Located in $LINUS24/utils/

Residue descriptor file for use with ribosome.py. The first two residue entries are given below:

# ALANINE
name ala numatm 7
n      1.329  116.200  180.000   -3   -2   -4 + none    N(i)    C(i-1)   CA(i-1)   N(i-1)
ca     1.458  121.700  180.000    1   -3   -2 + omega   CA(i)   N(i)     C(i-1)    CA(i-1)
c      1.525  111.200  -64.000    2    1   -3 + phi     C(i)    CA(i)    N(i)      C(i-1) 
o      1.231  120.800  137.000    3    2    1 + psi     O(i)    C(i)     CA(i)     N(i)
cb     1.521  110.400 -122.000    2    1    3 + chi0    CB(i)   CA(i)    N(i)      C(i)
h      0.997  119.150  180.000    1    2   -3 - none
ha     1.080  110.000 -120.000    2    1    5 - none
# ARGININE
name arg numatm 13
n      1.329  116.200  180.000   -3   -2   -4 + none    N(i)    C(i-1)   CA(i-1)   N(i-1)
ca     1.458  121.700  180.000    1   -3   -2 + omega   CA(i)   N(i)     C(i-1)    CA(i-1)
c      1.525  111.200  -64.000    2    1   -3 + phi     C(i)    CA(i)    N(i)      C(i-1) 
o      1.231  120.800  137.000    3    2    1 + psi     O(i)    C(i)     CA(i)     N(i)
cb     1.530  110.500 -122.000    2    1    3 + chi0    CB(i)   CA(i)    N(i)      C(i)
cg     1.520  114.100  -67.000    5    2    1 + chi1
cd     1.520  111.300  180.000    6    5    2 + chi2
ne     1.460  112.000  180.000    7    6    5 + chi3
cz     1.329  124.200  180.000    8    7    6 + chi4
nh1    1.326  120.000  180.000    9    8    7 + chi5
nh2    1.326  120.000  180.000    9    8   10 + none
h      0.997  119.150  180.000    1    2   -3 - none
ha     1.080  110.000 -120.000    2    1    5 - none

.
.
.

Each residue is described in a Z-matrix style. The first line contains the four letter code for the amino-acid (can be less than four letters long) and the number of the atoms in the residue. Following this are N lines, one for each atom in the residue and the atoms it is connected to with the appropriate geometric variables. The file is free-format with arguments separated by spaces or tabs.

The first line for each residue contains the name and number of atoms in the residue. Thus,

name ala numatm 5

specifies the residue name as ala with 5 atoms in the residue. The residue name may be no longer than 4 characters.

Following the residue name line, there should be a line for each atom describing it's name, it's zmatrix parameters and indicators as to whether it is a default atom, and a pointer to any torsional angle that it may point to. The default descriptor is either a '+' or a '-' symbol, and is used to determine whether the coordinates for the atom are written to the output file. The file supplied has all hydrogens connected to carbons flagged with a '-' symbol. Thus, by default coordinates for these hydrogens are not written. Each line should begin with the atom name which should be four characters or less in length

The z-matrix description of an atom, specifies it's position in internal coordinates with respect to three other atoms, usual called parent, grand-parent and great grandparent. Consider the following description:

o 1.231 120.800 139.000 3 2 1

This line describes the atom with name "o" and specifies the distance between this atom and atom number 3 ( column 5) as 1.231 angstroms( column 2), the angle between this atom, atom number 3 and atom number 2 (column 6) as 120.8 degrees (column 3) and the dihedral between the atoms "o" , 3, 2 and 1 (column 7) as 139.0 degrees (column 4). A negative value in any of the columns 5, 6, or 7 specifies an atom from a previous residue.