Hi Charles,
Thanks. Xplor language is really hard for me. My goal is using all my
available chemical shift in structure refinement, not only proton. So it
seems instead of XplorPot term proton chemical shift restraints 'PROT',
Sparta can satisfy my requirement better. Besides, TALOS format is easy to
get.
I tried adding Sparta into my potList to do refinement, by adding this into
my python script:
from spartaPotTools import create_SpartaPot
sparta=create_SpartaPot('sparta',restraints="test.talos",format="TALOS")
potList.append(sparta)
There's no error in output file. However, the .stats file below shows
Sparta potential energy term is 0. Is that because Sparta term is not yet
supported?
type name Energy(dev) RMSD(dev) viols(dev)
Num
PotList TOTAL 6302.13( 66.57) 0.552( 0.003) 33.5( 4.9)
9605
PotList Vgyr 13.88( 0.06) 3.725( 0.008) 0.0( 0.0)
PotList noe 188.00( 5.61) 0.075( 0.001) 3.0( 0.0)
1108
PotList rdc 6.05( 0.38) 0.130( 0.004) 0.0( 0.0)
72
PotList sparta 0.00( 0.00) 0.000( 0.000) 0.0( 0.0)
...
On Tue, May 15, 2018 at 11:21 AM, Charles Schwieters <[email protected]
> wrote:
>
> Hi Qinhong--
>
> >
> > I see Proton Chemical Shift Restraints in Xplor manual. What's its
> corresponding
> > term in Python module? Is there an example showing how to use it?
>
> That is the XPLOR PROT term. In the Python interface you would use it
> like:
>
> from xplorPot import XplorPot
> potList.append( XplorPot('PROT') )
>
> xplor.command('''
>
> ! read chemical shift tables and configure term
> ''')
>
> where examples of the commands to be executed by xplor.command can be
> found in test/protoncshift.inp and test/protoncshift2.inp in the
> Xplor-NIH distribution.
>
> We also have two as-yet unpublished energy terms which have chemical
> shifts as target observables, one based on Sparta and the other on
> Camshift. Example use or these terms can be found in the spartaPot?.py
> and csPotTest.py files in the python/tests directory in the Xplor-NIH
> distribution.
>
> best regards--
> Charles
>
--
Qinhong Yu
Ames' Lab
Department of Chemistry
UC Davis
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