OK, so there are two things here: JavaScript and Jmol scripts. The
JavaScript just allows interaction on a web page so the user can have some
buttons or menus or links on the page that transmit Jmol script to the
applet.
If you want to try scripts with Integration.java, you can just change the
code in that file and re-run it.
final static String strScript = "delay; move 360 0 0 0 0 0 0 0 4;";
"delay...." -- that's the Jmol script. The scripting documentation is at
http://chemapps.stolaf.edu/jmol/docs. Lots of examples there. It doesn't
have to be very complex. But it can be.
On Mon, Nov 23, 2009 at 8:14 PM, Andy Lu <andylu0...@gmail.com> wrote:
> Are javascripts used only when trying to incorporate it onto html? because
> I want a script for it to able to run in Eclipse. Do I put those scripts in
> the integration.java?
> Do you have any sample examples of a finished script? I am not sure where
> to start.
> Thank you for your explanation!
>
> On Mon, Nov 23, 2009 at 7:50 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> Andy, welcome to Jmol. You are going to find it exceptionally easy to do
>> all the things you suggest.
>>
>> On Sun, Nov 22, 2009 at 7:15 PM, Andy Lu <andylu0...@gmail.com> wrote:
>>
>>> I just started programming with JMol java files and I got the
>>> Integration.java file to work from JMol website.
>>>
>>> I have 5 questions:
>>> 1) How can I set the ball and stick model as the default because when I
>>> tried to open a file through my file I/O and sending a pdb file to it, it
>>> shows up as ribbon.
>>>
>>
>> you just script anything you want. There is a command "set defaultScript"
>> that defines the script that will be run after any file is read. See
>> http://chemapps.stolaf.edu/jmol/docs
>>
>>
>>
>>> 2) Is there a way that I can read another pdb file containing a few
>>> number of residues and highlight only those (halo option) from a bigger
>>> protein file? I tried to put jmolviewer.setSelectionHalos(true); in my
>>> integration.java, but it didn't work.
>>>
>>
>> You should do all your interfacing with jmolviewer.evalString(....) if you
>> can. These are sequenced properly; the other methods are mostly deprecated.
>> You can do just about anything with scripting.
>>
>>
>>
>>> 3) Is there a way that I can have the info about a residue show up when I
>>> move my mouse over it?
>>
>>
>> We call that hovering, and you can catch that with a callback if you want
>> to totally customize it, or you can define a simple "hover label" template
>> that will be filled in for you with basic atom information to your detailed
>> specification. See the documentation for details.
>>
>>
>>>
>>> 4) Is there a way that I can write a code to draw a line connecting 2
>>> selected resides?
>>>
>>
>> draw or measure, depending upon what you want.
>>
>>
>>> 5) I know that there is a BFactor option, what does it do?
>>>
>>
>> there's a column in the PDF file that is the BFactor or temperature data.
>> Not sure about the "option" you are talking about.
>>
>>
>>>
>>> I would greatly appreciated if you can help me with my problems, I really
>>> need some help!
>>>
>>> Thank you!
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>> 30-Day
>>> trial. Simplify your report design, integration and deployment - and
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>>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> _______________________________________________
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>>
>>
>
>
> --
> Andy Lu
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now. http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
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trial. Simplify your report design, integration and deployment - and focus on
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