For building double stranded RNA stems with the Ideal RNA tool, make them all the same chain ID and a numbering where one strand is offset by say a 100 so I can rigid body an entire double stranded RNA helix into density without breaking the optimal H-bonding between the strands.
Currently ideal RNAs are imported as separate chain IDs, so its not possible to rigid body refine them both at the same time.
Another option is to pop up a dialog box and ask the user for numbering. (But window control/management is so funky in X that it may further clutter the user's desktop or be completely ambiguous to the user what to do next). An example of this is opening an mtz and having the column selector window appear behind(?) the main coot window (at least it does this on my X window setup in OS X). I normally have to hunt for this column selector window when I have multiple windows on my desktop... and the fact that some coot windows don't appear in OSX's expose mode makes it a little more challenging.
Cheers,
F
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Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
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