Re: [Jmol-users] Coloring A molecular dynamically....

[Jonathan G. <gu...@uw...>]

Jay,

I've actually started to work on a general version of this.  Do you  
want to help?  I am at the stage of outlining behavior and figuring  
out the best interface.  Here's what I've thought of so far.  If  your  
are interested in working on this let me know and we'll move the  
discussion to jmol-developers...

Interface:

a) A browser pop-up menu that includes a list of all atoms or residues  
(essentially duplicates the list in the Jmol menu).  This will require  
using callbacks to the applet to get the list of what is in the  
displayed molecule(s).  There are also some issues with making sure  
things update if the displayed molecule changes.

b) The color could be selected using the colorpicker widget that I  
developed for SAGE and is now included for picking the background  
color in the Jmol WebExport tool.  Some examples of how it looks are at:

http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/JmolColorPicker/Jmol%20Color%20Picker%20Test.html

(this example needs some updating but will give you an idea of how the  
color picker behaves.).

Jonathan
On Jun 11, 2010, at 7:36 AM, jmo...@li...  
wrote:

> Message: 1
> Date: Thu, 10 Jun 2010 15:59:59 -0400
> From: Jay Vyas <jay...@gm...>
> Subject: [Jmol-users] Coloring A molecular dynamically....
> To: jmo...@li...
> Message-ID:
> 	<AAN...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi : I want to allow users to color atoms in a protein by selecting  
> the
> residue numbers, and then selecting a color.  Im not sure how to do  
> this in
> dynamically.  For example, I know I could make a
> "select 1-20 ; color yellow" command.  But I want the user to be  
> able to
> select both the residue numbers, and the color.  Anyone know if  
> there is a
> simple way to add this feature using jmol controls ??
> If not, I think some dynamic javascript could do the trick.
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>
> Message: 2
> Date: Thu, 10 Jun 2010 16:15:36 -0500
> From: Robert Hanson <ha...@st...>
> Subject: Re: [Jmol-users] Coloring A molecular dynamically....
> To: jmo...@li...
> Message-ID:
> 	<AAN...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> We have a nice color widget now, and it could be adapted....  
> Jonathan, does
> the color widget allow you to tie it to any script command?
>
> The basic idea is
>
> 1) set a pick callback so you know what residue(s) were clicked. --  
> or I
> guess just use set picking select.
> 2) in response to a color pick -- say it's "[xFF00FF]" you would  
> construct
> the script
>
> var scr = "select within(group, selected);color [xFF00FF]"
>
> and send that to Jmol using
>
> jmolScript(scr)
>

                          Dr. Jonathan H. Gutow
Chemistry Department                                 gu...@uw...
UW-Oshkosh                                           Office:920-424-1326
800 Algoma Boulevard                                 FAX:920-424-2042
Oshkosh, WI 54901
                  http://www.uwosh.edu/facstaff/gutow