Hello Charles,
Thanks for your fix on the script, now this problem is solved.
But I met an new problem using the script for a protein-DNA complex. I modified
the script as attachment gen1.py, but in output PDB, both HD1 and HE2 of 2nd
HIS been deleted (I want to delete HE2 only). While I used your script
(attachment gen.py), the problem is fixed, but there is error as below in later
structure calculation:
> "SystemError: xplor-nih error: error reading restraint: selection string
> resid 124 and name HN'' selects no atoms
> PyInterp::command: error executing: >execfile('newRefine_c.py')<
So I compared two output PDBs, there are some different atom names between
them.
The difference between there two scripts only as follows:
in your script:
> import psfGen
>psfGen.pdbToPSF(open('complex1.pdb').read(),startResid=1)
I changed this into:
>import psfGen
>psfGen.seqToPSF(open('protein.seq').read(),startResid=1)
>from atomSelAction import SetProperty
>#dna
>#
>psfGen.seqToPSF("./nuc.seq",startResid=101,seqType='dna',
customRename=True)
>#break
>psfGen.seqToPSF("./nuc2.seq",startResid=113,seqType='dna',
customRename=True)
So can you help me modify the new script (gen1_py) to fix the problem? Thanks
very much.
Best regards,
Qianwen
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simWorld.setRandomSeed(5521)
proteinSeq="""
three character residue name sequence
"""
import psfGen
psfGen.seqToPSF(open('protein.seq').read(),startResid=1)
from atomSelAction import SetProperty
#dna
#
psfGen.seqToPSF("./nuc.seq",startResid=101,seqType='dna',
customRename=True)
#break
psfGen.seqToPSF("./nuc2.seq",startResid=113,seqType='dna',
customRename=True)
import protocol
protocol.initTopology('ion')
xplor.command("""
topology
AUTO ANGLe=False DIHEdral=False END
! patch to create Zn (Cys)2 (His)2
!
! 1 and 2 should be CYS
!
! 3 and 4 should be HIS
presidue ZnC2H2
delete atom 1hg end
delete atom 2hg end
delete atom 3hd1 end
delete atom 4he2 end
add bond 5ZN+2 1sg
add bond 5ZN+2 2sg
add bond 5ZN+2 3nd1
add bond 5ZN+2 4ne2
add angle 1SG 5ZN+2 2SG
add angle 1SG 5ZN+2 3nd1
add angle 1SG 5ZN+2 4ne2
add angle 2SG 5ZN+2 3nd1
add angle 2SG 5ZN+2 4ne2
add angle 3nd1 5ZN+2 4ne2
end
end
!add the Zn2 atom
segment
setup=true
number=401
chain
sequence ZN2 end
end
end
!do patch
patch ZnC2H2 reference=1=(resid 37)
reference=2=(resid 42)
reference=3=(resid 66)
reference=4=(resid 68)
reference=5=(resid 401)
end
""")
protocol.initCoords("complex1.pdb")
protocol.initParams("zn-finger_new.par")
protocol.addUnknownAtoms()
# This next line will change the coordinates somewhat, and may not be a
# good idea.
#
protocol.fixupCovalentGeom(maxIters=100,useVDW=1)
xplor.command("write psf output=new.psf end")
protocol.writePDB("new.pdb")
simWorld.setRandomSeed(5521)
proteinSeq="""
three character residue name sequence
"""
import psfGen
psfGen.pdbToPSF(open('complex1.pdb').read(),startResid=1)
import protocol
protocol.initTopology('ion')
xplor.command("""
topology
AUTO ANGLe=False DIHEdral=False END
! patch to create Zn (Cys)2 (His)2
!
! 1 and 2 should be CYS
!
! 3 and 4 should be HIS
presidue ZnC2H2
delete atom 1hg end
delete atom 2hg end
delete atom 3hd1 end
delete atom 4he2 end
add bond 5ZN+2 1sg
add bond 5ZN+2 2sg
add bond 5ZN+2 3nd1
add bond 5ZN+2 4ne2
add angle 1SG 5ZN+2 2SG
add angle 1SG 5ZN+2 3nd1
add angle 1SG 5ZN+2 4ne2
add angle 2SG 5ZN+2 3nd1
add angle 2SG 5ZN+2 4ne2
add angle 3nd1 5ZN+2 4ne2
end
end
!add the Zn2 atom
segment
setup=true
number=401
chain
sequence ZN2 end
end
end
!do patch
patch ZnC2H2 reference=1=(resid 37)
reference=2=(resid 42)
reference=3=(resid 66)
reference=4=(resid 68)
reference=5=(resid 401)
end
""")
protocol.initCoords("complex1.pdb")
protocol.initParams("zn-finger_new.par")
protocol.addUnknownAtoms()
# This next line will change the coordinates somewhat, and may not be a
# good idea.
#
protocol.fixupCovalentGeom(maxIters=100,useVDW=1)
xplor.command("write psf output=new.psf end")
protocol.writePDB("new.pdb")
