This is a hard thing to do.
Eric Westhof is one of the masters:
http://www-ibmc.u-strasbg.fr/upr9002/westhof/
[log in to unmask] wrote:
> HI ccp4ers, I have to model the structure of a 400nt RNA and I was
> wondering if there was free programs out there, similar to Modeller or
> other 3D prediction program, to predict the structure of my RNA or
> helping to built my pdb model. I have used several programs to model
> the base-pairing and the 2D structure, but for the 3D model, I've been
> googling a lot without success. Any helps will be appreciated. Thanks
>
>
> Jeff
>
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