Dear All,
I would like to refine the structure of a Zn finger peptide (Cys2, His2) I
calculated in CYANA, in xplor. I modified a script with the CYS/HIS patches
from 2019 I found on the xplor Listserver to test the patches (bottom). I get
some errors (below), is there something I should do differently?
Best,
Mark
[TomCatVI:Projects/ZF53/Cyana2Xplor_Zn_auto_20231103_2] markkelly% xplor
C2H2_2.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: 11-Nov-23 08:55:20
[stdin](1): xplor.execfile('C2H2_2.py')
C2H2_2.py(2): xplor.parseArguments()
C2H2_2.py(4): import protocol
C2H2_2.py(5): protocol.loadPDB("model.pdb")
loading pdb file: model.pdb [psf] initCoords: still 7 unknown atomic
coordinates
[coords]
C2H2_2.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
C2H2_2.py(8): import psfGen
C2H2_2.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: 1 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 8)
SELRPN: 22 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 6)
SELRPN: 11 atoms have been selected out of 459
PATCH>
PATCH> reference=4=(resid 19)
SELRPN: 18 atoms have been selected out of 459
PATCH>
PATCH> reference=5=(resid 23)
SELRPN: 18 atoms have been selected out of 459
PATCH>end
%PATCH-ERR: atom 1HG not found
%PATCH-ERR: atom 3HE2 not found
MAPIC: Atom numbers being modified
%PATCH-ERR: bond 5ZN+2 1SG not found
%PATCH-ERR: bond 5ZN+2 2SG not found
%PATCH-ERR: bond 5ZN+2 3NE2 not found
%PATCH-ERR: bond 5ZN+2 4NE2 not found
%PATCH-ERR: angle 1SG 5ZN+2 2SG not found
%PATCH-ERR: angle 1SG 5ZN+2 3NE2 not found
%PATCH-ERR: angle 1SG 5ZN+2 4NE2 not found
%PATCH-ERR: angle 2SG 5ZN+2 3NE2 not found
%PATCH-ERR: angle 2SG 5ZN+2 4NE2 not found
%PATCH-ERR: angle 3SG 5ZN+2 4NE2 not found
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 457(MAXA= 800) NBOND= 460(MAXB= 800)
NTHETA= 819(MAXT= 1600) NGRP= 195(MAXGRP= 200)
NPHI= 52(MAXP= 100) NIMPHI= 257(MAXIMP= 400)
NDON= 0(MAXPAD= 0) NACC= 0(MAXPAD= 0)
NNB= 138(MAXNB= 200)
X-PLOR>
X-PLOR>
X-PLOR>
X-PLOR>
X-PLOR>end
C2H2_2.py(89): xplor.command("write psf output=test.psf end")
X-PLOR>write psf output=test.psf end
ASSFIL: file test.psf opened.
X-PLOR>end
C2H2_2.py(91): from pdbTool import PDBTool
C2H2_2.py(92): PDBTool("test.pdb").write()
WARNING: PDBTool::writeAtoms: invalid coordinates for atom A 1 TYR HT1
WARNING: PDBTool::writeAtoms: invalid coordinates for atom A 1 TYR HT2
WARNING: PDBTool::writeAtoms: invalid coordinates for atom A 1 TYR HT3
WARNING: PDBTool::writeAtoms: invalid coordinates for atom A 15 HIS HE2
WARNING: PDBTool::writeAtoms: invalid coordinates for atom A 23 HIS HE2
WARNING: PDBTool::writeAtoms: invalid coordinates for atom A 27 THR OT2
WARNING: PDBTool::writeAtoms: invalid coordinates for atom 1 ZN2 ZN+2
HEAP: maximum use= 2304469 current use= 2197557
X-PLOR: total CPU time= 0.5035 s
X-PLOR: entry time at 08:55:20 11-Nov-23
X-PLOR: exit time at 08:55:21 11-Nov-23
SCRIPT
[TomCatVI:Projects/ZF53/Cyana2Xplor_Zn_auto_20231103_2] markkelly% cat C2H2_2.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 8)
reference=2=(resid 3)
reference=3=(resid 6)
reference=4=(resid 19)
reference=5=(resid 23)
end
""")
xplor.command("write psf output=test.psf end")
from pdbTool import PDBTool
PDBTool("test.pdb").write()
########################################################################
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