More details on setting up the molecular axis system

If your original .res file has sensible atom labels, you might be able to easily work out the NEIGHCRYS/DMACRYS internal atom labels, and choose sensible definitions for the axis system.

If you are not sure which atom labels NEIGHCRYS/DMACRYS will use within your molecule, you can run NEIGHCRYS with just the starting .res format file and the covalent bonds specification file, which will give you a fort.21 file with the following section:

Inequivalent basis atoms

atom atomic name input molecule invert
index number name number flag
1 6 C_F1_1____1____ C1 1 F
2 6 C_F1_2____2____ C2 1 F
3 6 C_F1_3____3____ C3 1 F
4 6 C_F1_4____4____ C4 1 F
5 6 C_F1_5____5____ C5 1 F
6 6 C_F1_6____6____ C6 1 F
7 6 C_F1_7____7____ C7 1 F
8 9 F_F1_1____8____ F1 1 F
9 1 H_F1_1____9____ H1 1 F
10 1 H_F1_2____10___ H2 1 F
11 1 H_F1_3____11___ H3 1 F
12 1 H_F1_4____12___ H4 1 F
13 1 H_F1_5____13___ H5 1 F
14 1 H_F1_6____14___ H6 1 F
15 1 H_F1_7____15___ H7 1 F

In this case, the atom that was labelled "C1" in the input .res file is called "C_F1_1____1____" in NEIGHCRYS. Please read the manual for a full desciption of the atom labelling convention within NEIGHCRYS/DMACRYS.

For this example, we will chose the following molecule definition

X LINE C_F1_1____ C_F1_4____ 3
Y PLANE C_F1_1____ C_F1_4____ 3 C_F1_2____ 1

This means that there is 1 molecule, the x-line of the molecule runs parallel to the line joining C_F1_1____ and C_F1_4____, which are 3 bonds apart, and the y-line is perpendicular to this where the xy-plane contains atoms C_F1_1____, C_F1_4____ (which is 3 bonds from C_F1_1____) and C_F1_2____ (which is 1 bond from C_F1_1____. The origin is always at the centre of mass of the molecule, and the z-axis always forms a right-handed set.