MSL Programs:getDihedrals

getDihedrals

A program to print out the dihedral angles of an input structure. Prints out backbone angles (phi/psi) and side chain angles (chi1-4). Optionally, will analyze each residue and report phi/psi probabilities and propensities, given a table of phi/psi counts. A table of phi/psi counts is provided in MSL ( found in MSLROOT/tables/phiPsiCounts.txt). Another feature is it will print out " ---- MISSING ATOMS ---- " when a side chain is missing expected atoms.

Options

--pdb      FILE.pdb    PDB structure to analyze
--phiPsiTable TABLE    Optional. Takes a phi/psi count table ( one is found in MSLROOT/tables/phiPsiCounts.txt)

Details

Using current phiPsiTable from MSL, which is a 5 degree bin table. Here are the definitions for each column when using phiPsiStatistics flag.

x= residue type
y = phi bin
z = psi bin

PP-COUNTS : #AminoAcids of type x, phi bin y, psi bin z that were found in the database.
PP-PROB       : #AA-Phi-Psi(x,y,z) / #AA(x)
PP-PROP       : 
		  (#AA-Phi-Psi(x,y,z)   / #AA(x)) 
		  ------------------------
		  (#AA-Phi-Psi(all,y,z) / #AA(all))

Examples

> getDihedrals --pdb ~/Downloads/1MEL.pdb
FILE CHAIN RESNUM RESICODE RESNAME PHI PSI CHI1 CHI2 CHI3 CHI4 
1MEL A   2  VAL    0.000    0.000   -48.33 
1MEL A   3  GLN -128.498  151.922   -54.54   175.87     2.40 
1MEL A   4  LEU -136.093  119.977   -67.95  -161.64 
1MEL A   5  GLN -122.931  106.282  -150.95    62.25   -96.60 
1MEL A   6  ALA  -81.301  160.911 
1MEL A   7  SER -147.966  163.295   -65.97 
1MEL A   8  GLY  102.273 -155.926 
1MEL A   9  GLY   74.483  176.706 
1MEL A  10  GLY  134.495 -148.689 
1MEL A  11  SER -120.655  155.091    53.03 
1MEL A  12  VAL -163.582  160.626    49.84 
1MEL A  13  GLN  -84.856  148.937  -174.85   175.80   -96.60 
....

getDihedrals --pdb ~/Downloads/1MEL.pdb --phiPsiTable ~/software/mslib/tables/phiPsiCounts.txt  
FILE CHAIN RESNUM RESICODE RESNAME PHI PSI PP-COUNTS PP-PROB PP-PROBALL PP-PROP CHI1 CHI2 CHI3 CHI4
1MEL A   2  VAL    0.000    0.000     0   0.00   0.00   0.00  -48.33 
1MEL A   3  GLN -128.498  151.922    29   0.00   0.00   1.03  -54.54   175.87     2.40 
1MEL A   4  LEU -136.093  119.977    18   0.00   0.00   0.90  -67.95  -161.64 
1MEL A   5  GLN -122.931  106.282     2   0.00   0.00   0.24 -150.95    62.25   -96.60 
1MEL A   6  ALA  -81.301  160.911    19   0.00   0.00   0.70
1MEL A   7  SER -147.966  163.295    33   0.00   0.00   1.08  -65.97 
1MEL A   8  GLY  102.273 -155.926     0   0.00   0.00   1.00
1MEL A   9  GLY   74.483  176.706     1   0.00   0.00   1.00
1MEL A  10  GLY  134.495 -148.689     0   0.00   0.00   1.00
1MEL A  11  SER -120.655  155.091    14   0.00   0.00   0.51   53.03 
1MEL A  12  VAL -163.582  160.626    21   0.00   0.00   0.81   49.84 
1MEL A  13  GLN  -84.856  148.937    17   0.00   0.00   1.13 -174.85   175.80   -96.60 
....