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Hello Jeff--
> 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?
>
Of course, using the Python interface would make this much easier to
figure out...
As it is, I'm not sure what's wrong. It's possible there's a bug, but
please see below.
>
> 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 )"
>
you might print out the analysis with this:
CPYTH "from simulationTools import analyze"
CPYTH "print analyze(planePot)"
Are you using the ivm? How is it set up?
best regards--
Charles
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