Defining non-standard residues
Non-standard residue types can be added to the residue library as additional entries. The procedure to add a new residue type to the library is as follows (see also the description of the format of the residue library file):
Create Cartesian coordinates for all atoms of the residue, for example with a molecular graphics program or using the attach and insert commands of the program COFIMA. Bond lengths, bond angles, and chiralities of this structure must be correct but the conformation, i.e. the values of the dihedral angles, does not matter. The coordinates of the overlap atoms at the beginning and at the end of the residue (for example N, CA, and C in amino acids) will also be needed. If the new residue type results from a slight modification of an existing residue type, it is usually most convenient to start from the coordinates of the existing residue type and to modify them. Order the atoms such that their order is compatible with the tree structure of dihedral angles that will be defined, i.e. such that the following two rules are fulfilled:
- A change of a dihedral angle must not affect the positions of the first, second, third, or forth atom in any preceding dihedral angle definition.
- The set of atoms whose positions will be affected by a change of a dihedral angle consists of all atoms following the third atom in the dihedral angle definition up to the fifth (last) atom in the dihedral angle definition (or the end of the main chain for backbone dihedral angles).
Convert the coordinates into the format of the library file (for example with a text editor). Add atom types, connectivities, and the information about diastereotopic partners. Add the dihedral angle definitions to the new entry. These two steps are best done using the library format in which connectivities and angle definitions are given by atom names rather than by atom numbers (see the option names of the write lib command). Make sure that the header line starting with RESIDUE is correct. Add the new entry to (a copy of) the residue library file. Test the new entry, for example in the following way:
- Create a sequence file that contains the new residue type, preferably in the interior of the chain, i.e. not as the first or last residue.
- Using this sequence file and the new residue library in the program CYANA, create angle and coordinate files for a conformer with randomized dihedral angles.
- Start CYANA again (with the same sequence and residue library file), read the previously produced coordinate file, and write again angle and coordinate files without making any minimization.
- Check whether the angles and coordinates produced by the second run of CYANA coincide closely with those from the first run. If this test fails, then there is probably a format error in the new library entry or the ordering rules listed above are violated. However, this test does not detect errors in nomenclature, connectivities, or pointers to pseudo atoms.
- Check the coordinates produced by CYANA on a molecular graphics system, for example with the program MOLMOL (Koradi et al., 1996).