id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1157	need to change initial display of nucleotides	Elaine Meng	Eric Pettersen	"The current initial display of nucleotides has the same issues I wanted to avoid from Chimera… namely a bunch of mysterious blue blocks.  See the attached image, with variations:

(1) current initial display, blue slabs and all-atom ribose.  The problem is that heteroatom coloring is good for atom representations, but the slab color is slaved to that of the base N1, and blue is dark and not good for the slab.  A second problem is that it abstracts the interesting part of the nucleotide and leaves atomic detail for the less interesting part.

(2) all atom… lots of detail but you can see the H-bonds that come with the mmCIF file.

(3) more abstracted tube instead of ribose atoms, more pleasing slab shape (to me :-) ), and slab color the same as the cartoon instead of distracting color-blocking.  I’m not set on the slab shape, the other issues are more important.

(4) most abstracted, nucleotide stubs (half-rungs).  Could also do ladder (full rungs where there are H-bonds) but then the representation of the same structure would vary depending on whether there were H-bonds or not, so I like all-stubs a little better.

I’d vote for any of (2)-(4) over the current (1).  However (3) would require some way of changing slab color without changing the heteroatom coloring.  If we choose something abstracted, nother thing to think about is how to make it easier/more obvious how to switch to showing atoms.
Elaine

from Conrad:
I like (3) but (4) would look good with round caps too.

Other notes:
#1156 use cartoon color for slabs is blocker for (3)
#1155 round caps on stubs pertains to (4)"	defect	closed	major		Depiction		fixed		chimera-programmers				all	ChimeraX