[filename].rib

A command input file for the program ribosome.py. Each command must be given on a separate line. Keywords are case insensitive . All white space and tab characters are ignored. All blank lines and lines beginning with a "#" character are ignored.

[TITLE   "string"]
DEFAULT "options"
ALLH
RES ACE
RES "3-letter code" [phi "val"] [psi "val"] [omega "val"][chi1 "val"] [chi2 "val"]
RES "3-letter code" [phi "val"] [psi "val"] [omega "val"][chi1 "val"] [chi2 "val"]
.
.
.
RES NME

The TITLE command permits the input of a title for the molecule. The title may contain white spaces, tabs etc. Only the first 70 characters of the title, including spaces and tabs are printed. This is an optional command.

The DEFAULT command is used to specify the default conformation for the residues. Valid options are:
"ang" "val"
where ang is one of phi,psi,omega,chi1,chi2,chi3,chi4,chi5 and
val is the dihedral angle value.

For example: PHI 120

The RESidue command is used to specify the sequence. Each residue should be on a separate line. This command can also be used to specify the conformation of the residue and will override the default command values. Syntax for options is as above in the DEFAULT command and chi values out to chi5 may be used.

A minimal .rib example is:

TITLE      UBIQUITIN
DEFAULT PHI -120.0
DEFAULT PSI  130.0
ALLH
RES ACE
RES MET
RES GLN
RES ILE
RES PHE
RES VAL
RES LYS
RES THR
RES LEU
RES THR
RES GLY
RES LYS
RES THR
RES ILE
RES THR
RES LEU
RES GLU
RES VAL
RES GLU
RES NME

A more complicated .rib example is:

TITLE   PROTEIN
DEFAULT PHI -120.0
DEFAULT PSI 130.0
ALLH
RES ACE
RES  MET PHI  999.99  PSI 145.00  OMEGA -179.49  CHI1  175.82  CHI2  112.35  CHI3   43.93  CHI4 999.99
RES  THR PHI  -94.12  PSI 130.16  OMEGA  178.77  CHI1  -53.43  CHI2  999.99  CHI3  999.99  CHI4 999.99
RES  TYR PHI -118.91  PSI 150.32  OMEGA  179.21  CHI1  -70.60  CHI2  -77.61  CHI3  999.99  CHI4 999.99
RES  LYS PHI -119.14  PSI 154.06  OMEGA  174.78  CHI1 -166.50  CHI2 -173.64  CHI3 -122.43  CHI4 -49.74
RES  LEU PHI -130.24  PSI 126.59  OMEGA  175.58  CHI1  170.61  CHI2   68.09  CHI3  999.99  CHI4 999.99
RES  ILE PHI -102.91  PSI 122.21  OMEGA -178.00  CHI1  -64.65  CHI2  173.96  CHI3  999.99  CHI4 999.99
RES  LEU PHI -102.99  PSI 122.37  OMEGA  178.22  CHI1  -62.88  CHI2  136.30  CHI3  999.99  CHI4 999.99
RES  ASN PHI -130.49  PSI  61.26  OMEGA  179.26  CHI1  171.08  CHI2   58.40  CHI3  999.99  CHI4 999.99
RES  GLY PHI  -85.39  PSI 179.91  OMEGA -178.79  CHI1  999.99  CHI2  999.99  CHI3  999.99  CHI4 999.99
RES  LYS PHI  -73.01  PSI -36.64  OMEGA -178.19  CHI1  -45.70  CHI2 -174.10  CHI3  -65.64  CHI4  78.64
RES NME

Other examples of .rib files may be found in the Examples section under the "Build Helix" and "Build Sheet" menu items.