Scripts of the NMRPipe System
pdb2gmc.tcl: Create a DYNAMO Initial/Extended Structure from PDB Sequence Info.

Input Options:

Flag	Argument	Default	Description
`-in`	`pdbName`	`ref.pdb`	Name of Input for Sequence Info.
`-r1`	`firstRes`	`First`	First Residue of Input to Use.
`-rN`	`lastRes`	`Last`	Last Residue of Input to Use.
`-pdb`			Input is PDB Format (Default).
`-tab`			Input is Table with DATA SEQUENCE Info.

Input Modes:

`-protein`			Input is a Protein Sequence.
`-dna`			Input is a DNA Sequence.
`-rna`			Input is an RNA Sequence.
`-seqres`			Use SEQRES Info (-pdb Mode Only). Not implemented yet.

Output Specification:

`-seg`	`segName`	`PROT`	Output Segment Name (Also: DNA RNA).
`-out`	`outName`	`ext.pdb`	Name of PDB Extended Structure Output.
`-gmc`	`gmcName`	`ref.gmc`	GMC Directory Name for Structure.
`-mod`	`modName`	`None`	GMC Modification Text, if Any.
`-r0`	`firstRes`	`First`	Value to Give for Output First ResID.
`-reset`			Reset Output Segment Name to Blanks.
`-nogmc`			Don't Create GMC Tables. Creates GMC Sequence Information Only.

Repeated Use for Multiple Segments:

`-cont`			Sequence Info Will Be Continued.
`-append`			Append Sequence Info to Existing GMC.

Annealing Options:

`-tInit`	`t`	`4000`	Initial Temperature.
`-initSteps`	`iN`	`1000`	Number of Initialization Steps.
`-highSteps`	`hN`	`2000`	Number of High-Temperature Steps.
`-coolSteps`	`cN`	`4000`	Number of Cooling Steps.
`-print`	`pCount`	`10`	Increment for Report Printing.
`-rasmol`	`rCount`	`0`	Increment for Rasmol Drawing.
`-noext`			No Simulated Annealing for Extended PDB. Creates GMC Info Random PDB Only (-nosa).
`-novdw`			No VDW Terms.
`-wireframe`			Use Rasmol Wrireframe Draw Mode.

Backbone Angle Options (Currently, Protein Only):

`-bb`	`bbName`	`None`	Start with Backbone Angles from PDB.
`-nohelix`			Don't Set Final Angles to Helix Values. Backbone Angles will be 'random'.
`-cis`			Identify cis vs trans Peptide Bonds.
`-nocis`			All Peptide Bonds are trans (Default).

Special Options:

`-unk`	`resName`	`gly`	Substitute Name for Unknown Residues.
`-water`	`wCount`	`0`	Number of Water Molecules to Add.
`-frag`	`fLength`	`0`	Homology Fragment Length.
`-offset`	`fOffset`	`0`	Homology Fragment Offset.
`-heme`			Search for Heme to HIS Connections. Requires PDB Input.
`-disu`			Search for Disulfide Bonds. Requires PDB Input.