gorex.pl

Usage

usage:   convpdb.pl [options] [PDBfile]
options: [-center] [-translate dx dy dz] [-orient]
         [-rotate m11 m12 m13 m21 m22 m23 m31 m32 m33]
         [-rotatex phi] [-rotatey phi] [-rotatez phi]
         [-biomt num] [-smtry num]
         [-scale factor] [-diff PDBfile] [-difflsqfit] [-add PDBFile]
         [-nmode file amplitude weight]
         [-nmodesample file prefix from to delta] [-skipzero]
         [-sel list] [-exclude list]
         [-chain id] [-model num] [-firstmodel] [-nohetero]
         [-selseq abbrev]
         [-nsel Selection]
         [-merge pdbfile]
         [-renumber start] [-addres value]
         [-renumwatersegs]
         [-match pdbfile]
         [-setchain id] [-setseg id] [-setall]
         [-readseg] [-chainfromseg] [-splitseg] [-alternate]
         [-charmm19] [-amber]
         [-out charmm19 | charmm22 | amber | generic]
         [-genres]
         [-crd] [-crdext] [-crdinp]
         [-segnames]
         [-fixcoo]
         [-ssbond res1:res2[=res1:res2]] [-nossbond]
         [-solvate] [-cutoff value] [-solvcut value]
         [-octahedron] [-cubic]
         [-ions NAME:num[=NAME:num]]
         [-replace PDB:num]
         [-info] [-listseg] [-residues] [-rescount]
         [-fill inx:seq]
         [-mol2]
         [-cleanaux]
         [-setaux1 value] [-setaux2 value]
         [-removeclashes] [-clashes] [-clashcut value]
         [-wrap boxx boxy boxz] [-by chain|atom|system]
         [-reimage cx cy cz]

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