Hello Charles,
I have uploaded a file called charles.tar.gz under the login of santhu.
Let me know if that did not work out or any other comments.
Thanks
Santhosh
On Wed, Sep 11, 2013 at 10:00 AM, Charles Schwieters wrote:
>
> Hello Santhos--
>
> >
> > My concern is this :
> >
> > The force o
Hello Santhos--
>
> My concern is this :
>
> The force on the conformation whose weight is 0.1 is too low to drive it to
> the minimum. The possible solution is that increase the force constant by
> using rdc.setScale or something similar but that would mean the conformation
> with weight 0.9 w
Hi Charles,
My concern is this :
The force on the conformation whose weight is 0.1 is too low to drive it to
the minimum. The possible solution is that increase the force constant by
using rdc.setScale or something similar but that would mean the
conformation with weight 0.9 would have a large fo
Hello Santhos--
>
> I was able to set up weights during refinement but I have a doubt on how they
> are implemented in the program.
>
> Suppose I have a 2 member ensemble and their weights are assigned as
> [0.9,0.1]. Now while computing the weighted averages of NOE's and RDC's the
> individua
Hi Charles,
I was able to set up weights during refinement but I have a doubt on how
they are implemented in the program.
Suppose I have a 2 member ensemble and their weights are assigned as
[0.9,0.1]. Now while computing the weighted averages of NOE's and RDC's the
individual members contributio
Hello Santhos--
>
> Thanks for the information. I have used rdc.setEnsWeights and
> rdc.useSimEnsWeight = False and the same for NOE.
If you call setEnsWeights, useSimEnsWeight should be set False.
>
> Is there any test script or documentation available for the weight
> optimization facilit
Hi Charles,
Thanks for the information. I have used rdc.setEnsWeights and
rdc.useSimEnsWeight = False and the same for NOE.
Is there any test script or documentation available for the weight
optimization facility? We are working on a similar idea and would like to
know XPLOR's capabilities.
Than
Hello Santhos--
>
> This is more of confirmation than anything.
> I know that RDCpot is a weighted average, where the weights provided by:
>
> #weights is a list of weights
> esim = EnsembleSimulation("ensemble",ensembleSize)
> memberIndex = esim.member().memberIndex()
> esim.setWeights(weight
Hello Charles,
This is more of confirmation than anything.
I know that RDCpot is a weighted average, where the weights provided by:
#weights is a list of weights
esim = EnsembleSimulation("ensemble",ensembleSize)
memberIndex = esim.member().memberIndex()
esim.setWeights(weights)
are used for com
Hello Santhos--
>
> While I was going through example scripts, in eginput/gb3_ensemble and
> comparing against eginput/gb3_rdc [single structure refinements], I found
> some thing that looks weird.
>
> In eginput/gb3_ensemble:
> dyn = ivm.IVM(esim) #manipulator for T-A dynamics
> dynx = ivm.IV
Hello Charles,
While I was going through example scripts, in eginput/gb3_ensemble and
comparing against eginput/gb3_rdc [single structure refinements], I found
some thing that looks weird.
In eginput/gb3_ensemble:
dyn = ivm.IVM(esim) #manipulator for T-A dynamics
dynx = ivm.IVM(esim) #manipulator
Hello Charles,
Thanks. That makes sense and it works. :-)
Good day,
Santhosh
On Tue, Aug 27, 2013 at 12:15 PM, Charles Schwieters wrote:
>
> Hello Santhos--
>
> >
> > I was able to successfully load the pdb files using both loadPDB and
> > initCoords [i generated a psf file using pdb2psf and
Hello Santhos--
>
> I was able to successfully load the pdb files using both loadPDB and
> initCoords [i generated a psf file using pdb2psf and since the psf would be
> the same for all the ensemble simulation members I think thats OK].
>
> But I am not really sure if its doing the right thing
Hi Charles/Gabriel,
I was able to successfully load the pdb files using both loadPDB and
initCoords [i generated a psf file using pdb2psf and since the psf would be
the same for all the ensemble simulation members I think thats OK].
But I am not really sure if its doing the right thing. Just to b
Hello Santhosh--
>
> No I did not load a psf before I loaded the structure.
>
> Should I make a psf file using psfGen [or some tool] and then use
> initCoords?
Well, I think you can simply use protocol.loadPDB instead of the
two-step initStruct/initCoords and do without a psf.
best regards--
Hello Charles,
No I did not load a psf before I loaded the structure.
Should I make a psf file using psfGen [or some tool] and then use
initCoords?
Thanks,
Santhosh
On Tue, Aug 27, 2013 at 8:35 AM, Charles Schwieters
wrote:
>
> Hello Santhosh--
>
> >
> > Thanks for the tip. I am running into w
Hello Santhosh--
>
> Thanks for the tip. I am running into weird error now.
>
> The command protocol.initCoords(fileName) does not recognize any of the atoms
> while protocol.loadPDB(fileName) loads the pdb file correctly. It does not
> make sense as protocol.loadPDB internally calls initCoord
Hi Charles,
Thanks for the tip. I am running into weird error now.
The command protocol.initCoords(fileName) does not recognize any of the
atoms while protocol.loadPDB(fileName) loads the pdb file correctly. It
does not make sense as protocol.loadPDB internally calls initCoords [As I
see from the
Hello Santhosh--
>
> We are trying to refine an ensemble against RDC and NOE data. The ensemble
> size for now is 2. While going through the examples in eginput/gb3_ensemble,
> I have a few questions.
>
> 1). In the script provided, the starting structure for all the ensemble
> members is prov
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