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Hello Mueller, Geoffrey (NIH/NIEHS) [E] <mueller3 at niehs.nih.gov> wrote:
>
> I was trying to use the DANI term in conjunction with the refine.py script.
>
> Is the diffusion anisotropy module set up with the python interface, i.e.
> With the potlist and initialize functions? I counldn't find it in the
> python documentation.
>
unfortunately, I don't have helpers for the Python interface yet, so you
must do this manually. Please see the snippets included below.
best regards--
Charles
#first, set up dani potential
xplor.command("""
param @par_axis.pro
end
structure @axis_new.psf end
coor @axis_new_alternate.pdb
evaluate ($kdani = 0.001)
dani
nres=300
class relax
force $kdani
potential harmonic
coef 10.59 1.55 0.01 750 76.00
set echo off message off end
@r2_r1_ein_rho_1ezac_750.tbl
set echo on message on end
end""")
potList.append( XplorPot("DANI") )
rampedParams.append( MultRamp(1,1000,"potList['DANI'].setScale(VALUE)") )
# then make sure you set all IVMs correctly
dyn.group( 'resid 500' )
dyn.hinge( "rotate", 'resid 500' )
minc.group( 'resid 500' )
minc.hinge( "rotate", 'resid 500' )
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