[modeller_usage] Restraints to apply for nucleic acid

[Charlotte Habegger-Polomat <chpoloma AT rsvs.ulaval.ca>]

Hello!

Modeller has been quite successful at modelling my protein of interest
and I am very happy with the results. I am now using Modeller to model
my protein in complex with a nucelic acid (tNRA), as there is a homolog
complex of known structure.

The family of models  I obtained is quite good but the nucleic acid
seems a little out of shape. It looks like some of the base pairing
and/or stacking has been lost.

I have been thinking of adding restraints to the modelling process.

Do you have any ideas on the best type of restraints to use (H-bonds,
distance, etc.)?

Thanks!

-Charlotte Habegger-Polomat, Quebec