Thank you for your response Dr. Schwieters,
Unfortunately moving the setThreshold command into the noe potential
declaration did not work (although no error was reported). I've tried
several iterations of the setThreshold command, as can be seen in the
script below, however the structures are still being checked only for
noe violations of .5A.
At present, the only way that I've been able to successfully set the noe
threshold to .15A was to change the default value in noePotTools.py.
I'm sure this problem is simply due to a syntax error on my part
somewhere in the script as I'm only passingly familiar with python,
however I'm unable to find it. I can, however, get everything to work
by manipulating default values, so I think I'll leave the in-depth
troubleshooting for a time when I am not trying to finish my thesis.
Thanks,
Andrew Borgert
# set up NOE potential
noe=PotList('noe')
potList.append(noe)
from noePotTools import create_NOEPot
for (name,scale,file) in [('all',1,"D_R.rst"),
#add entries for additional tables
]:
pot = create_NOEPot(name,file)
# pot.setPotType("soft") - if you think there may be bad NOEs
pot.setScale(scale)
# potList['noe'].setThreshold( 0.15 ) <--- no effect, no error message
# potList['all'].setThreshold( 0.15 ) <--- produced error
potential type 'all' does not exist
noe.setThreshold( 0.15 ) <--- no effect, no
error message
noe.append(pot)
rampedParams.append( MultRamp(5,40, "noe.setScale( VALUE )") )
Charles at Schwieters.org wrote:
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> Hello Andrew--
>
>
>> I am using the eginput/gb1_rdc/refine.py script, and I am noticing a
>> discrepancy in the NOE violation threshold that I set and the threshold
>> listed in the .viols file created by the script. Specifically, I set
>> the violation threshold to .15 A, while all of the .viols files list an
>> noe threshold of of 0.5 A (which is the default value).
>>
>
> To get this to do what you want, you need to set the threshold for each
> noe term individually. The noe setup is thus changed to:
>
>
>> noe=PotList('noe')
>> potList.append(noe)
>> from noePotTools import create_NOEPot
>> for (name,scale,file) in [('all',1,"D_R.rst"),
>> #add entries for additional tables
>> ]:
>> pot = create_NOEPot(name,file)
>> # pot.setPotType("soft") - if you think there may be bad NOEs
>> pot.setScale(scale)
>> potList['noe'].setThreshold( 0.15 )
>> noe.append(pot)
>> rampedParams.append( MultRamp(5,40, "noe.setScale( VALUE )") )
>>
>
> hope this helps--
> Charles
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