On 03/22/2013 12:55 AM, Robert Hanson wrote:
I just want to be clear before I change 50 methods: You need actual
colors, not values that can be mapped to colors, right?
Dear Bob,
sorry for being late in my reply - time zone issues. Yes, I'd need the
actual color. None of those properties would do for me.
Thanks for taking the time to do this, best regards
Paolo
On Thu, Mar 21, 2013 at 6:04 PM, Robert Hanson <[email protected]
<mailto:[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]
<mailto:[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] <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)
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
