Dear Bob,
glad to hear that!
Thanks a lot, cheers
p.
On 03/21/2013 11:47 PM, Robert Hanson wrote:
Ah, good. I was looking for that an missed it!
Since the clipping of surfaces is completely flexible in Jmol now --
z-clipping of just the surface and not the model, clipping on a sphere
or plane, within a given distance of one or more atoms, clipping based
on mapped data value -- it hardly seems necessary to add per-vertex
translucency. also you can "ghost" the surface in if you want to have
the effect you are describing. This is fairly new; not sure it's well
documented.
Let me adapt the readers to allow for vertex coloring, add that to the
efvet reader, and get back to you.
Bob
On Thu, Mar 21, 2013 at 3:12 PM, Paolo Tosco <[email protected]
<mailto:[email protected]>> wrote:
Dear Bob,
thanks a lot for your answer. Not really a surface format - what I
am doing is re-generate a surface out of Povray data, which
include vertices, faces, and per-vertex aRGB information. I did
that with success with PyMOL using CGO_OBJs, which support
per-vertex color and translucency.
There is a format which is already supported by Jmol which carries
per-vertex RGB information, which is Efvet. Currently RGB fields
are ignored by the parser, but modifying the Efvet format parser
would probably be the least painful way to implement it.
Per-vertex translucency would be a plus - it is nice because you
can "peek" inside without z-clipping the surface.
Thanks again for your interest in this, best regards
p.
On 03/21/2013 08:58 PM, Robert Hanson wrote:
Let's think about how to do this. Generally what we do is to
create a surface and then color it by vertex in a second
"mapping" pass. What you want is to do that in one pass. I don't
see why that would be a problem; we just don't have it in place
right now. Is there a simple format you know of that has vertex
coloring? If so, let's just write a surface reader for that.
But translucency by vertex -- that would take some thinking.
Bob
On Thu, Mar 21, 2013 at 9:40 AM, Paolo Tosco
<[email protected] <mailto:[email protected]>> wrote:
Dear all,
I have been studying the Jmol code trying to find a way to
color the
vertices of a pmesh surface imported in Jmol. As far as I could
understand, it should be doable by defining as many colors as
required,
and then defining the appropriate color indexes for each
vertex. This
should also allow setting a per-vertex alpha value. Is this
correct?
My concern is: maybe I can succeed in implementing a surface
reader to
assign appropriate colors to the surface. But can such a
coloring scheme
fit in the JVXL format and therefore be loadable by a
JSMol-enabled
webserver? Otherwise, my effort would be useless
Any help is very appreciated
Best regards
Paolo
--
==========================================================
Paolo Tosco, Ph.D.
Department of Drug Science and Technology
Via Pietro Giuria, 9 - 10125 Torino (Italy)
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Robert M. Hanson
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Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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==========================================================
Paolo Tosco, Ph.D.
Department of Drug Science and Technology
Via Pietro Giuria, 9 - 10125 Torino (Italy)
Tel:+39 011 670 7680 <tel:%2B39%20011%20670%207680> | Mob:+39 348 5537206
<tel:%2B39%20348%205537206>
Fax:+39 011 670 7687 <tel:%2B39%20011%20670%207687> |
E-mail:[email protected] <mailto:[email protected]>
http://open3dqsar.org |http://open3dalign.org
==========================================================
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<mailto:[email protected]>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
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--
==========================================================
Paolo Tosco, Ph.D.
Department of Drug Science and Technology
Via Pietro Giuria, 9 - 10125 Torino (Italy)
Tel: +39 011 670 7680 | Mob: +39 348 5537206
Fax: +39 011 670 7687 | E-mail: [email protected]
http://open3dqsar.org | http://open3dalign.org
==========================================================
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