Allow the user to apply torsional changes (also called dihedral rotations) to a molecule. Such rotations are made around bonds. Two commands are available; one requires a database entry that provides a description of what angles can be changed and what atoms are affected,. The other command allows the user to define a set of linked bonds that will be affected by the torsional rotations. Changes are made via the dials (or mouse equivalents).
A third command, allows the user to flip over the carbonyl oxygen while maintaining the peptide plane
tor_residue <id an atom> or <mol res atom>
This allows one to make dihedral rotations around bonds between pairs of atoms. All of the torsional angles associated with the identified residue can be changed via the dials. The number of dials activated depends on how many angles are defined for the particular residue. Therefore, dial_previous or dial_next may have to be used. Use Yes/No to accept or reject the result.
The program need to know what angles are associated with the residue and how they are defined. This torsional information is kept in the data base as an entry .torsion_information. The distributed version of this information can be loaded from $ODAT/torsion.o and is also in $ODAT/startup.o. It is very easy to add new residues to this entry. For example, a serine residue is encoded as
RESIDUE SER
TORSION PHI -57. C- N CA C C O N+ CB OG
TORSION PSI -47. N CA C N+ N+ O CB OG
TORSION CHI1 -60. N CA CB OG OG
In this residue there are 3 torsion angles (PHI, PSI and CHI1) with preferred values 57., 47., 60 respectively. The first four atom names describe how each angle is defined, the remaining names specify which atoms are affected by the angle. The CHI1 angle is, therefore, defined by looking along the CA-CB bond and measuring the angle subtended by the lines N-CA and CB-OG. Only ther OG atom moves when this angle is changed.
Note that atoms from last and next residues have '-' and '+' signs in their names. In the distributed database, we have chosen to move the N of the next residue as PHI and PSI change. If the list of atoms is too long, you can go into the next line by typing a back-slash character \. Begin the next line with at least 6 spaces for tidiness's sake.
IF YOU DO NOT FOLLOW THE STANDARD ATOMIC NAMING CONVENTION, OR IF YOU HAVE EXTRA ATOMS (E.G. HYDROGENS) IN YOUR RESIDUES, YOU MUST MAKE A NEW VERSION OF .torsion_information.
The program reports atoms that are defined in the torsion database but not present in the residue. If an atom is in the residue but not defined as a moving atom, it will never move.
We would love to receive entries for new types of residues, and will place them on the ftp server for the benefit of other O users.
tor_general <Id 2 connected atoms>
This command allows one to change torsion angles by identifying two atoms that define the angles to be changed. The identified atoms must be connected and there cannot be a ring between them. One angle requres 4 connected atoms, 2 angles needs 5 etc. A maximum of 8 angles can change.
Flip_peptide <id an atom> or <mol res atom>
This is an easy but dirty way to flip peptides, since the peptide group simply is rotated 180° around the Ca - Ca direction. After the flip, the geometry of the peptide group of the current and adjacent residues are slightly distorted. The operation should therefore be followed by a regularization or a database fragment fit. This is an immediate action command, there is no need to accept/reject the new coordinates. If you regret the flip, simply activate the command once more.
You must identify any atom in the residue whose carbonyl oxygen gets flipped. A number of people have identified the nitrogen atom N of the next residue, thinking that will define the peptide. They are surprised to see the 'next' oxygen flip!
.torsion_information Containing the torsion database.