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 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
>
>
> ------------------------------------------------------------------------------
> 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
>
>
--
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
