality     # We need to define allowed symbols
_atomSet_conformer_absolute_configuration   # values as per _chemical_absolute_configuration
_atomSet_conformer_Zprime       # 
_atomSet_conformer_occupation   # occupation number of this conformer in the crystal
_atomSet_conformer_details

 With several 'conformers' you need these additional values to be given here.
 I do not agree at all with David's proposal of putting copies of the occupation number with the individual atom information of the conformer. The occupation applies to the whole conformer and must go here. Putting occupation values on the individual atoms leaves the gate wide open for those who might be tempted to 'doctor' their results to get around an error message from a checking programme.



#6L893>loop_
_tecton_geom_atom_id    # List-reference, child of _tecton_topology_atom_id
_tecton_geom_atom_conformer_label  # Child of _tecton_conformer_equiv_label
_tecton_geom_atom_coord_x          # Coordinates of atom in Angstrom
_tecton_geom_atom_coord_y          # 
_tecton_geom_atom_coord_z          # 
_tecton_geom_atom_details
 
 should be

_atomSet_geom_atom_id    # List-reference, child of _tecton_topology_atom_id
_atomSet_geom_atom_conformer_label  # Child of _tecton_conformer_equiv_label
_atomSet_geom_atom_coord_x          # Coordinates of atom in Angstrom
_atomSet_geom_atom_coord_y          # 
_atomSet_geom_atom_coord_z          # 
_atomSet_geom_atom_chirality        #  chirality of chiral centre on atom as per CIP
_atomSet_geom_atom_details



#6L919>loop_
_tecton_geom_dist_id              # List-reference
_tecton_geom_dist_conformer_label # Child of _tecton_geom_equiv_label
_tecton_geom_dist_atom1_id        # Child of _tecton_topology_atom_id
_tecton_geom_dist_atom2_id        # Child of _tecton_topology_atom_id
_tecton_geom_dist_distance        # Distance atom1-atom2 in Angstroms
1  all   T.C7   T.C1    1.54                # TNT methyl group
2  all   T.C7   T.H71   1.05
3  all   T.C7   T.H72   1.05
4  all   T.C7   T.H73   1.05
5  all   T.N4   T.C4    1.43                # TNT N4 nitro group
6  all   T.N4   T.O41   1.18
7  all   T.N4   T.O42   1.18
8  all   T.N2   T.C2    1.43                # TNT N2 nitro group
9  all   T.N2   T.O21   1.18
10 all   T.N2   T.O22   1.18
11 all   T.N6   T.C6    1.43                # TNT N6 nitro group
12 all   T.N6   T.O61   1.18
13 all   T.N6   T.O62   1.18

 should be as follows since _dist_id serves no purpose.

loop_
_atomSet_geom_dist_conformer_label # Child of _tecton_geom_equiv_label
_atomSet_geom_dist_atom1_id        # Child of _tecton_topology_atom_id
_atomSet_geom_dist_atom2_id        # Child of _tecton_topology_atom_id
_atomSet_geom_dist_distance        # Distance atom1-atom2 in Angstroms
all   T.C7   T.C1    1.54                # TNT methyl group
all   T.C7   T.H71   1.05
all   T.C7   T.H72   1.05
all   T.C7   T.H73   1.05
all   T.N4   T.C4    1.43                # TNT N4 nitro group
all   T.N4   T.O41   1.18
all   T.N4   T.O42   1.18
all   T.N2   T.C2    1.43                # TNT N2 nitro group
all   T.N2   T.O21   1.18
all   T.N2   T.O22   1.18
all   T.N6   T.C6    1.43                # TNT N6 nitro group
all   T.N6   T.O61   1.18
all   T.N6   T.O62   1.18



