6.9 Add hydrogens
In order to add hydrogens to a
molecule, you can use a specific dialog that can be shown by Edit
Add
Hydrogens main menu item:
6.9.1 Dialog options
In this dialog, you can select the molecule type (Generic organic,
Protein, Nucleic acid), the nomenclature type (normal progressive
number or IUPAC nomenclature), the possibility to process the selected atoms only (Consider
selected atoms only) and where the hydrogens are placed in the molecule file
(After each heavy atom or at Residue end). Check Use the bond
order to assign the atom types if the molecule has uncertain geometry (e.g.
2D instead of 3D structure) and the bond order is correctly assigned.
Finally, you user must click Add to
add the hydrogens.
6.9.2 About the method
To add hydrogens, the recognition of atom types and valences is
needed. The powerful ATDL geometry-independent engine can't be used because the atom valences are
incomplete due to the missing hydrogens and so the implemented method is based
on the original code included in Babel 1.6 (© 1992-96, W. Patrick Walters, Matthew T.
Stahl) that detects the atom valences considering the atomic distances and the
bond angles. Unluckily, this is the method limit, because some structures don't
have a canonical geometry and so the valence detection can be wrong. VEGA
introduces an algorithm that fixes the atom type and the valence detection when
the user specify the type of the molecule. You must remember that this check
is disabled selecting Generic organic molecule type.
The method can be summarized in the following steps:
All hydrogens are removed in order to allow the correct atom type detection.
Atom type and valence attribution: the atom types are detected using the Meng convention (E. Meng and R. Lewis, J. Comp. Chem., 12, pp 891-898, 1991) updating it with Nim atom type to detect the nitrogens in five member rings.
Optionally, to fix the incorrect atom types, VEGA ZZ uses two templates (NA.hyb for nucleic acids and PROTEIN.hyb for proteins) placed in the Data directory. They are text files witch format is explained in the header.
The required hydrogens are placed and bonded.