please explain the following statement
document.location.search.split("JMOLJAR=")[1].split("&")[0] ;
On Fri, Nov 27, 2009 at 11:29 PM,
<jmol-users-requ...@lists.sourceforge.net>wrote:
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> Today's Topics:
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> 1. Re: Questions about basic JMol featuers (Robert Hanson)
> 2. synchronisation of two but not all applets (Julia Fischer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 24 Nov 2009 11:35:20 -0600
> From: Robert Hanson <hans...@stolaf.edu>
> Subject: Re: [Jmol-users] Questions about basic JMol featuers
> To: jmol-users@lists.sourceforge.net
> Message-ID:
> <ba9c0bd60911240935i6412c30epf31f6e54698c9...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> set drawHover on
> set defaultColorScheme JMOL
>
>
>
> On Mon, Nov 23, 2009 at 11:56 PM, Andy Lu <andylu0...@gmail.com> wrote:
>
> > Thank you so much, the JMol script is really useful!
> >
> > Just one last thing, how come the following is giving me errors:
> > viewer.evalString("defaultColorScheme JMOL;");
> > viewer.evalString("drawHover on;");
> >
> > I am not sure how to set those values. I am sensing I am missing
> something
> > in front of quotes. Thanks once again!
> >
> >
> > On Mon, Nov 23, 2009 at 11:17 PM, Robert Hanson <hans...@stolaf.edu
> >wrote:
> >
> >> 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
> >>>>> 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
> >>>
> >>>
> >>
> >>
> >> --
> >> 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
> >
> >
>
>
> --
> 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
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 2
> Date: Fri, 27 Nov 2009 17:59:18 +0000
> From: Julia Fischer <julia.fisc...@ebi.ac.uk>
> Subject: [Jmol-users] synchronisation of two but not all applets
> To: jmol-users@lists.sourceforge.net
> Message-ID:
> <f84e3340911270959xc56f35ag2978326fd32bc...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I have 4 applets (jmolApplet0, jmolApplet0a, jmolApplet1, jmolApplet1a),
> and
> I would like to synchronize 0 with 0a (both as drivers) and 1 with 1a (both
> as drivers), but the 0s should rotate independent from the 1s. My code is
> below, but for some reason all 4 applets rotate around the same centre of
> gravity all together when I move one. Interestingly the choice of the
> centre
> of gravity depends on which applet I click on first.
>
> What am I doing wrong? Please help.
>
> Julia.
>
>
> <script src="jmol/Jmol.js
> <view-source:
> http://wwwdev.ebi.ac.uk/thornton-srv/databases/CoFactor_dev/jmol/Jmol.js>"
> type="text/javascript"></script>
>
> <script type="text/javascript">
> jmolInitialize("jmol");
> jmolSetAppletColor("white");
>
> jmolApplet(400, "script jmolscripts/0.jmol", "0");
> </script>
>
> <script src="jmol/Jmol.js
> <view-source:
> http://wwwdev.ebi.ac.uk/thornton-srv/databases/CoFactor_dev/jmol/Jmol.js>"
> type="text/javascript"></script>
>
> <script type="text/javascript">
> jmolInitialize("jmol");
> jmolSetAppletColor("white");
>
> jmolApplet(400, "script jmolscripts/0a.jmol" , "0a");
> jmolScript("sync jmolApplet0","0a");
> </script>
>
>
> <script src="jmol/Jmol.js
> <view-source:
> http://wwwdev.ebi.ac.uk/thornton-srv/databases/CoFactor_dev/jmol/Jmol.js>"
> type="text/javascript"></script>
>
> <script type="text/javascript">
> jmolInitialize("jmol");
> jmolSetAppletColor("white");
>
> jmolApplet(400, "script jmolscripts/1.jmol", "1");
> </script>
>
> <script src="jmol/Jmol.js
> <view-source:
> http://wwwdev.ebi.ac.uk/thornton-srv/databases/CoFactor_dev/jmol/Jmol.js>"
> type="text/javascript"></script>
>
> <script type="text/javascript">
> jmolInitialize("jmol");
> jmolSetAppletColor("white");
>
> jmolApplet(400, "script jmolscripts/1a.jmol" , "1a");
> jmolScript("sync jmolApplet1","1a");
> </script>
>
> --
> Julia Fischer
> EBI - Thornton group (julia.fisc...@ebi.ac.uk)
> -------------- next part --------------
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>
> ------------------------------
>
>
> ------------------------------------------------------------------------------
> 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
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>
>
> End of Jmol-users Digest, Vol 42, Issue 26
> ******************************************
>
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