Scripts of the NMRPipe System
rama.tcl: display and adjust TALOS prediction results.

Directory Settings:

Flag	Argument	Default	Description
`-talosDir`	`mDir`	`.`	TALOS Main Directory: TALOS_DIR.
`-predDir`	`pDir`	`pred`	Directory of existing predictions.
`-tabDir`	`tDir`	`tab`	Subdirectory of TALOS master tables.

Other Options:

`-in`	`inName`	`None`	Input shifts for predictions.
`-sum`	`sumName`	`pred.tab`	Prediction summary input/output.
`-ref`	`refName`	`None`	PDB Reference (for testing).
`-db`	`dbName`	`talos.tab`	TALOS triplet database file.
`-rand`	`rcName`	`randcoil.tab`	Random coil shifts table.
`-count`	`mc`	`10`	Max match count per triplet.
`-cols`	`cCount`	`10`	Column Count for Sequence Display.
`-first`	`resID1`	`First`	First residue to display.
`-last`	`resIDN`	`Last`	Last residue to display.
`-sd`			Display shift distributions.
`-ras`			Display PDB Reference using RasMol.
`-auto`			Display predictions in progress.

Examples:
Typical inspection:
rama.tcl -in ubiq.tab
Inspection when a PDB structure is known:
rama.tcl -in ubiq.tab -ref ubiq.pdb
Inspection when a PDB structure is known, including Molecular Viewer:
rama.tcl -in ubiq.tab -ref ubiq.pdb -ras
Display predictions in progress while talos.tcl is running:
rama.tcl -in ubiq.tab -auto
See also:
talos.tcl Creates predictions by shift homology.
vina.tcl Summarize predictions in a single table.
Notes:
Option -ras requires that RasMol2 is installed and available
via the command 'rasmol', and that no other instances of RasMol
are using the screen.
RasMol Reference:
Roger Sayle and E. James Milner-White.
RasMol: Biomolecular graphics for all
Trends in Biochemical Sciences (TIBS),
September 1995, Vol. 20, No. 9, p. 374.
http://www.umass.edu/microbio/rasmol

Frank Delaglio, Ph.D.