Hello Adedolapo--
>
> Thanks for your help. My script is running now. However, I am
> getting high Da value and my structures are unfolded. I am trying to
> get a better understanding of the refinement process. I already have
> a starting structure for UBQ from PDB. I am just trying to test my
> script by refining the structure with PCS. So the only input
> restraint is the PCS data. If I have a folded starting structure,
> I'm not sure why the calculations result in an unfolded
> structure.
Probably the PCS data by themselves are insufficient to restrain the
structure. You will likely have to add additional restraints, or
use the initial structure as a restraint:
refRMSD = create_PosDiffPot("refRMSD","name CA or name C or name N",
pdbFile=referencePDB, cmpSel="not name H*")
potList.append( refRMSD )
then it shouldn't change too much.
You can also allow a range of motion using:
refRMSD.setUpperBound(1) # no penalty for up to 1 Angstrom RMSD change
Of course, this will do nothing to preserve local structure. That
could be done using distance and dihedral restraints generated from
the initial structure.
>
> Secondly:
> I already calculated pretty good ax and rh values from paramagpy software and
> I put
> these as my initalTensor in the script like below:
> lanthanides = ['TM'] # list of lanthanide metals
> initialTensors = [(37.116, 14.692)] # list of tensors, specified as tuple
> (Xax, Xrh) 1e-32
> m^3
If you simply add this to the script after pcs = create_RDCPot(...) :
from pcsTools import calcXTensor
calcXTensor( oTensor )
print( oTensor.Da(), oTensor.Rh() )
if you have a reasonable structure, then this will tell you
approximate values for checking your scaling.
> Then I allow the tensors to vary using this line in the script.
> for m in metals.values():
> # m.setFreedom("fixDa, fixRh") #fix tensor Rh, Da, vary orientation
> m.setFreedom("varyDa, varyRh") #vary tensor Rh, Da, vary
> orientation
Initially, I would fix Da, Rh until the calculation is stable. The
tensor orientation would still change, as would the metal position.
>
> VarTensor::setDa: WARNING: abs(Da=4.10873e+07) > DaMax. Resetting to DaMax
This is likely a result of the calculation not being stable- but do
check the Da value computed by calcXTensor.
I hope this helps.
Charles
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