[Proteopedia] Surface computation &rendering (changed fromScript compiler error)

Karl Oberholser oberhols at messiah.edu
Tue Feb 3 13:20:33 EST 2009


Eran,
Great!  Very little delay in producing the surface.  Could you change the
orientation so that the view is more into the depth of the pocket.  The
following should give the desired orientation 'moveto /* time, axisAngle */
0 { -825 230 -516 140.78} /* zoom, translation */  205.94 -6.0 8.0  /*
center, rotationRadius */ {24.349142 -1.9670883 46.6426} 110.124054 /*
navigation center, translation, depth */ {0.0 0.0 0.0} -54.660324 7.7672005
50.0;'.
 
Thanks!
 
Karl
 

>>> Eran Hodis <eran.hodis at weizmann.ac.il> 2/3/2009 10:03 AM >>>
Hi Karl,

Ok, fixed the script. Try the green link.

Eran

On Feb 2, 2009, at 10:28 PM, Karl Oberholser wrote:

> Eran,
> The command that gives the desired effect for 'this surface' link is
> 'isosurface surface_cn "../images/b/ba/1kyo_cn.jvxl" backlit'.  The  
> position
> of the structure needs to be the same.
>
> Karl
>
>
>
>>>> Eran Hodis <eran.hodis at weizmann.ac.il> 2/2/2009 10:40 AM >>>
> Karl,
>
> Which green scene link(s) do you want to have recall this jvxl file?
>
> Eran
>
> -----Original Message-----
>> From Karl Oberholser <oberhols at messiah.edu>
> Sent Mon 2/2/2009 5:15 PM
> To Forum for the Proteopedia User Community
> <proteopedialist-for-users at bioinformatics.org>
> Subject Re: [Proteopedia] Surface computation & rendering
> (changedfromScript compiler error)
>
> I have been able to render a surface using a jvxl file.  The Jmol  
> command
> that I used was isosurface surface_cn "../images/b/ba/1kyo_cn.jvxl  
> ".  The
> file url is relative to the url of the page.  When I sent the command
> through the Jmol console, the surface appeared in one or two  
> seconds.  But
> through the green link the rendering take five minutes or more, but  
> then
> ever since last Friday it has been taking all the green links to  
> respond.
>
> Karl
>
>
>>>> Eran Hodis <eran.hodis at weizmann.ac.il> 1/30/2009 3:04 PM >>>
> Karl,
>
> Changed it so that jvxl is now a permitted file upload type.  Give  
> it a
> try.
>
> What Angel said is exactly what we've wanted to do for a while now.   
> We
> know that Proteopedia is not handling surface creation and display
> optimally, both with the  menu offered for creation and manipulation  
> of
> the
> surface in the Scene Authoring Tools, as well as with the fact that  
> the
> surfaces must be recalculated each time rather than having them  
> saved on
> the
> server for quick loading. Now seems like a good time to address the  
> these
> issues on Proteopedia.
>
> Eran
>
> -----Original Message-----
>> From Karl Oberholser <oberhols at messiah.edu>
> Sent Fri 1/30/2009 9:23 PM
> To Forum for the Proteopedia User Community
> <proteopedialist-for-users at bioinformatics.org>
> Subject Re: [Proteopedia] Script compiler error
>
> Eran and Jaim,
> If jvxl could be made to be an acceptable file type for uploading, I  
> think
> that I will be able to display a surface in PP by drawing it using a  
> jvxl
> data file, and thereby avoid the long computation time.  At least I  
> would
> like to try doing it.
>
> Karl
>
>>>> "Angel Herraez" <angel.herraez at uah.es> 1/30/2009 10:05 AM >>>
> I've managed to reach the source of the script files saved for
> scenes. Those contain the isosurface command, as expected.
> So the solution would be to implement in the SAT a way to substitute
> the isosurface generation code for an isosurface loading code, plus
> to save the isosurface to a file on the server.
> Not trivial at all!
>
>
>
> _______________________________________________
> Proteopedialist-for-users mailing list
> Proteopedialist-for-users at bioinformatics.org 
> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users

> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
>
<http://www.bioinformatics.org/pipermail/proteopedialist-for-users/attachments/20090130/5feb3109/attachment.html

> >
> _______________________________________________
> Proteopedialist-for-users mailing list
> Proteopedialist-for-users at bioinformatics.org 
> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users

>
>
> _______________________________________________
> Proteopedialist-for-users mailing list
> Proteopedialist-for-users at bioinformatics.org 
> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users

> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
>
<http://www.bioinformatics.org/pipermail/proteopedialist-for-users/attachments/20090202/f111657f/attachment.html

> >
> _______________________________________________
> Proteopedialist-for-users mailing list
> Proteopedialist-for-users at bioinformatics.org 
> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users

>
>
> _______________________________________________
> Proteopedialist-for-users mailing list
> Proteopedialist-for-users at bioinformatics.org 
> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users

> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
<http://www.bioinformatics.org/pipermail/proteopedialist-for-users/attachments/20090202/cf4f3108/attachment.html

> >
> _______________________________________________
> Proteopedialist-for-users mailing list
> Proteopedialist-for-users at bioinformatics.org 
> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users


Eran Hodis
eran.hodis at weizmann.ac.il 




_______________________________________________
Proteopedialist-for-users mailing list
Proteopedialist-for-users at bioinformatics.org 
http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/proteopedialist-for-users/attachments/20090203/c505fe2d/attachment.html>


More information about the Proteopedialist-for-users mailing list