#6L942>loop_
_tecton_geom_angle_id              # List-reference
_tecton_geom_angle_conformer_label # Child of _tecton_geom_equiv_label
_tecton_geom_angle_atom1_id        # Child of _tecton_topology_atom_id
_tecton_geom_angle_atom2_id        # Child of _tecton_topology_atom_id
_tecton_geom_angle_atom3_is        # Child of _tecton_topology_atom_id
_tecton_geom_angle_angle           # Angle in degrees
1  all    T.C1   T.C7   T.H71  109     # TNT Methyl group
2  all    T.C1   T.C7   T.H72  109
3  all    T.C1   T.C7   T.H73  109
4  all    T.H71  T.C7   T.H72  109
5  all    T.H72  T.C7   T.H73  109
6  all    T.H73  T.C7   T.H71  109
7  all    T.O41  T.N4   T.C4   117     # TNT N4 nitro group
8  all    T.O42  T.N4   T.C4   117 
9  all    T.O41  T.N4   T.O42  126
10 all    T.O21  T.N2   T.C2   117     # TNT N2 nitro group
11 all    T.O22  T.N2   T.C2   117 
12 all    T.O21  T.N2   T.O22  126 
13 all    T.O61  T.N6   T.C6   117     # TNT N6 nitro group
14 all    T.O62  T.N6   T.C6   117 
15 all    T.O61  T.N6   T.O62  126 

  should be as _angle_id serves no purpose

loop_
_atomSet_geom_angle_conformer_label # Child of _tecton_geom_equiv_label
_atomSet_geom_angle_atom1_id        # Child of _tecton_topology_atom_id
_atomSet_geom_angle_atom2_id        # Child of _tecton_topology_atom_id
_atomSet_geom_angle_atom3_is        # Child of _tecton_topology_atom_id
_atomSet_geom_angle_angle           # Angle in degrees
all    T.C1   T.C7   T.H71  109     # TNT Methyl group
all    T.C1   T.C7   T.H72  109
all    T.C1   T.C7   T.H73  109
all    T.H71  T.C7   T.H72  109
all    T.H72  T.C7   T.H73  109
all    T.H73  T.C7   T.H71  109
all    T.O41  T.N4   T.C4   117     # TNT N4 nitro group
all    T.O42  T.N4   T.C4   117 
all    T.O41  T.N4   T.O42  126
all    T.O21  T.N2   T.C2   117     # TNT N2 nitro group
all    T.O22  T.N2   T.C2   117 
all    T.O21  T.N2   T.O22  126 
all    T.O61  T.N6   T.C6   117     # TNT N6 nitro group
all    T.O62  T.N6   T.C6   117 
all    T.O61  T.N6   T.O62  126 



#6L975>loop_
_tecton_geom_torsion_id              # List-reference
_tecton_geom_torsion_conformer_label # Child of _tecton_geom_equiv_label
_tecton_geom_torsion_atom1_id        # Child of _tecton_topology_atom_id
_tecton_geom_torsion_atom2_id        # Child of _tecton_topology_atom_id
_tecton_geom_torsion_atom3_id        # Child of _tecton_topology_atom_id
_tecton_geom_torsion_atom4_id        # Child of _tecton_topology_atom_id
_tecton_geom_torsion_angle           # Torsion angle in degrees
1 all  T.C3   T.C4   T.N4   T.O41   90
2 aa   T.C1   T.C2   T.N2   T.O21   10.5
3 aa   T.C1   T.C6   T.N6   T.O61   10.5
4 bb   T.C1   T.C2   T.N2   T.O21  -10.5
5 bb   T.C1   T.C6   T.N6   T.O61  -10.5
6 ab   T.C1   T.C2   T.N2   T.O21   10.5
7 ab   T.C1   T.C6   T.N6   T.O61  -10.5
8 ba   T.C1   T.C2   T.N2   T.O21  -10.5
9 ba   T.C1   T.C6   T.N6   T.O61   10.5

