DEF mdw 13:15 30/Sep/11 0.0.1 prosmart prosmart: comparative structural analysis CPdbDataFile True False True CPdbDataFile True False True Reference CDataFile txt False False CDataFile True True True False CRefmacRestraintsDataFile CString ALIGN_RESTRAIN,ALIGN,RESTRAIN align structures and generate restraints,align structures,generate restraints 1 ALIGN_RESTRAIN Use Prosmart to CString NONE,LIB,HELIX,STRAND No,Use helix and strand,Use ideal helix only,Use representative strand only 1 NONE Perform fragment-based analysis CString 0 0,1,2 1 use mainchain,use CA atoms,superpose mainchain and score CA atoms For alignment CInt Fragment length CFloat Alignment threshold CFloat Helix gap penalty threshold CFloat Helix gap penalty CBoolean True Reward sequence-identical fragments CBoolean True Perform alignment refinement CFloat Procrustes superposition threshold CBoolean False Include backbone atoms in side chain scores CBoolean Allow side chain flips True CBoolean Perform rigid substructure identification True CFloat Procrustes score threshold CFloat Intrafragment rotation score threshold CInt Minimum number of fragments per substructure CFloat Single linkage clustering threshold CFloat Final cluster rigidity CString MAIN,SIDE 1 Main chain atoms only,Main and side chain atoms Generate restaints using CString ALL,BEST 1 all reference chains for all target chains,only the best-matching chain for each target chain Select CBoolean False Include self-restraints CFloat Maximum restraint distance Size of sphere around atom in which restraints can exist CFloat Minimum restraint distance Restraints of length below this value are not included CFloat Default sigma used to weight atomic distance restraints CFloat Minimum allowed sigma CString DEFAULT,CONSTANT,DD 1 'default sigma,constant estimated sigma,distant-dependent estimated sigma Use sigma estimation mode CFloat Procrustes alignment score cutoff for restaints Default 10.0 means this is effectively off CFloat Side chain average score cutoff CFloat Outlier removal threshold multipier of restraint sigma to create cutoff of extreme restaints (default 10.0 is effectivly off) CFloat Linear scale sigmas by factor Default 1.0 - lower values increase effect of restaints CBoolean False Force removal of bonds/angles CString TYPE0,TYPE1,TYPE2 1 Replace existing bond type restraints,Add to existing bond type restraints,External restraints Treat as Refmac restraint type CBoolean False Generate generic self-restraints CBoolean False Generate H-bond or generic restraints CBoolean false Generate restraints for helices (alpha, pi and 3-10) CBoolean False Generate restraints For beta-sheets CBoolean False Generate restraints For 3_10 helices CBoolean False Generate restraints For alpha helices CBoolean False Generate restraints For pi helices CBoolean False Require strict structural conservation to helix/strand fragment CFloat Target restraint value CFloat Minimum interatomic distance for restrained atom-pairs CFloat Maximum interatomic distance for restrained atom-pairs CInt Minimum number of residues between restrained atom-pairs CInt Maximum number of residues between restrained atom-pairs CString TYPE1,TYPE2,TYPE3 1 Only O-N restraints (for helices),O-N And N-O restraints (for main chain and sheets),No selection - all main chain atom pairs Atom type selection CInt Maximum number of bonds per atom CBoolean False Output cluster distance matrices CBoolean True Display angular scores in degrees CBoolean False Output restraints for individual chains CBoolean False Merge all chains within each PDB file CString Regenerate PDB file with single chain ID CBoolean False Structures are NMR/MD ensembles