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.