should be since _torsion_id serves no purpose

loop_
_atomSet_geom_torsion_conformer_label # Child of _tecton_geom_equiv_label
_atomSet_geom_torsion_atom1_id        # Child of _tecton_topology_atom_id
_atomSet_geom_torsion_atom2_id        # Child of _tecton_topology_atom_id
_atomSet_geom_torsion_atom3_id        # Child of _tecton_topology_atom_id
_atomSet_geom_torsion_atom4_id        # Child of _tecton_topology_atom_id
_atomSet_geom_torsion_angle           # Torsion angle in degrees
all  T.C3   T.C4   T.N4   T.O41   90
aa   T.C1   T.C2   T.N2   T.O21   10.5
aa   T.C1   T.C6   T.N6   T.O61   10.5
bb   T.C1   T.C2   T.N2   T.O21  -10.5
bb   T.C1   T.C6   T.N6   T.O61  -10.5
ab   T.C1   T.C2   T.N2   T.O21   10.5
ab   T.C1   T.C6   T.N6   T.O61  -10.5
ba   T.C1   T.C2   T.N2   T.O21  -10.5
ba   T.C1   T.C6   T.N6   T.O61   10.5



#6L1045>loop_
_map_tecton_atom_map_id        # List reference
_map_tecton_atom_atom1_id      # Child of _tecton_topology_atom_id
_map_tecton_atom_atom2_id      # Child of _tecton_topology_atom_id
1   B.C1    T.C1    # mapping 1,2,4,6 benzene moiety onto TNT
2   B.C2    T.C2
3   B.C3    T.C3
etc etc

should be since _map_id serves no purpose

loop_
_map_atomSet_atom_atom1_id      # Child of _tecton_topology_atom_id
_map_atomSet_atom_atom2_id      # Child of _tecton_topology_atom_id
B.C1    T.C1    # mapping 1,2,4,6 benzene moiety onto TNT
B.C2    T.C2
B.C3    T.C3
etc etc



#6L1085># The occupation number indicates how much of each conformer (or isomer) is
# present. The occupation numbers of the atoms in the crystal are defined in
# the atom_site loop and must not be less than the sum of the corresponding
# occupation numbers of the conformers.  

  should be

# The occupation number indicates how much of each conformer (or isomer) is
# present. The occupation numbers of the atoms in the crystal are defined in
# the atom_site loop and must approximately equal within 2 or 3 standard
# uncertainties to the sum of the corresponding occupation numbers of the conformers.  



#6L1118>loop_
_map_tecton2crystal_atom_id           # List-reference
_map_tecton2crystal_atom_atom_id      # Child of _tecton_topology_atom_id
_map_tecton2crystal_atom_conformer_label 
                                   # Child of _tecton_conformer_equiv_label
_map_tecton2crystal_atom_occup_number # Occupation number of tecton atom
_map_tecton2crystal_atom_atom_site_label # child of _atom_site_label
_map_tecton2crystal_atom_symop_id     # child of _space_group_symop_id
1  T.C1  all 1   C1   1
2  T.C2  all 1   C2   1
3  T.C3  all 1   C3   1
4  T.C4  all 1   C4   1
5  T.C5  all 1   C3   2
6  T.C6  all 1   C2   2
7  T.H3  all 1   H3   1
8  T.H5  all 1   H3   2
9  T.C7  all 1   C7   1
10 T.H71 all 1   H71  1
11 T.H72 all 1   H72  1
12 T.H73 all 1   H71  2
13 T.N4  all 1   N4   1
14 T.O41 all 1   O41  1
15 T.O42 all 1   O42  1
# SIDE CHAINS
16 T.N2  aa 0.5  N2a  1
17 T.O21 aa 0.5  O21a 1
18 T.O22 aa 0.5  O22a 1
19 T.N6  aa 0.5  N2a  2
20 T.O61 aa 0.5  O21a 2
21 T.O62 aa 0.5  O22a 2
22 T.N2  bb 0.5  N2b  1
23 T.O21 bb 0.5  O21b 1
24 T.O22 bb 0.5  O22b 1
25 T.N6  bb 0.5  N2b  2
26 T.O61 bb 0.5  O21b 2
27 T.O62 bb 0.5  O22b 2

  should be  because (a) _atom_id serves no purpose and (b) the occupations do not belong here

