Everyone has been a great help with the questions I had about final
structures, thank you. Now I need to convert the xplor format to pdb
format. I need to change the atom names, add a chainID etc.
I found the PDBTool module command and commands in PDBTool such as
read()
useIupacNames()
setUseChainID()
useChainID()
However, I have not been successful in getting it to write out a file with
the changes. Can someone help me out here.
Here is my script that doesn't seem to work. I have a feeling I am not
using the commands properly because the out.pdb is the same as the
ave.pdbin regards to atom records, names etc.
xplor.parseArguments()
psffile="sh3.psf"
import protocol
protocol.initParams("protein")
proteocol.initStruct(psffile)
from pdbTool import PDBTool
PDBTool("ave.pdb").read()
PDBTool("ave.pdb").useIupacNames()
#I have also tried the setIupacNames and addRemark to no avail.
PDBTool("A").useChainID()
PDBTool("out.pdb").write()
Thanks in advance,
Andrew Severin
Graduate student
Iowa State University
Biophysics, Biochemistry
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