Jonathan,
I'm not sure I understand the goal here. Is it to select a single atom or
residue and color it? Is it to select all lysines and color them red? Is it
to select residues 50-73 and color them blue? Is it to find all alpha helices
and color them purple?
Jeff
***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[email protected]
***********************************************
On Jun 11, 2010, at 10:24 AM, Jonathan Gutow wrote:
> 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, [email protected]
> wrote:
>
>> Message: 1
>> Date: Thu, 10 Jun 2010 15:59:59 -0400
>> From: Jay Vyas <[email protected]>
>> Subject: [Jmol-users] Coloring A molecular dynamically....
>> To: [email protected]
>> Message-ID:
>> <[email protected]>
>> 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.
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 10 Jun 2010 16:15:36 -0500
>> From: Robert Hanson <[email protected]>
>> Subject: Re: [Jmol-users] Coloring A molecular dynamically....
>> To: [email protected]
>> Message-ID:
>> <[email protected]>
>> 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 [email protected]
> UW-Oshkosh Office:920-424-1326
> 800 Algoma Boulevard FAX:920-424-2042
> Oshkosh, WI 54901
> http://www.uwosh.edu/facstaff/gutow
>
>
>
>
>
>
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