loop_
_map_atomSet2crystal_atom_atom_id      # Child of _atomSet_topology_atom_id
_map_atomSet2crystal_atom_conformer_label 
                                   # Child of _atomSet_conformer_equiv_label
_map_atomSet2crystal_atom_atom_site_label # child of _atom_site_label
_map_atomSet2crystal_atom_symop_id     # child of _space_group_symop_id
T.C1  all C1   symop1
T.C2  all C2   symop1
T.C3  all C3   symop1
T.C4  all C4   symop1
T.C5  all C3   symop2
T.C6  all C2   symop2
T.H3  all H3   symop1
T.H5  all H3   symop2
T.C7  all C7   symop1
T.H71 all H71  symop1
T.H72 all H72  symop1
T.H73 all H71  symop2
T.N4  all N4   symop1
T.O41 all O41  symop1
T.O42 all O42  symop1
# SIDE CHAINS
T.N2  aa  N2a  symop1
T.O21 aa  O21a symop1
T.O22 aa  O22a symop1
T.N6  aa  N2a  symop2
T.O61 aa  O21a symop2
T.O62 aa  O22a symop2
T.N2  bb  N2b  symop1
T.O21 bb  O21b symop1
T.O22 bb  O22b symop1
T.N6  bb  N2b  symop2
T.O61 bb  O21b symop2
T.O62 bb  O22b symop2



#6L1163>                        4.2 SECOND SAMPLE CIF
  4.2 should be 3.2



#6L1240>loop_
         _space_group_symop_id
         _space_group_symop_operation_xyz
1         ' X, Y, Z'
2         '-X, Y,-Z+1/2'
3         '-X,-Y,-Z'
4         ' X,-Y, Z+1/2'
5         ' X+1/2, Y+1/2, Z'
6         '-X+1/2, Y+1/2,-Z+1/2'
7         '-X+1/2,-Y+1/2,-Z'
8         ' X+1/2,-Y+1/2, Z+1/2'

  would be nicer as 

loop_
         _space_group_symop_id
         _space_group_symop_operation_xyz
symop1         ' X, Y, Z'
symop2         '-X, Y,-Z+1/2'
symop3         '-X,-Y,-Z'
symop4         ' X,-Y, Z+1/2'
symop5         ' X+1/2, Y+1/2, Z'
symop6         '-X+1/2, Y+1/2,-Z+1/2'
symop7         '-X+1/2,-Y+1/2,-Z'
symop8         ' X+1/2,-Y+1/2, Z+1/2'



#6L1291>loop_
_tecton_topology_id          # List reference 
_tecton_topology_formula
_tecton_topology_special_details
1 'Ca Cr F5' 'The formula unit'

  would be nicer as:

loop_
_atomSet_topology_id          # List reference 
_atomSet_topology_formula
_atomSet_topology_special_details
atomSet1 'Ca Cr F5' 'The formula unit'



#6L1309># _tecton_topology_atom_label is included for the benefit of the user.  It has
# no parent or child and is not required for CIF management.  The CIF
# identifies the atom by _tecton_topology_atom_id.

  I don't see what possible benefit this _atom_label is for the user. In fact I think things are clearer if you leave it out.



#6L1318>loop_
_tecton_topology_atom_id            # List-reference
_tecton_topology_atom_tecton_id     # Child of _tecton_topology_id
_tecton_topology_atom_label            
_tecton_topology_atom_type_symbol   # Child of _atom_type_symbol
_tecton_topology_atom_valence
_tecton_topology_atom_coord_number  # Number of bonds formed by this atom
_tecton_topology_atom_details
Ca 1 Ca1 Ca  2 7  ?
Cr 1 Cr1 Cr  3 6  ?
F1 1 F1  F  -1 3  ?
F2 1 F2  F  -1 2  ?
F3 1 F3  F  -1 3  ?
F4 1 F4  F  -1 3  ' Related to F1 by crystallographic symmetry'
F5 1 F5  F  -1 2  ' Related to F2 by crystallographic symmetry'

