Make interactions darker

Moved opacity up to 0.7 so interaction lines would be darker and more visible.
Add a button for toggline long range interactions

This can turn on or off long range interactions. However this interacts with
the base pair family buttons. So it will only turn them off if the family
button is off as well as turning off the lr button. Not sure this is best
behavior but it is good enough for dev.
Add a data-pdb attribute to the 2D

It's a nicer way of storing what pdb we looking at instead of generating
javascript.
Add basic coloring by RsR

This can now color 2D's by RsR if it exists. This uses the API to get the RsR
values and then can color the 2D. This a very crude version of the needed
functionality.
Merge branch 'dev' of github.com:BGSU-RNA/RNA-3D-Hub into dev
Add a primitive way to select nts by ranges

Similar to the stuff used in R3D Align. I need to consolidate the two things by
having one api end point I understand. Probably just some study of anton's stuff
will do. Also the text box added is not aligned right, but I'm in a rush.
Add motif chainbreak to json output
Rename short tags to ?php echo

The new server does not enable short tags by default.
Fix another short tag.
RNA 3D Hub has been published it is not beta

Remove the beta symbol as this has already been published and there is no reason
to mark it as beta anymore.
Add some js scripts

These scripts were loaded from rna.bgsu.edu without looking at the baseurl. This
was probably done so they can be easily shared across different sites, but this
means this site is not self-contained. This means the content is blocked when
running in the new test server. For this reason I'm adding the scripts to this
site.
Use short tags and load using baseurl

This way we don't point at outside resources making our site more self
contained.
Merge branch 'dev' of github.com:BGSU-RNA/RNA-3D-Hub into dev
Fix links

The links I just added were wrong. Now fixed.
Move jmol

The site was not finding jmol. By moving it we should be able to load it easily.
Filename fix
Add links to NDB from popups as well

It is useful to have links back to NDB as well. This adds them in a bunch of
places.
Update wording

Updating the landing page for the RNA 3D Hub to have cleaner wording.
Fix spelling issue
Merge branch 'dev'