Hi Charles,
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. Here are the sections of the script where
I loaded the starting structure.
*initialPDB = '1ubqH_S57C_Tm_updated_metalpos.pdb'fastaSEQ =
NonereferencePDB = None*
*# read an existing modelprotocol.loadPDB(initialPDB,
deleteUnknownAtoms=True)protocol.fixupCovalentGeom(maxIters=100, useVDW=1)*
*#a PotList contains a list of potential terms. This is used to specify
which# terms are active during refinement.from potList import
PotListpotList = PotList()# parameters to ramp up during the simulated
annealing protocolfrom simulationTools import MultRamp, StaticRamp,
InitialParamsrampedParams=[]highTempParams=[]# compare atomic Cartesian
rmsd with a reference structure# - backbone / heavy atom RMSDs will be
printed in the output structure filesfrom posDiffPotTools import
create_PosDiffPot# if no reference PDB file is available or specified, it
will use the initial# PDB as reference structureif not referencePDB:
referencePDB = initialPDBrefRMSD = create_PosDiffPot("refRMSD","name CA or
name C or name N", pdbFile=referencePDB,
cmpSel="not name H*")*
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 metalsinitialTensors =
[(37.116, 14.692)] # list of tensors, specified as tuple (Xax, Xrh) 1e-32
m^3*
The unit of the Xax and Xrh from paramagpy is *1E-32 m^3* from paramagpy
but I'm not sure what unit or format XPLOR uses during the calculation.
Also regarding the nomenclature, is there a difference between the
unit/expression of X*ax and Da* or Xrh and rh? I want to make sure that
setting the initial tensor to *[(37.116, 14.692)]* is okay.
I had set the Damax like the below snippet from the script. Could you
please help clarify how the Da and Rh are handled in Xplor during
refinement and what unit is used? I keep getting warnings that my Da values
are exceeding the Damax (the unfolded structure is likely contributing to
this too).
*from varTensorTools import create_VarTensormetals = {}for (metal, tensor)
in zip(lanthanides, initialTensors): oTensor = create_VarTensor(metal)
Xax, Xrh = tensor oTensor.setDaMax(6000)
oTensor.setDa(Xax*10000/(12.0*math.pi)) oTensor.setRh(Xrh/Xax)
metals[metal] = oTensorprint(metals)*
*Then I allow the tensors to vary using this line in the script.*
f
*or m in metals.values(): # m.setFreedom("fixDa, fixRh") #fix
tensor Rh, Da, vary orientation m.setFreedom("varyDa, varyRh")
#vary tensor Rh, Da, vary orientationprotocol.torsionTopology(dyn)# minc
used for final cartesian minimization#minc =
IVM()protocol.initMinimize(minc)for m in metals.values():
m.setFreedom("varyDa, varyRh") #allow all tensor parameters float
here # m.setFreedom("fixDa, fixRh") #fix tensor Rh, Da, vary
orientation passprotocol.cartesianTopology(minc)*
*Here is a sample of the warning:*
VarTensor::setDa: WARNING: abs(Da=4.10873e+07) > DaMax. Resetting to DaMax
*--- Dynamics ---- step= 0 ---- time= 0 ---- delta_t=
0.0065334 --*
| E(kin)+E(poten)= 3613.702 E(kin)= 19.872 temperature= 50.891
|
| E(poten)= 3593.8298201 grad= 9.1798459 ANGL= 1.2924317
|
| BOND= 0.0737858 HBDA= 0.0000000 HBDB= -1.2690000
|
| IMPR= 4.2898050 pcs= 737.8541154 repel= 2.1321972
|
| repel14= 83.4258917 torsionDB= 2766.0305933
|
*------------------------------------------------------------------------------*
*--- Dynamics ---- step= 44 ---- time= 0.20398 ---- delta_t= 0.004774
--*
| E(kin)+E(poten)= 3600.984 E(kin)= 14.814 temperature= 37.937
|
| E(poten)= 3586.1702464 grad= 8.3600760 ANGL= 0.6870755
|
| BOND= 0.2473332 HBDA= 0.0000000 HBDB= -0.3750000
|
| IMPR= 1.8661041 pcs= 737.8422472 repel= 1.9504212
|
| repel14= 86.9663796 torsionDB= 2756.9856856
|
*------------------------------------------------------------------------------*
Thanks for your help
Adedolapo
########################################################################
To unsubscribe from the XPLOR-NIH list, click the following link:
http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
