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Hello David--
> How do I modify addAtoms.py (eginput/PSF_generation) to operate on a PDB
> file with the chainid's set? Is it an option to PDBTools or is it set
> when I enter the protein sequence?
Xplor-NIH does not use the ChainID internally. However, when
1) reading a PDB file you can read the ChainID PDB field as the segid
value by
a) specifying useChainID=True in protocol.initCoords. This is the
default behavior for initCoords and also for protocol.loadPDB.
b) setting PDBTool's useChainID value to True, if you're working
directly with a PDBTool.
2) write a PDB file you can write the segid value into the ChainID PDB
field (if it is a single character) by
a) specifying writeChainID=True in protocol.writePDB
b) setting writeChainID to True if you are using a PDBTool.
Please see the documentation for pdbTool and protocol for more
information.
in addAtoms, PDBTool oibjects are used directly, so you would need to
modify the script as shown below. Please let me know if you have
problems.
best regards--
Charles
import protocol
protocol.initTopology(('protein'))
protocol.initParams(('protein'))
import psfGen
psfGen.seqToPSF(seq,seqType='prot',startResid=117)
from pdbTool import PDBTool
reader=PDBTool('start.pdb')
reader.setUseChainID(True)
reader.read()
notKnown=AtomSel("not known")
protocol.addUnknownAtoms(dyn_stepsize=0.01)
protocol.fixupCovalentGeom(sel=notKnown)
xplor.command("write psf output=new.psf end")
writer=PDBTool("new.pdb")
writer.setWriteChainID(True)
writer.write()
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