Thanks a lot for your suggestions!
The script is modified as below for testing one set of RDCs:
###########
ptensor = create_VarTensor('gel')
ptensor.setFreedom('varyDa, varyRh')
rdcNH = create_RDCPot("NH",oTensor=ptensor,file='./Restraints/rdc_hn.tbl')
calcTensor(ptensor)
command("" write coordinates output=test.pdb end "")
###########
test.pdb is the starting structure of structureLoop since 7 atoms were
added.
###########
def setRdcForce(k_rdc):
rdcNH.setScale( k_rdc )
calcTensor(ptensor)
print "current tensor: ", ptensor.Da(), ptensor.Rh()
print "(setRdcForce) current k_rdc: ", k_rdc
return
###########
In the manual of varTensorTools:
"If there is an ensemble of structure, a single orientatin tensor is
calculated"
Is it what you said that in denatured ensemble, all conformations only use a
single tensor to calculated their RDCs, thus cause problem in energy
minimization?
Can I have a different set of OO1 PA1 PA2 atoms for each conformer and
obtain (floating) alignment tensor for each one during calculation? Any
suggestions? Thanks a lot!!
Best wishes,
Jie-rong
2008/6/3 <Charles at schwieters.org>:
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>
> Hello Jie-rong--
>
> >
> > I want to put measured RDCs (only in one alignment medium) into this
> script
> > from your distribution now in addition to PRE restraints. However, I
> have
> > some trouble in reading RDC restraints, here is the error message:
> > ##########
> > SELRPN: 1 atoms have been selected out of 2784
> > SELRPN> ( resid 500 and name Z )
> > SELRPN: 1 atoms have been selected out of 2784
> > SELRPN> ( resid 500 and name X )
> > SELRPN: 1 atoms have been selected out of 2784
> > SELRPN> ( resid 500 and name Y )
> > SELRPN: 1 atoms have been selected out of 2784
> > SELRPN> ( resid 2 and name N )
> > SELRPN: 2 atoms have been selected out of 2784
> > %SANI-ERR: more than 1 atom in sel for atom l. Using first:
> > ( resid 2 and name N )
>
> the SANI term doesn't handle averaging- you'll need to use the DIPO (or
> Python RDCPot) for that. I problem with using RDCs for disordered
> proteins is that each ensemble member may have a different alignment
> tensor. Depending on timescales, different portions of the molecule may
> experience different alignment tensors. So use these with care.
>
> Charles
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