Thanks. If I'm going to use the initial structure as a restraint, is that
what this line you mentioned does? *potList.append( refRMSD )*
Also, I thought using Talosn restraints would have helped with the proper
folding of the structure as well. I had these line in the script but only
the helices are formed during structure calculations
*# Set up dihedral anglesfrom dihedralPotTools import
create_DihedralPotdihePot =
create_DihedralPot('dihePot',"talosn.tbl")potList.append( dihePot
)highTempParams.append( StaticRamp("dihePot.setScale(10)")
)rampedParams.append( StaticRamp("dihePot.setScale(200)") )*
Adedolapo Ojoawo
On Thu, Dec 7, 2023 at 12:12 PM Charles Schwieters <[email protected]>
wrote:
>
> 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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