looks nicer as

loop_
_atomSet_topology_atom_id            # List-reference
_atomSet_topology_atom_tecton_id     # Child of _tecton_topology_id            
_atomSet_topology_atom_type_symbol   # Child of _atom_type_symbol
_atomSet_topology_atom_valence
_atomSet_topology_atom_coord_number  # Number of bonds formed by this atom
_atomSet_topology_atom_details
Ca atomSet1 Ca  2 7  ?
Cr atomSet1 Cr  3 6  ?
F1 atomSet1 F  -1 3  ?
F2 atomSet1 F  -1 2  ?
F3 atomSet1 F  -1 3  ?
F4 atomSet1 F  -1 3  ' Related to F1 by crystallographic symmetry'
F5 atomSet1 F  -1 2  ' Related to F2 by crystallographic symmetry'



#6L1393>## the finite bond graph, i.e. that atoms in the tecton from which the
  should be
## the finite bond graph, i.e. those atoms in the tecton from which the



#6L1403>loop_
_tecton_geom_dist_id            # List-reference
_tecton_geom_dist_atom1_id      # Child of _tecton_topology_atom_id
_tecton_geom_dist_atom2_id      # Child of _tecton_topology_atom_id
_tecton_geom dist_distance      # Ideal bond distance in Angstroms
_tecton_geom_dist_valence           # Same as _tecton_topology_bond_valence
_tecton_geom_dist_details
A  Cr F1 1.93  0.48  'Bond distances calculated from bond valences'
B  Cr F4 1.93  0.48  'Bond distances calculated from bond valences'
C  Cr F2 1.84  0.61  'Bond distances calculated from bond valences'
D  Cr F5 1.84  0.61  'Bond distances calculated from bond valences'
E  Cr F3 1.99  0.41  'Bond distances calculated from bond valences'
F  Cr F3 1.99  0.41  'Bond distances calculated from bond valences'
G  Ca F1 2.34  0.26  'Bond distances calculated from bond valences'
H  Ca F1 2.34  0.26  'Bond distances calculated from bond valences'
I  Ca F4 2.34  0.26  'Bond distances calculated from bond valences'
J  Ca F4 2.34  0.26  'Bond distances calculated from bond valences'
K  Ca F2 2.19  0.39  'Bond distances calculated from bond valences'
L  Ca F5 2.19  0.39  'Bond distances calculated from bond valences'
M  Ca F3 2.48  0.18  'Bond distances calculated from bond valences'

 since _dist_id serves no purpose should be

loop_
_atomSet_geom_dist_atom1_id      # Child of _atomSet_topology_atom_id
_atomSet_geom_dist_atom2_id      # Child of _atomSet_topology_atom_id
_atomSet_geom dist_distance      # Ideal bond distance in Angstroms
_atomSet_geom_dist_valence           # Same as _atomSet_topology_bond_valence
_atomSet_geom_dist_details
Cr F1 1.93  0.48  'Bond distances calculated from bond valences'
Cr F4 1.93  0.48  'Bond distances calculated from bond valences'
Cr F2 1.84  0.61  'Bond distances calculated from bond valences'
Cr F5 1.84  0.61  'Bond distances calculated from bond valences'
Cr F3 1.99  0.41  'Bond distances calculated from bond valences'
Cr F3 1.99  0.41  'Bond distances calculated from bond valences'
Ca F1 2.34  0.26  'Bond distances calculated from bond valences'
Ca F1 2.34  0.26  'Bond distances calculated from bond valences'
Ca F4 2.34  0.26  'Bond distances calculated from bond valences'
Ca F4 2.34  0.26  'Bond distances calculated from bond valences'
Ca F2 2.19  0.39  'Bond distances calculated from bond valences'
Ca F5 2.19  0.39  'Bond distances calculated from bond valences'
Ca F3 2.48  0.18  'Bond distances calculated from bond valences'


#6L1434># Note that atoms F4 and F5 in the molecular unit map onto
  should be
# Note that atoms F4 and F5 in the atomSet map onto



