<< >> Contents

FORMAT OF THE MODEL FILE


This file is designed to be the new interface from QUEST3D to commercial molecular modelling packages.

The file format adheres to the STAR/CIF conventions (Hall, Allen and Brown, 1991). As such the file is internally self-documented, consisting of a series of data names followed by data items which may occur in looped lists.

Some data names are not contained in the CIF Core Dictionary (1991) and these are prefaced by "_csd".

Two types of MODEL entry can be saved:

Example 1.

The example shown below has been generated using the ALL setting:

data_DMSNCL01_text
_refine_ls_R_factor_obs 8.60
_csd_average_sigma(C-C) > 0.031A
_csd_matching_status perfect match
_csd_remarks
0.25 ADDED TO ALL COORDINATES TO ALLOW FOR NON-STANDARD ORIGIN
_csd_crystal_conn_bond_tolerance 0.40
........................................................................
loop_
_atom_type_symbol
_atom_type_radius_bond
Cl 0.99
C 0.68
Sn 1.35
........................................................................
data_DMSNCL01_structure
loop_
_csd_atom_site_number
_csd_atom_site_name
_atom_site_type_symbol
_csd_atom_site_chem_conn_nca
_csd_atom_site_chem_conn_nh
_csd_atom_site_chem_conn_charge
_csd_atom_site_crystal_ncon
_csd_atom_site_crystal_residue
_csd_atom_site_orth_x
_csd_atom_site_orth_y
_csd_atom_site_orth_z
 1 CL1 CL 1 0 0 1 1 2.6463 1.9375 4.3198
 2 C1 C 1 0 0 1 1 4.3900 3.8905 1.6188
 3 SN1 SN 1 0 0 4 1 4.3900 1.9375 2.6649
 4 CL1B CL 1 0 0 1 1 6.1337 1.9375 4.3198
 5 C1D C 1 0 0 1 1 4.3900 -0.0155 1.6188
........................................................................
loop_
_csd_crystal_conn_bond_atom_1
_csd_crystal_conn_bond_atom_2
_csd_crystal_conn_bond_type
 1 3 1
 2 3 1
 3 4 1
 5 3 1

For convenience of description dotted lines have been introduced, dividing the entry into 4 sections.

Section1:

The data block delimiter always begins with:

data_refcode_text

This is followed by a set of data items summarising various information in the CSD entry:

	_refine_ls_R_factor_obs
	_csd_average_sigma(C-C)
	_csd_matching_status
	_csd_remarks
	_csd_errors
	_csd_disorder
	_csd_crystal_conn_bond_tolerance

In Ex.1 there are no comments in the CSD entry relating to "errors" or "disorder".

Section 2:

This is a looped list of the element types with their radii (in Å).

	loop_
	_atom_type_symbol
	_atom_type_radius_bond

These radii, together with the bond tolerance in section 1, are used to determine the crystal connectivity. Section 2 completes the general information which is output to all MODEL entries.

Section 3:

The delimiter for MODEL file structural information for the complete CSD entry is:

data_refcode_structure

This is followed by a looped list of crystallographic atom information:

	loop_

_csd_atom_site_number atom serial no. _csd_atom_site_name atom label _atom_site_type_symbol element type _csd_atom_site_chem_conn_nca nca value in chem. conn. _csd_atom_site_chem_conn_nh nh value in chem. conn. _csd_atom_site_chem_conn_charge nch value in chem. conn. _csd_atom_site_crystal_ncon no. of connected atoms _csd_atom_site_crystal_residue crystal residue number _csd_atom_site_orth_x orthogonal x (in Å) _csd_atom_site_orth_y orthogonal y (in Å) _csd_atom_site_orth_z orthogonal y (in Å)

Section 4:

Finally the crystal connectivity is described in a looped list:

	loop_
	_csd_crystal_conn_bond_atom_1		atom serial no. in Section 3
	_csd_crystal_conn_bond_atom_2		atom serial no. in Section 3
	_csd_crystal_conn_bond_type		chemical bond type

Example 2.

The example shown below has been generated using the FRAG setting.

This involved a search for two carbon atoms linked by a triple bond.

