Difference between revisions of "MSL Programs:getDihedrals"
From MSL-Libraries
Jump to navigationJump to search (Created page with '==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 analyz…') |
(→Options) |
||
| (4 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==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). | + | 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== | ==Options== | ||
| − | --pdb FILE.pdb | + | --pdb FILE.pdb PDB structure to analyze |
| − | --phiPsiTable TABLE | + | --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== | ==Examples== | ||
| Line 28: | Line 43: | ||
| + | |||
| + | 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 | ||
| + | .... | ||
==Source from SourceForge== | ==Source from SourceForge== | ||
Latest revision as of 17:05, 31 March 2010
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 ....
