Hi Mark-- I have refreshed the script here:
https://bit.niddk.nih.gov/out/toMark-20231113.py to properly specify and load parameters, and I also made a little fix to the script. thanks-- Charles On Mon, 13 Nov 2023 09:49:15 -0500, Kelly, Mark wrote: > > [1 <multipart/alternative (7bit)>] > [1.1 <text/plain; utf-8 (base64)>] > [1.2 <text/html; utf-8 (base64)>] > 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: > Bad URL Removed - see why - > https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=XPLOR-NIH&A=1 > [2 20231113.txt <text/plain (base64)>] > > 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: > Bad URL Removed - see why - > https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=XPLOR-NIH&A=1 ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
