Volume 2 Chapter 10 Search Menu SAVE MODEL

Function

SAVE MODEL is used to specify that, for all kept hits, an interface MODEL file is saved.

Remarks

The interface file to be saved by this command is intended for input to external molecular modelling packages.

The command differs from the other SAVE file commands in that it toggles over three settings:

NONE: MODEL file is not to be saved (this is the default)
ALL: MODEL file is to be saved as complete entries for hits which are kept
FRAG: MODEL file is to be saved as kept hit crystal fragments from a geometric search

It should be remembered that if the number of accepted hits is large then sufficient disk space must be available to accommodate the saved output file.
Examples

Ex.1 Suppose that the default is displayed, viz. MODEL NONE

Select MODEL

MODEL NONE is replaced by MODEL ALL enclosed in a red box.

Re-select MODEL to change setting.

A MODEL ALL file will be saved for all hits which are kept.

A sample MODEL file is shown below for entry AACMAL.

data_AACMAL_text
_refine_ls_R_factor_obs 9.20
_csd_average_sigma(C-C) not recorded
_csd_matching_status perfect match
_csd_errors
In ATOM-table atom labels C(1) and C(2) should be interchanged
_csd_crystal_conn_bond_tolerance 0.40
loop_
_atom_type_symbol
_atom_type_radius_bond
C 0.68
O 0.68
N 0.68
Al 1.35
data_AACMAL_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 AL1 Al 4 0 -1 4 1 -0.1316 3.1161 1.5586
 2 O1 O 1 0 0 1 1 -1.9642 2.2837 5.0004
 3 O2 O 2 0 0 2 1 -0.8252 2.5744 3.1661
 4 N1 N 4 0 1 4 2 1.8603 1.4512 -3.1356
 5 C2 C 1 3 0 1 1 -2.4388 4.3251 3.7528
 6 C1 C 3 0 0 3 1 -1.7273 3.0060 4.0323
 7 C3 C 1 3 0 1 1 -1.5797 2.7726 0.2010
 8 C4 C 1 3 0 1 1 1.4633 1.8498 1.2941
 9 C5 C 1 3 0 1 1 0.5009 5.0210 1.6976
 10 C6 C 1 3 0 1 2 0.5439 0.9602 -2.4598
 11 C7 C 1 3 0 1 2 3.0091 0.6452 -2.5642
 12 C8 C 1 3 0 1 2 1.7626 1.1275 -4.6047
 13 C9 C 1 3 0 1 2 2.1056 2.8761 -2.8883
loop_
_csd_crystal_conn_bond_atom_1
_csd_crystal_conn_bond_atom_2
_csd_crystal_conn_bond_type
 1 3 1
 2 6 2
 3 6 1
 4 10 1
 5 6 1
 7 1 1
 8 1 1

Ex2. Suppose that the default is displayed, viz. MODEL NONE

Select MODEL
MODEL NONE is replaced by MODEL ALL enclosed in a red box.
```
Re-select MODEL to change setting.
```
Select MODEL
MODEL ALL is replaced by MODEL FRAG enclosed in a red box.
```
Re-select MODEL to change setting.
```
A MODEL FRAG file will be saved for all hit crystal fragments which are kept.
A sample MODEL file is shown below for a fragment found in the entry AACMAL.

Note

Select SAVE

Please select individual items. (REFC, ASER, FDAT, FCON, FBIB, POSTSCRIPT,
MODEL)

data_AACMAL_text
_refine_ls_R_factor_obs 9.20
_csd_average_sigma(C-C) not recorded
_csd_matching_status perfect match
_csd_errors
In ATOM-table atom labels C(1) and C(2) should be interchanged
_csd_crystal_conn_bond_tolerance 0.40
loop_
_atom_type_symbol
_atom_type_radius_bond
C 0.68
O 0.68
N 0.68
Al 1.35
data_AACMAL_fragment_1_of_1
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 C3 C 1 3 0 1 1 -1.5797 2.7726 0.2010
 2 AL1 Al 4 0 -1 4 1 -0.1316 3.1161 1.5586
 3 C4 C 1 3 0 1 1 1.4633 1.8498 1.2941
 4 C5 C 1 3 0 1 1 0.5009 5.0210 1.6976
 5 O2 O 2 0 0 2 1 -0.8252 2.5744 3.1661
loop_
_csd_crystal_conn_bond_atom_1
_csd_crystal_conn_bond_atom_2
_csd_crystal_conn_bond_type
 1 2 1
 2 5 1
 2 3 1
 2 4 1

Related Command

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Volume 2 Chapter 10 Search Menu SAVE MOL2 .