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Hello Sadia--
>
> I wanted to model an RNA-RNA interaction in XPlor between two NMR
> structures. I was wondering is their any standard script I could
> follow to carry out the modelling of the interaction? Any advice would
> be extremely grateful.
>
I assume you have NMR data.
With that assumption, you might try working from
eginput/diffTens/dock/dock.py
adding your NMR data (such as NOE's) and the rna-rna positional database
using
#initialize the nucliotide-nucliotide positional database
xplor.command("@rna_orient.setup")
potList.append(AvePot(XplorPot,"orie") )
rampedParams.append( StaticRamp("potList['ORIE'].setScale(0.2)") )
where the file rna_orient.setup should be based on
eginput/rna_refi/rna_orient.setup
(you will have to edit this file to change the rna pair definitions)
please let me know if you'd like further help.
Charles
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