now, are you sure you don't just want to read the property value there? You
have five options:
1 electrostatic_potential
2 hydrophobicity
3 temperature_factor
4 minimum_curvature
5 maximum_curvature
Is there something the color itself adds to that?
Bob
On Thu, Mar 21, 2013 at 5:58 PM, Paolo Tosco <[email protected]> wrote:
> 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]>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
>
>
>
> ------------------------------------------------------------------------------
> 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
------------------------------------------------------------------------------
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
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