Scripts of the NMRPipe System
talos.tcl: predicts angles from chemical shift homology.

Directory Settings:
Flag Argument Default Description
 -talosDir mDir . TALOS Main Directory: TALOS_DIR.
 -shiftDir sDir shifts Subdirectory of master shifts.
 -pdbDir pDir pdb Subdirectory of master structures.
 -tabDir tDir tab Subdirectory of master tables.
 -predDir pDir pred Directory for prediction results.
File Name Settings:
 -in inName None Input Shift Table.
 -sum sumName Prediction Summary Output.
 -homo hName Residue Homology Table.
 -map mName vina.dat Ramachandran Map Name.
 -db dbName TALOS triplet database file.
 -w wName TALOS triplet weighting file.
Random Coil and Secondary Shift Tables:
 -rand rName Random Coil Shift Table.
 -adj aName Adjustment Table. (None for no adjustment).
 -prev pName Previous Residue Adjustment. (None for no adjustment).
 -next nName Next Residue Adjustment. (None for no adjustment).
 -limits lName Secondary Shift Limits. (Used only with -clip).
Other Options:
 -excl eList List of Proteins to Exclude.
 -first resID1 First First RESID to use.
 -last resIDN Last Last RESID to use.
 -thresh tVal 200.0 Max Distance Threshold.
 -count mc 10 Max Match Count per Triplet.
 -clip Clip Extreme Shifts (Default).
 -noclip No Clipping of Shifts.
 -compile Re-compile triplet database.
Allowable Percentage of Undefined Shifts
 -dbpct defPct 59.0 Minimum, Database Triplet.
 -tpct tPct 15.0 Minimum, Target Triplet.
Special Fast-Mode Searching (Only Availble on Some Systems):
 -fast Use Fast Mode When Available (Default).
 -nofast Use Ordinary TCL-Based Search.
 -sleep sTime 5 Sleep Time After Fast Mode Search, Sec.
  talos.tcl -in Form predictions from the given shifts.
  talos.tcl -compile Re-compile the triplet database.
See Also:
  vina.tcl Summarize predictions in a single table.
  rama.tcl Graphical interface to inspect results.

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