#6L1441>loop_
_map_tecton2crystal_atom_id              # List reference
_map_tecton2crystal_atom_atom_id         # Child of _tecton_topology_atom_id
_map_tecton2crystal_atom_atom_site_label # Child of _atom_site_label
_map_tecton2crystal_atom_symop_id        # Child of _space_group_symop_id
_map_tecton2crystal_atom_trans_x
_map_tecton2crystal_atom_trans_y
_map_tecton2crystal_atom_trans_z
1   Ca  Ca1 1 0 0 0
2   Cr  Cr1 1 0 0 0
3   F1  F1  1 0 0 0
4   F2  F2  1 0 0 0
5   F3  F3  1 0 0 0
6   F4  F1  3 0 0 0
7   F5  F2  3 0 0 0

 should be nicer as:

loop_
_map_atomSet2crystal_atom_atom_id         # Child of _atomSet_topology_atom_id
_map_atomSet2crystal_atom_atom_site_label # Child of _atom_site_label
_map_atomSet2crystal_atom_symop_id        # Child of _space_group_symop_id
_map_atomSet2crystal_atom_trans_x
_map_atomSet2crystal_atom_trans_y
_map_atomSet2crystal_atom_trans_z
Ca  Ca1 symop1 0 0 0
Cr  Cr1 symop1 0 0 0
F1  F1  symop1 0 0 0
F2  F2  symop1 0 0 0
F3  F3  symop1 0 0 0
F4  F1  symop3 0 0 0
F5  F2  symop3 0 0 0



#6L1477>loop_
_map_tecton2crystal_bond_id                # List reference
_map_tecton2crystal_bond_bond_id           # Child of _tecton_topology_bond_id
_map_tecton2crystal_bond_atom_site_label_1 # Child of _atom_site_label
_map_tecton2crystal_bond_symop_1           # Child of _space_group_symop_id 
_map_tecton2crystal_bond_trans_x_1
_map_tecton2crystal_bond_trans_y_1
_map_tecton2crystal_bond_trans_z_1
_map_tecton2crystal_bond_atom_site_label_2 # Child of _atom_site_label
_map_tecton2crystal_bond_symop_2           # Child of _space_group_symop_id 
_map_tecton2crystal_bond_trans_x_2
_map_tecton2crystal_bond_trans_y_2
_map_tecton2crystal_bond_trans_z_2
_map_tecton2crystal_bond_dist               # Observed distance (optional)
_map_tecton2crystal_bond_details
1  Cr.F1       Cr1 1 0 0 0  F1 1 0 0 0    1.918   ?
2  Cr.F4       Cr1 1 0 0 0  F4 1 0 0 0    1.918   ?
3  Cr.F2       Cr1 1 0 0 0  F2 1 0 0 0    1.848   ?
4  Cr.F5       Cr1 1 0 0 0  F5 1 0 0 0    1.848   ?
5  Cr.F3.1     Cr1 1 0 0 0  F3 1 0 0 0    1.940   ?
6  Cr.F3.2     Cr1 1 0 0 0  F3 3 0 0 0    1.940   link

7  Ca.F1.1     Ca1 1 0 0 0  F1 5 0 0 0    2.391   link
8  Ca.F1.2     Ca1 1 0 0 0  F1 6 0 0 0    2.292   link
9  Ca.F4.1     Ca1 1 0 0 0  F4 5 0 -1 0   2.391   link
10 Ca.F4.2     Ca1 1 0 0 0  F4 6 0 -1 0   2.292   link
11 Ca.F2       Ca1 1 0 0 0  F5 1 0 0 0    2.215   ?
12 Ca.F5       Ca1 1 0 0 0  F2 4 1 0 0    2.215   link
13 Ca.F3       Ca1 1 0 0 0  F3 5 0 0 0    2.494   link

  would be nicer as:

loop_
_map_atomSet2crystal_bond_bond_id           # Child of _tecton_topology_bond_id
_map_atomSet2crystal_bond_atom_site_label_1 # Child of _atom_site_label
_map_atomSet2crystal_bond_symop_1           # Child of _space_group_symop_id 
_map_atomSet2crystal_bond_trans_x_1
_map_atomSet2crystal_bond_trans_y_1
_map_atomSet2crystal_bond_trans_z_1
_map_atomSet2crystal_bond_atom_site_label_2 # Child of _atom_site_label
_map_atomSet2crystal_bond_symop_2           # Child of _space_group_symop_id 
_map_atomSet2crystal_bond_trans_x_2
_map_atomSet2crystal_bond_trans_y_2
_map_atomSet2crystal_bond_trans_z_2
_map_atomSet2crystal_bond_dist               # Observed distance (optional)
_map_atomSet2crystal_bond_details
Cr.F1       Cr1 symop1 0 0 0  F1 symop1 0 0 0    1.918   ?
Cr.F4       Cr1 symop1 0 0 0  F4 symop1 0 0 0    1.918   ?
Cr.F2       Cr1 symop1 0 0 0  F2 symop1 0 0 0    1.848   ?
Cr.F5       Cr1 symop1 0 0 0  F5 symop1 0 0 0    1.848   ?
Cr.F3.1     Cr1 symop1 0 0 0  F3 symop1 0 0 0    1.940   ?
Cr.F3.2     Cr1 symop1 0 0 0  F3 symop3 0 0 0    1.940   link
Ca.F1.1     Ca1 symop1 0 0 0  F1 symop5 0 0 0    2.391   link
Ca.F1.2     Ca1 symop1 0 0 0  F1 symop6 0 0 0    2.292   link
Ca.F4.1     Ca1 symop1 0 0 0  F4 symop5 0 -1 0   2.391   link
Ca.F4.2     Ca1 symop1 0 0 0  F4 symop6 0 -1 0   2.292   link
Ca.F2       Ca1 symop1 0 0 0  F5 symop1 0 0 0    2.215   ?
Ca.F5       Ca1 symop1 0 0 0  F2 symop4 1 0 0    2.215   link
Ca.F3       Ca1 symop1 0 0 0  F3 symop5 0 0 0    2.494   link



#6L1545>              5. SAMPLE CIFS WITH COMMENTS REMOVED
  Parts of section 5 are already out of date with respect to the content of section 3




PMR>One of the most important contributions would be to require that EVERY atom is reported.

   Yes I agree with that.

PMR>Are conformers only relevant for disordered structures or might a species such as TNT have one NO2 tecton with three conformations (I would argue against that)
    
   In my view the word 'conformer' is badly chosen. One topology might well correspond to the two opposite enantiomers and perhaps several diastereoisomers.


PMR>It would be useful to see an example of a simple structure without problems, and perhaps one without disorder but either symmetry or multiple molecules. I think the present example is trying to tackle too many problems at once

   I agree that the final document should contain more including simpler examples. I'm prepared to provide some concerned with chiral molecules. At the moment, I think it would not be too helpful to overload an already long text with more examples at the moment.

PMR> There are many groups that are not isomorphic to a point group. They include permutation groups and products. I spent some time many years ago looking at whether such groups could usefully be represented geometrically.

   It sounds as though we should drop the automorphism group.



PMR>> # 3) only one molecule can be described

PMR Response
-------------------
CML can store multi-molecules - e.g. hexane+urea. The problem seems to come from conformers

   There are problems with racemates as well. Of course the racemate is not really 'one molecule' although it is often incorrectly treated as though it were. (i.e. despite the fact that every molecule in a racemate is chiral, most chemists think of the racemate as being achiral!)



PMR>CML is only just starting to tackle the problem of describing molecules as assemblies of fragments. Do your fragments have unfilled valences, dummy atoms, etc.?

   I've come to the opinion that describing the molecules in terms of fragments i.e. TNT formed of substituted benzene, nitro group, etc is the part of the spec which has the least potential practical application. It looks like a chemical decomposition of the molecule. I wondered whether it would not be better to shelve it at least for the time being. I can't think of what practical application I would use it for.  


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