Dear Charles,
I don't get the indent syntax error anymore with your script, but I now get
what looks like errors for missing '%CODBON-ERR: missing bond parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%"
for what looks like the ligands to the Zn (3, 6, 19 & 23) - see below
I attach your script (I changed to extension to .txt).
Best,
Mark
[TomCatVI:Projects/ZF53/Cyana2Xplor_Zn_auto_20231103_2] markkelly% xplor
20231113.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: 13-Nov-23 06:45:43
[stdin](1): xplor.execfile('20231113.py')
20231113.py(2): xplor.parseArguments()
20231113.py(4): import protocol
20231113.py(5): protocol.loadPDB("model.pdb")
loading pdb file: model.pdb [psf] initCoords: still 7 unknown atomic
coordinates
[coords]
20231113.py(6): protocol.initTopology('ion')
X-PLOR>rtf @TOPPAR:ion.top end
ASSFIL: file /Applications/xplor-nih-3.5/toppar/ion.top opened.
RTFRDR>!contributed by Jack Howarth
RTFRDR>!updated for Xplor-NIH 2007/05/15 CDS
RTFRDR>
RTFRDR>remarks file toppar/ion.top
RTFRDR>remarks topology and masses for common ions
RTFRDR>remarks Dingle atom ion residues are given the name of the element.
RTFRDR>remarks By default the atom will be uncharged (eg. the residue MG will
RTFRDR>remarks contain the atom called MG with zero charge).
RTFRDR>remarks To use the charged species the charge state is appended to
RTFRDR>remarks the atom name (eg to use MG2+ the residue name is MG2, and the
RTFRDR>remarks atom name is MG+2 and has charge +2.0).
RTFRDR>remarks NOTE: not all ionic species are represented
RTFRDR>remarks PDA 02/09/99
RTFRDR>
RTFRDR>set echo=false end
EVALUATE: symbol $LOADFILE set to FALSE (logical)
NEXTCD: condition evaluated as false
EVALUATE: symbol $LOADFILE set to TRUE (logical)
NEXTCD: condition evaluated as true
EVALUATE: symbol $IONTOPOINIT set to TRUE (logical)
RTFRDR> end
X-PLOR>end
20231113.py(8): import psfGen
20231113.py(10): xplor.command("""
X-PLOR>
X-PLOR>
X-PLOR> topology
RTFRDR>
RTFRDR> AUTO ANGLe=False DIHEdral=False END
RTFRDR>
RTFRDR>! patch to create Zn (Cys)2 (His)2
RTFRDR>!
RTFRDR>! 1 and 2 should be CYS
RTFRDR>!
RTFRDR>! 3 and 4 should be HIS
RTFRDR>
RTFRDR> presidue ZnC2H2
RESIDUE>
RESIDUE> delete atom 1hg end
RESIDUE>
RESIDUE> delete atom 2hg end
RESIDUE>
RESIDUE> delete atom 3he2 end
RESIDUE>
RESIDUE> delete atom 4he2 end
RESIDUE>
RESIDUE> add bond 5ZN+2 1sg
RESIDUE>
RESIDUE> add bond 5ZN+2 2sg
RESIDUE>
RESIDUE> add bond 5ZN+2 3ne2
RESIDUE>
RESIDUE> add bond 5ZN+2 4ne2
RESIDUE>
RESIDUE> add angle 1SG 5ZN+2 2SG
RESIDUE>
RESIDUE> add angle 1SG 5ZN+2 3ne2
RESIDUE>
RESIDUE> add angle 1SG 5ZN+2 4ne2
RESIDUE>
RESIDUE> add angle 2SG 5ZN+2 3ne2
RESIDUE>
RESIDUE> add angle 2SG 5ZN+2 4ne2
RESIDUE>
RESIDUE> add angle 3SG 5ZN+2 4ne2
RESIDUE>
RESIDUE> end
RTFRDR>
RTFRDR>end
X-PLOR>
X-PLOR>!add the Zn2 atom
X-PLOR>
X-PLOR>segment
SEGMENT>
SEGMENT>setup=true
SEGMENT>
SEGMENT>number=401
SEGMENT>
SEGMENT>chain
CHAIN>
CHAIN>sequence ZN2 end
CHAIN>
CHAIN>end
SEGMENT>
SEGMENT>end
SEGMNT: 401 residues were inserted into segment " "
SCRATC-warning: STORe selections erased.
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 459(MAXA= 800) NBOND= 462(MAXB= 800)
NTHETA= 822(MAXT= 1600) NGRP= 195(MAXGRP= 200)
NPHI= 52(MAXP= 100) NIMPHI= 258(MAXIMP= 400)
NDON= 0(MAXPAD= 0) NACC= 0(MAXPAD= 0)
NNB= 138(MAXNB= 200)
X-PLOR>
X-PLOR>!do patch
X-PLOR>
X-PLOR>patch ZnC2H2 reference=1=(resid 6)
SELRPN: 11 atoms have been selected out of 459
PATCH>
PATCH> reference=2=(resid 3)
SELRPN: 11 atoms have been selected out of 459
PATCH>
PATCH> reference=3=(resid 19)
SELRPN: 18 atoms have been selected out of 459
PATCH>
PATCH> reference=4=(resid 23)
SELRPN: 18 atoms have been selected out of 459
PATCH>
PATCH> reference=5=(resid 401)
SELRPN: 1 atoms have been selected out of 459
PATCH>
PATCH>
PATCH>end
MAPIC: Atom numbers being modified
%PATCH-ERR: angle 3SG 5ZN+2 4NE2 not found
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 455(MAXA= 800) NBOND= 462(MAXB= 800)
NTHETA= 821(MAXT= 1600) NGRP= 195(MAXGRP= 200)
NPHI= 52(MAXP= 100) NIMPHI= 256(MAXIMP= 400)
NDON= 0(MAXPAD= 0) NACC= 0(MAXPAD= 0)
NNB= 138(MAXNB= 200)
X-PLOR>
X-PLOR>
X-PLOR>
X-PLOR>end
20231113.py(90): try:
20231113.py(91): protocol.addUnknownAtoms()
[stdin](1): xplor.execfile('20231113.py')
%CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
bond energy constant missing.
