Hello Tian--
>
> I am trying to determine a membrane protein structure using the new
> eef-membrane
> script. I downloaded the recent example. I just realize that there is no RDC
> restraints used in the example folder. Does anyone know how to initiate rdc
> restraint in the fold_EEF.py script?
>
> I tried to change if False: ... rdcs= to if True, but it seems that I need to
> input value for tensor. also, I am not sure if this is the correct way with Da
> and Rh determined automatically.
>
In addition to changing that False to True, you will need to specify a
nonzero value of force constant. I suggest changing the snippet to
if True:
from rdcPotTools import create_RDCPot
rdcs = PotList('rdc')
for (name, file, tensor, scale) in [('rdcNH_F', rdcNH1_data, mem, 1)]:
rdc=create_RDCPot(name=name, file=file, oTensor=tensor)
rdc.setScale(scale)
rdc.setThreshold(1.0) # dflt [0.0]
rdc.setShowAllRestraints(1)
rdcs.append(rdc)
pots.append(rdcs)
rampedParams.append(MultRamp(0.05, 5.0, "rdcs.setScale(VALUE)"))
Rhombicity can be optimized by setting
memfreedom="fixAxis, varyDa, varyRh"
And an initial value of Da and rhombicity might be obtain by the
calcDaRh helper distributed with Xplor-NIH.
https://nmr.cit.nih.gov/xplor-nih/doc/current/helperPrograms/calcDaRh.html
best regards--
Charles
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