Dear Charles,
I incorporated the additional commands, but get a syntax error (below). I
attach the current script (bottom). Did I insert the new commands in the right
place?
Best wishes,
Mark
[TomCatVI:Projects/ZF53/Cyana2Xplor_Zn_auto_20231103_2] markkelly% xplor
C2H2_4.py
Xplor-NIH version 3.5
C.D. Schwieters, J.J. Kuszewski, Progr. NMR Spectr. 48, 47-62 (2006).
N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003).
http://nmr.cit.nih.gov/xplor-nih based on X-PLOR 3.851 by A.T. Brunger
User: markkelly on: TomCatVI.l(darwin/x86_64 ) at: 12-Nov-23 19:55:04
[stdin](1): xplor.execfile('C2H2_4.py')
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/Applications/xplor-nih-3.5/python/trace.py", line 180, in run
exec(cmd, dict, dict)
File "<string>", line 1, in <module>
File "/Applications/xplor-nih-3.5/python/xplorInit.py", line 136, in execfile
code = compile(fh.read(), filename, 'exec')
File "C2H2_4.py", line 91
except protocol.CovalentViolation::
^
SyntaxError: invalid syntax
HEAP: maximum use= 628650 current use= 616818
X-PLOR: total CPU time= 0.1813 s
X-PLOR: entry time at 19:55:04 12-Nov-23
X-PLOR: exit time at 19:55:05 12-Nov-23
[TomCatVI:Projects/ZF53/Cyana2Xplor_Zn_auto_20231103_2] markkelly% cat C2H2_4.py
xplor.parseArguments()
import protocol
protocol.loadPDB("model.pdb")
protocol.initTopology('ion')
import psfGen
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 3he2 end
delete atom 4he2 end
add bond 5ZN+2 1sg
add bond 5ZN+2 2sg
add bond 5ZN+2 3ne2
add bond 5ZN+2 4ne2
add angle 1SG 5ZN+2 2SG
add angle 1SG 5ZN+2 3ne2
add angle 1SG 5ZN+2 4ne2
add angle 2SG 5ZN+2 3ne2
add angle 2SG 5ZN+2 4ne2
add angle 3SG 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 6)
reference=2=(resid 3)
reference=3=(resid 19)
reference=4=(resid 23)
reference=5=(resid 401)
end
""")
protocol.addUnknownAtoms()
except protocol.CovalentViolation::
pass
xplor.command("write psf output=test.psf end")
from pdbTool import PDBTool
PDBTool("test.pdb").write()
> On Nov 12, 2023, at 9:21 AM, Charles Schwieters <[email protected]>
> wrote:
>
>
> Hi Mark--
>
>>
>> thanks for the corrections to the script. I am seeing that the ZN
>> atom does not have valid coordinates (below). I pasted my current
>> script below. Also, is there something I need to do to fix the same
>> errors for the termini, or should I not worry about them.
>>
>
> Please try adding this snippet before writing out the coordinates:
>
> try:
> protocol.addUnknownAtoms()
> except protocol.CovalentViolation::
> pass
>
>
> Charles
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