target bond length missing.
ATOM1: SEGId=" ", RESId="401 ", NAME="ZN+2", CHEMical="ZN+2"
ATOM2: SEGId="A ", RESId="6 ", NAME="SG ", CHEMical="S "
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
bond energy constant missing.
target bond length missing.
ATOM1: SEGId=" ", RESId="401 ", NAME="ZN+2", CHEMical="ZN+2"
ATOM2: SEGId="A ", RESId="3 ", NAME="SG ", CHEMical="S "
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
bond energy constant missing.
target bond length missing.
ATOM1: SEGId=" ", RESId="401 ", NAME="ZN+2", CHEMical="ZN+2"
ATOM2: SEGId="A ", RESId="19 ", NAME="NE2 ", CHEMical="NB "
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
bond energy constant missing.
target bond length missing.
ATOM1: SEGId=" ", RESId="401 ", NAME="ZN+2", CHEMical="ZN+2"
ATOM2: SEGId="A ", RESId="23 ", NAME="NE2 ", CHEMical="NB "
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
BOMLEV= 0 reached. Program execution will be terminated.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Subroutine DIE called . Terminating
20231113.py(92): except protocol.CovalentViolation:
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 137, in execfile
exec(code, globals, locals)
File "20231113.py", line 91, in <module>
protocol.addUnknownAtoms()
File "/Applications/xplor-nih-3.5/python/regularize.py", line 982, in
addUnknownAtoms
addUnknownAtoms_fast(verbose,
File "/Applications/xplor-nih-3.5/python/regularize.py", line 924, in
addUnknownAtoms_fast
fixupCovalentGeom(useVDW=1,maxIters=maxFixupIters,sel=unknownSel,
File "/Applications/xplor-nih-3.5/python/regularize.py", line 523, in
fixupCovalentGeom
minState = fixupLoop(ivm,maxIters,verbose,maxViols,minState)
File "/Applications/xplor-nih-3.5/python/regularize.py", line 217, in
fixupLoop
viols=covalentViols(lSim.fastCommand)
File "/Applications/xplor-nih-3.5/python/regularize.py", line 162, in
covalentViols
ret = [int(xplorCmd(
File "/Applications/xplor-nih-3.5/python/regularize.py", line 162, in
<listcomp>
ret = [int(xplorCmd(
File "/Applications/xplor-nih-3.5/python/wrappers/xplorSimulation.py", line
339, in fastCommand
return self.wrap().fastCommand(c,r)
File "/Applications/xplor-nih-3.5/python/wrappers/xplorWrap.py", line 92, in
fastCommand
return _xplorWrap.XplorWrap_fastCommand(self, *args, **kwargs)
SystemError: xplor-nih error: XplorWrapProc: error. XPLOR interpreter has died.
________________________________
From: Charles Schwieters <[email protected]>
Sent: Monday, November 13, 2023 6:02
To: Kelly, Mark <[email protected]>
Cc: Xplor-NIH mailing list <[email protected]>; Kelly, Mark
<[email protected]>
Subject: Re: Refine CYANA Structure with Cys2, His2 ZN finger
Hi Mark--
It seems like indentation got lost in email formatting. The script
here:
https://urldefense.com/v3/__https://bit.niddk.nih.gov/out/toMark-20231113.py__;!!LQC6Cpwp!ppON2o9BBTCMUJ-qBTgIU-LS2P-K6ticD0gvgc8A4FuoYXxX6HHImCOm0pe-yJ69zxLNsGeZ59Zzm66zxKDT_t4$
should work ok.
Charles
On Sun, 12 Nov 2023 23:00:24 -0500,
Kelly, Mark wrote:
>
> 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).
>
> https://urldefense.com/v3/__http://nmr.cit.nih.gov/xplor-nih__;!!LQC6Cpwp!ppON2o9BBTCMUJ-qBTgIU-LS2P-K6ticD0gvgc8A4FuoYXxX6HHImCOm0pe-yJ69zxLNsGeZ59Zzm66zNJJAx0Q$
> 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
>
########################################################################
To unsubscribe from the XPLOR-NIH list, click the following link:
http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
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
""")
try:
protocol.addUnknownAtoms()
except protocol.CovalentViolation:
pass
xplor.command("write psf output=test.psf end")
from pdbTool import PDBTool
PDBTool("test.pdb").write()
########################################################################
To unsubscribe from the XPLOR-NIH list, click the following link:
http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
