set hermiteLevel and smoother cartoons
Jmol 10.9.93 introduces a more sophisticated look for cartoons and other
secondary structure depictions. The smoothness level of the Hermite
curves can be increased or decreased using "set hermiteLevel n" where n
is 0 to 8. The default is 4; 0 returns to the Jmol 10.2 standard flat
ribbons and rough rope-like traces. A word of caution: Setting the
hermite level to 8 can significantly slow processing and possibly result
in out-of-memory conditions.
load 1crn.pdb;restrict none;select *;cartoons on;color structure
moveto 1.0 { 140 -957 -255 50.6} 277.4 {10.5935 10.2105 6.079} 17.4;
set hermitelevel 1
set hermitelevel 2
set hermitelevel 3
set hermitelevel 4
set hermitelevel 5
set hermitelevel 6
set hermitelevel 7
set hermitelevel 8
load 1mbo.cif;restrict none;select *;cartoons on;color structure;select
HEM;wireframe 0.1;color cpk;set hermitelevel 4;moveto 1.0 { 422 126 898
117.4} 192.2 {15.027501 19.463001 6.660001} 35.7;
set hermitelevel 0
------------
I'd like input on what to use as the default. Right now I've set the
defaults to
set hermiteLevel 4
set ribbonAspectRatio 16
set traceAlpha false
The Jmol 10.2 "flat" ribbon look is:
set hermiteLevel 0
set ribbonAspectRatio 0
set traceAlpha false
We need to discuss if this slower but fancier rendering is acceptable as
a default.
This rendering uses a totally different means of rendering than was used
before. Instead of painting a ribbon or other flat surface in 2D, and
instead of using a sequence of spheres to generate a trace, what this
does is create a 3D surface that is displayed using the same mechanism
as for orbitals. (It's a mesh of quadrilaterals.)
It uses significantly more memory, and I'm a bit worried that extremely
large molecules will choke. So please give it a good run-through. You
may notice a bit of jerkiness; this is because the surfaces are being
constructed on the fly, only when needed.
Also, it is set so that if the structure being drawn is very small (low
zoom, far-away small, that is), then it reverts to the simpler
"hermiteLevel 0" mode. This may or may not be effective. The objective
is to speed rendering when you can't see the difference anyway. We need
to test that out.
Something else I added that should make quite a difference for large
systems: There is now a preliminary check to see if the alpha carbon of
a group is well outside the window frame, and if it is, then the whole
group is skipped in terms of rendering. (It may surprise you to learn
that in 10.2 if an atom is far outside the window, it is still
processed, but that's the way it was.) My preliminary tests suggest this
is very effective at high zoom level.
I haven't done the arrow heads, but it's not a big deal to do them as well.
Rockets? Maybe....
Please let me know if you start seeing "render mesh error" in the
console at any time.
Bob
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