Hi Robin
Here's my two pence:
> 1)PyMol has that great object/selection/etc list on the right
> hand side, where the user can quickly change the color, style, etc of
> everything displayed
Not in Jmol. There might be something in Jmol-including suites like
Bioclipse.
> 2)Pymol has a "mutation" wizard (actually so does a Package
> called KiNG), where you can select a residue, mutate it, and rotate
> through all the rotamers, in addition it will show collisions as red
> circles
That's hard stuff, as it requires molecular mechanics computation.
Unlikely in Jmol, at least in the present incarnation.
> 3)DSV has a "Hierchy" window, a simple tree browser showing
> the chains, amino acids, atoms. Which allows selections
I think there is enough code base in Jmol for this to be easily
achived by a programmer. It could be a plugin or complement to Jmol.
> 4)PyMol and DSV both have a "sequence" view
There is some code support in Jmol to recognize sequences ("within"
command). I'd bet this is already in place in Bioclipse, but haven't
checked it out.
Others will surely follow with more specific details.
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