MakeTNT-toolkit User Documentation

MakeTNT-toolkit

Formatting and content of REFMAC restraint dictionaries

Copyright © 2004-2006 Global Phasing Limited

All rights reserved.

This software is proprietary to and embodies the
confidential technology of Global Phasing Limited (GPhL).
Possession, use, duplication or dissemination of the software is
authorised only pursuant to a valid written licence from GPhL.

Author: (2004-2006) M. Brandl

Conversion and editing of REFMAC restraint dictionaries by MakeTNT and EditREFMAC was originally developed using template files generated by commercial software (e.g. CORINA) rather than the mmCIF standard as such. Depending on how you obtain your own REFMAC restraint files, you may find that you cannot use them directly in this release of our software. Please use the guidelines below to check that the formatting of your files is suitable for input to MakeTNT and EditREFMAC.

If you would like us to consider changing our mmCIF input processing in a future release to enable the full flexibility of the CIF-standard to be used, please DO let us know (buster-dev@globalphasing.com).

Do NOT use Multi-line text

Please keep records within one line. Multi-lined semi-column separated text is NOT supported.

Comments

To be on the safe side, please remove all comments from your mmCif input file before submitting to MakeTNT, unless your files seem to process absolutely fine

loop_ keyword, loop headers and looped data

Please DO USE, e.g:
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_es
ACE O C CH3 123.000 3.000
Please DO NOT USE, e.g:
loop_
_chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 ...

Quoted Data

Quotes need to be used consistently between different data categories. The example below will not work in MakeTNT:
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
NAG 'C1' C 0 1.0770 -0.3850 0.1210
NAG 'C2' C 0 -0.2080 0.1120 0.7850
...
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
NAG C1 C2 SING
...

Data items used by MakeTNT -REFMAC

  • chem_comp_atom:
      Required: _chem_comp_atom.atom_id _chem_comp_atom.type_symbol
      Optional: _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z
  • chem_comp_bond:
      Required: _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd
  • chem_comp_angle:
      Required: _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd
  • chem_comp_tor:
      Required: _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.id
      Optional: _chem_comp_tor.period
  • chem_comp_chir:
      Required: _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign
      Currently, chiral volume terms are only translated into TNT-dictionaries, if 3D coordinates are present in the input mmCIF-file
  • chem_comp_plane:
      Required: _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd
    Problem: presence of _chem_comp_plane