Authors: Alex Nip, Albert Leung, David Wishart

Input File Format

The file "infile" is expected to contain the dihedral angle information and can be in one of the following three formats.

Sample 1:

1     MET      360.0     153.6     -179.8 
2     GLN      -93.1     132.6      175.0  
3     PHE     -123.1     -92.6      177.0  
4     MET      -33.7     122.9     -174.0 
5     GLN      -53.1      97.9      177.5  
6     PHE     -123.4     154.6      175.5  
        

Sample 2: single letter IUPAC amino acid code

1     M       360.0      153.6     -179.8
2     Q       -93.1      132.6      175.0
3     F      -123.1      -92.6      177.0
4     M       -33.7      122.9     -174.0
5     Q       -53.1       97.9      177.5
6     F      -123.4      154.6      175.5
        

Sample 3: single letter IUPAC amino acid code with an assumed omega angle of 180°

1     M       360.0      153.6
2     Q       -93.1      132.6
3     F      -123.1      -92.6
4     M       -33.7      122.9
5     Q       -53.1       97.9
6     F      -123.4      154.6
        
The first number nearest to the amino acid is the PHI, followed by the PSI, and lastly the OMEGA value.

Program Output

The output from PepMake is a standard PDB file containing the backbone coordinates.

ATOM     1     N      MET     1     2.067     -1.206      0.000     1.00     1.00 
ATOM     2     CA     MET     1     3.519     -1.436      0.000     1.00     1.00 
ATOM     3     C      MET     1     4.213     -0.073      0.000     1.00     1.00 
ATOM     4     O      MET     1     3.655      0.929     -0.473     1.00     1.00 
ATOM     5     CB     MET     1     3.913     -2.210     -1.259     1.00     1.00
ATOM     6     N      GLN     2     5.420     -0.085      0.536     1.00     1.00 
ATOM     7     CA     GLN     2     >6.26     >1.116      0.642     1.00     1.00 
ATOM     8     C      GLN     2     7.164      1.172     -0.592     1.00     1.00 
ATOM     9     O      GLN     2     7.790      0.171     -0.970     1.00     1.00 
ATOM     10    CB     GLN     2     7.123      1.026      1.903     1.00     1.00 
TER
        

More Information

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