Hi,
I have used classic xplor plane restraints to orient a protein with respect
to a plane. The plane (plnSA_4_ORIENT_4_sl1.pdb below) was created by
setting all the Z coordinates in the protein pdb file to 0. The code for
setup of the plane restraints and the associated flags are shown below under
Xplor plane restraints code. Here three CA atoms along a single helical
stretch are aligned along the plane by undergoing restrained dynamics and
energy minimization. The rest of the script is derived from and very similar
to eginput/prot_prot/sa_cross_tor.inp. The result is as one expects, the
protein moves from its starting position so that the three specified CA
atoms are on the plane plnSA_4_ORIENT_4_sl1.pdb.
I would prefer to use PlaneDistPot instead of the classic plane restraints
and have set up the same type of calculation as above, it is listed below
under PlaneDistPot code. The same protein was used in both cases but in the
second the plane was defined by three atoms of a PHE ring which was not part
of the protein and not contacting it. All code not shown is the same in both
cases. In the PlaneDistPot case the restraints were set to 20+/-2 and the
restrained protein atoms in the starting structure were close to the plane
and did not change position as a result of the calculation. The plane force
constant was set high (1000) and the final SCRI energy was also high. Why
did the protein not move with respect to the plane in this calculation?
Thanks,
Jeff Ellena
Xplor plane restraints code
{* read in the PSF file and initial structure *}
structure @SA_4_ORIENT_4_sl1.psf end
coor @SA_4_ORIENT_4_sl1.pdb
coor disposition=reference @plnSA_4_ORIENT_4_sl1.pdb
vector do (harmonic = 0.0) (all)
vector do (harmonic = -20.0) (resid 145 and name ca)
vector do (harmonic = -20.0) (resid 152 and name ca)
vector do (harmonic = -20.0) (resid 163 and name ca)
restraints harmonic exponent=2 normal=(0 0 1) end
{* set the weights for the experimental and a priori energy terms *}
Later in script the potentials are specified with
flags
exclude *
include bonds angles impr vdw rama harm
end
PlaneDistPot code
{* read in the PSF file and initial structure *}
structure @dsbbandpln3_test.psf end
coor @sa4_o43.pdb
coor @phe3.pdb
!set up the potential term
evaluate ($plane_k=1000.0)
CPYTH "from planeDistTools import create_PlaneDistPot"
! specify plane using equation A x + B y + C z + D = 0 !
CPYTH "c= create_PlaneDistPot"
!this next line can't be longer than 132 characters!
CPYTH "p=c('plane',restraintsFile='p.tbl',oAtom='name CE1 and resi
200',xAtom='name CZ and resi 200',yAtom='name HZ and resi 200')"
CPYTH "planePot=p"
CPYTH "planePot.setShowAllRestraints(True)"
CPYTH "plane_k = float( xplor.command('','plane_k')[0] )"
CPYTH "planePot.setScale(plane_k)"
CPYTH "planePot.setFreedom('fix')"
CPYTH "xplor.simulation.potList().append( planePot )"
{* set the weights for the experimental and a priori energy terms *}
Later in script the potentials are specified with
flags
exclude *
include bonds angles impr vdw rama SCRIpting
end
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