data_BASLUC_text
_refine_ls_R_factor_obs 6.50
_csd_average_sigma(C-C) 0.006-0.010A
_csd_matching_status perfect match
_csd_crystal_conn_bond_tolerance 0.40
........................................................................
loop_
_atom_type_symbol
_atom_type_radius_bond
C 0.68
H 0.23
O 0.68
N 0.68
........................................................................
data_BASLUC_fragment_1_of_2
loop_
_csd_atom_site_number
_csd_atom_site_name
_atom_site_type_symbol
_csd_atom_site_chem_conn_nca
_csd_atom_site_chem_conn_nh
_csd_atom_site_chem_conn_charge
_csd_atom_site_crystal_ncon
_csd_atom_site_crystal_residue
_csd_atom_site_orth_x
_csd_atom_site_orth_y
_csd_atom_site_orth_z
 1 C2 C 2 0 0 2 1 25.0170 4.1106 5.7273
 2 C1 C 2 0 0 2 1 24.0156 4.4967 5.2525
........................................................................
loop_
_csd_crystal_conn_bond_atom_1
_csd_crystal_conn_bond_atom_2
_csd_crystal_conn_bond_type
 1 2 3
........................................................................
data_BASLUC_fragment_2_of_2
loop_
_csd_atom_site_number
_csd_atom_site_name
_atom_site_type_symbol
_csd_atom_site_chem_conn_nca
_csd_atom_site_chem_conn_nh
_csd_atom_site_chem_conn_charge
_csd_atom_site_crystal_ncon
_csd_atom_site_crystal_residue
_csd_atom_site_orth_x
_csd_atom_site_orth_y
_csd_atom_site_orth_z
 1 C11 C 2 0 0 2 1 22.8101 4.9405 4.6848
 2 C12 C 2 0 0 2 1 21.7594 5.2822 4.2115
........................................................................
loop_
_csd_crystal_conn_bond_atom_1
_csd_crystal_conn_bond_atom_2
_csd_crystal_conn_bond_type
 1 2 3

For convenience of description dotted lines have been introduced, dividing the entry into 6 sections.

Section 1:

This section contains the same type of information as in Ex.1

Section 2:

This section contains the same type of information as in Ex.1

Section 3:

The delimiter for MODEL file structural information for fragment n of the N crystal fragments located within entry refcode during a 3D search is:

data_refcode_fragment_n_of_N

This is followed by a looped list of crystallographic atom information for fragment 1 of the 2 fragments located in the search (for details see Ex.1).

Section 4:

The crystal connectivity of fragment 1 is described in a looped list.

Section 5:

The delimiter indicates that crystallographic atom information for fragment 2 now follows.

Section 6:

Finally the crystal connectivity of fragment 2 is described in a looped list.

Example 3.

The example shown below has been generated using the ALL setting.

data_KHACDC_text
_refine_ls_R_factor_obs 6.00
_csd_average_sigma(C-C) 0.001-0.005A
_csd_matching_status partial match
_csd_remarks
INTERMOLECULAR HYDROGEN BOND HAS H1 MIDWAY BETWEEN ATOMS O2 AND O2F
_csd_crystal_conn_bond_tolerance 0.40
.......................................................................
loop_
_atom_type_symbol
_atom_type_radius_bond
C 0.68
H 0.20
K 1.33
O 0.68
.......................................................................
data_KHACDC_structure
loop_
_csd_atom_site_number
_csd_atom_site_name
_atom_site_type_symbol
_csd_atom_site_chem_conn_nca
_csd_atom_site_chem_conn_nh
_csd_atom_site_chem_conn_charge
_csd_atom_site_crystal_ncon
_csd_atom_site_crystal_residue
_csd_atom_site_orth_x
_csd_atom_site_orth_y
_csd_atom_site_orth_z
 1 C1 C 3 0 0 3 1 2.0459 1.4073 4.4005
 2 C2 C 2 0 0 2 1 3.3151 1.2940 3.6739
 3 H1 H 1 0 0 2 1 0.0000 1.0900 4.4385
 4 K1 K 0 0 1 0 2 3.8342 3.9153 0.4234
 5 O1 O 1 0 0 1 1 1.9999 2.0370 5.4452
 6 O2 O 1 1 0 2 1 1.0582 0.8193 3.8263
 7 C2F C 2 0 0 2 1 4.3534 1.2940 3.0908
 8 O2F O ? ? ? 2 1 -1.0582 0.8193 5.0507
 9 C1F C 3 0 0 3 1 5.6225 1.4073 2.3643
 10 C1F C ? ? ? 1 1 -2.0459 1.4073 4.4765
 11 O1F O 1 0 0 1 1 5.6685 2.0370 1.3195
 12 O2F O 1 0 -1 1 1 6.6102 0.8193 2.9385
.......................................................................
loop_
_csd_crystal_conn_bond_atom_1
_csd_crystal_conn_bond_atom_2
_csd_crystal_conn_bond_type
 1 2 1
 2 7 3
 3 6 1
 5 1 2
 6 1 1
 7 9 1
 8 3 ?
 9 11 2
 10 8 ?
 12 9 1

For this CSD entry there is only partial matching of the crystal and chemical connectivities - see line 4.

For partially matched and unmatched connectivities certain data items can not be resolved.

These include:

Unresolved data items are indicated by ?

For examples, see atoms 8 and 10 in section 3; also the bond types of bonds 8-3 and 10-8 in section 4.


<< >> Contents