MSL Programs:getDihedrals - Revision history

Dwkulp: /* Options */

2010-03-31T17:05:18Z

‎Options

Dwkulp: /* Examples */

2010-03-31T17:04:30Z

‎Examples

Dwkulp: /* Examples */

2010-03-31T16:57:32Z

‎Examples

Dwkulp at 16:44, 31 March 2010

2010-03-31T16:44:38Z

Dwkulp: /* Options */

2010-03-31T16:41:16Z

‎Options

Dwkulp: 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…'

2010-03-31T16:40:47Z

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…'

New page

==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).

==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)

==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
....

==Source from SourceForge==

[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/getDihedrals.h?&view=markup getDihedrals.h]

[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/getDihedrals.cpp?&view=markup getDihedrals.cpp]

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[[Documentation|Documentation index]]

← Older revision		Revision as of 17:04, 31 March 2010
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		+
		+
	getDihedrals --pdb ~/Downloads/1MEL.pdb --phiPsiTable ~/software/mslib/tables/phiPsiCounts.txt		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		FILE CHAIN RESNUM RESICODE RESNAME PHI PSI PP-COUNTS PP-PROB PP-PROBALL PP-PROP CHI1 CHI2 CHI3 CHI4

← Older revision		Revision as of 16:57, 31 March 2010
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−		+	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==

@@ Line 6: / Line 6: @@
   --pdb      FILE.pdb    PDB structure to analyze
   --phiPsiTable TABLE    Optional. Takes a phi/psi count table ( one is found in MSLROOT/tables/phiPsiCounts.txt)
 ==Examples==

@@ Line 1: / Line 1: @@
 ==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==