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Hello Raik--
> >>>
> import psfGen, protocol, pdbTool
> ## see also xplor-2.23/eginput/PSF-generation/addAtoms.py
>
> simWorld.setRandomSeed(5521)
>
> import protocol
> protocol.initTopology(('protein'))
> protocol.initParams(('protein'))
>
> seq = open('01_sequence.txt').read()
>
> psfGen.seqToPSF(seq,seqType='prot',startResid=1)
>
> pdbTool.PDBTool('01_domain1.pdb').read()
> pdbTool.PDBTool('01_domain2.pdb').read()
>
> notKnown=AtomSel("not known")
>
> protocol.addUnknownAtoms()
>
> protocol.fixupCovalentGeom(sel=notKnown)
>
> xplor.command("write psf output=new.psf end")
> pdbTool.PDBTool("system1.pdb").write()
> <<<
>
> The seq content looks like this:
> "GLY VAL GLN VAL GLU THR ILE SER PRO GLY ASP..." and is exactly the
> sequence of PDB 1 plus sequence of the linker plus sequence of PDB 2
> (generated directly from the PDB files).
>
> The first PDB has residue numbering from 1 to N_res, consecutive atom
> numbering from 1 to N_atoms, no H and no END or TER record. The second
> PDB has a residue numbering that starts exactly with N_res +
> len(linker) + 1. I didn't yet adapt the atom numbering but there seems
> to be a problem before that anyway.
>
> The script hangs at protocol.addUnknownAtoms().
It's probably not hung- this routine takes a while. In fact, it will
take a *very* long while if the coordinates for a whole domain/subregion
are not defined. Instead, you should probably do this:
1) generate psf info.
2) genExtendedStructure()
3) initCoords
4) fixupCovalentGeom()
let me know how this works.
Charles
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