|
Authors: Alex Nip, Albert Leung, David Wishart Input File FormatThe 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 OutputThe 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
If you have any questions or wish to know more information, please contact |