I just want to be clear before I change 50 methods: You need actual colors,
not values that can be mapped to colors, right?
On Thu, Mar 21, 2013 at 6:04 PM, Robert Hanson <[email protected]> wrote:
> 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
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>>>
>>> _______________________________________________
>>> Jmol-users mailing
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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
>>> ==========================================================
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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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>>>
>>>
>>
>>
>> --
>> 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
>
>
--
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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