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]> 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]> 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)
>> Tel: +39 011 670 7680 <%2B39%20011%20670%207680> | Mob: +39 348
>> 5537206<%2B39%20348%205537206>
>> Fax: +39 011 670 7687 <%2B39%20011%20670%207687> | E-mail:
>> [email protected]
>> http://open3dqsar.org | http://open3dalign.org
>> ==========================================================
>>
>>
>>
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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
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:http://p.sf.net/sfu/appdyn_d2d_mar
>
>
>
> _______________________________________________
> Jmol-users mailing
> [email protected]https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> --
> ==========================================================
> 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
> ==========================================================
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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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