Message 2
Re: [Jmol-users] Link Jmol to other programme
Hi, Robert:
Did you mean I cannot link Jmol to other program just by using script in a
running Jmol application. I have to embed Jmol to other program?
I am trying to do the following things using Jmol script.
1. read in 2 structure files
2. call an external program to change the atom order of one structure file
and pass back the new structure file to Jmol
3. Display the 2 structures.
I'd like to know when I use "load" to read in the files in Jmol. How can I
get the information of the structure file? Will Jmol create an object of it
and I can use this object to get all the atom information such as
coordinates and connectivity matrix,etc?
If I can do that, I plan to use "message" command to pass these information
to external program and pass back the result by a call-back function.
Then I can use Jmol to display the structures.
Thank you.
On Tue, Sep 10, 2013 at 9:14 PM,
<[email protected]>wrote:
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> Today's Topics:
>
> 1. Re: JSmol too slow! (Robert Hanson)
> 2. Re: Link Jmol to other programme (Robert Hanson)
> 3. Re: JSmol in wordpress (Robert Hanson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 10 Sep 2013 19:37:35 -0400
> From: Robert Hanson <[email protected]>
> Subject: Re: [Jmol-users] JSmol too slow!
> To: "[email protected]"
> <[email protected]>
> Message-ID:
> <CAF_YUvVyiyeCqchDjV6qJmJ1vMuy3dEhrBbR4=
> [email protected]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> The distribution includes a file
>
> jmol2.js
>
> which allows the older jsmol.js syntax such as
>
> jmolButton()
>
> jmolScript()
>
> etc.
>
> to be used without change. I think they are all implemented.
>
> But the new way is recommended:
>
> Jmol.jmolButton(appletID, "script", "label")
>
>
> see
>
> http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Conversion_using_the_Jmol2.js_.27adapter.27_library
>
>
> On Tue, Sep 10, 2013 at 7:26 PM, Paul Pillot <
> [email protected]> wrote:
>
> > Try:
> >
> > Jmol.script(jmolAppletObjectNameComesHere,"load =PDBID")
> >
> > where jmolAppletObjectNameComesHere is the name you gave to your jmol
> > object instance at creation
> >
> > Paul
> >
> > Le 10 sept. 2013 ? 18:01, Amjad Farooq a ?crit :
> >
> > Bob,
> >
> > I checked out your new JSmol page with the protein loaded in at:
> > http://chemapps.stolaf.edu/jmol/jsmol/simple.htm
> >
> > The response time for this JSmol page is very fast and on par with Jmol.
> I
> > see no differences between the two with this new JSmol javascript that
> you
> > are using. So, kudos to you! And this is really cool development. Heck
> with
> > this Java nonsense. I am gonna switch to JSmol and use it exclusively
> from
> > now on. It is much easier and more widely acceptable as many of my
> > collaborators do not have Java installed on their machines. Thank you!
> >
> > One quick question:
> > I notice that you also incorporated JmolButton, JmolCheckbox and JmolMenu
> > into JSmol. But, how do I use JmolScript feature of Jmol in JSmol?! For
> > example, I use the following javascript a lot in my Jmol:
> >
> > <script type="text/javascript">
> > function pdb() {
> > jmolScript("load =PDBID")
> > </script>
> > <button onClick="pdb();">Load PDB</button>
> >
> > How do I use the JmolScript syntax in JSmol?
> >
> > Thanks,
> > Amjad
> >
> >
> >
> >
> >
> >
> >
> >
> > On Tue, Sep 10, 2013 at 3:18 PM, Robert Hanson <[email protected]>
> wrote:
> >
> >> Angel, I'd appreciate your assessment of
> >>
> >> set platformSpeed
> >>
> >> Are there settings that you prefer for specific types of compounds? What
> >> would you recommend for proteins in general?
> >>
> >> Bob
> >>
> >>
> >>
> >> On Mon, Sep 9, 2013 at 12:51 PM, Angel Herr?ez <[email protected]
> >wrote:
> >>
> >>> > Something odd there. That's not been our experience.
> >>>
> >>> Well, my experience is that Java Jmol is faster than JSmol. Of course
> >>> this has improved a lot in the las few months and now it's rather
> >>> tolerable, and all depends on the size of the molecule loaded and
> >>> even personal perception, but for me yes, Java is still more agile in
> >>> both loading and responsiveness of the model.
> >>>
> >>> I am not denying the need to move forward into non-Java systems and
> >>> the excellent achievement in JSmol and prospects for the future.
> >>>
> >>>
> >>>
> >>>
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> >>> Jmol-users mailing list
> >>> [email protected]
> >>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> >>>
> >>
> >>
> >>
> >> --
> >> Robert M. Hanson
> >> Larson-Anderson Professor of Chemistry
> >> St. Olaf College
> >> Northfield, MN
> >> http://www.stolaf.edu/people/hansonr
> >>
> >>
> >> 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
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> How ServiceNow helps IT people transform IT departments:
> >> 1. Consolidate legacy IT systems to a single system of record for IT
> >> 2. Standardize and globalize service processes across IT
> >> 3. Implement zero-touch automation to replace manual, redundant tasks
> >>
> >>
> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
> >> _______________________________________________
> >> Jmol-users mailing list
> >> [email protected]
> >> https://lists.sourceforge.net/lists/listinfo/jmol-users
> >>
> >>
> >
> >
> ------------------------------------------------------------------------------
> > How ServiceNow helps IT people transform IT departments:
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> > 2. Standardize and globalize service processes across IT
> > 3. Implement zero-touch automation to replace manual, redundant tasks
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> >
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> >
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> >
> >
> >
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> > How ServiceNow helps IT people transform IT departments:
> > 1. Consolidate legacy IT systems to a single system of record for IT
> > 2. Standardize and globalize service processes across IT
> > 3. Implement zero-touch automation to replace manual, redundant tasks
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
> > _______________________________________________
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> >
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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: Tue, 10 Sep 2013 19:42:38 -0400
> From: Robert Hanson <[email protected]>
> Subject: Re: [Jmol-users] Link Jmol to other programme
> To: "[email protected]"
> <[email protected]>
> Message-ID:
> <CAF_YUvXqtQo0Y-3nMToaGeHX4BAR19AyPX+qR5F=
> [email protected]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> You would embed Jmol.jar in some other program, then create a JmolViewer
> object and call JmolViewer.script(...), for instance. If you wanted the
> Jmol script to wait while it called your Java method, then use the MESSAGE
> command and create a callback for that for your program. The basic idea is
> illustrated in /examples/basic/org/jmol/Export.java in the source
> distribution.
>
>
>
>
> On Tue, Sep 10, 2013 at 3:26 PM, jiayi.zhou <[email protected]> wrote:
>
> > Hi, I have a piece of java codes which can do some changes to the
> > structure file. What I want to do is to write a Jmol script, which can
> read
> > in a structure file and then call my piece of java codes to make some
> > changes to the structure file and then display the structure in Jmol. Can
> > any Jmol script commands import and run the export java codes?
> >
> > Thank you.
> >
> > --
> > Aiden/Jiayi Zhou
> >
> > Office Tel: 709-864-4891
> > Master Candidate
> > Dept. of Computer Science
> > Memorial University of Newfoundland
> > St. John's, NL, Canada, A1B 3X5
> >
> > P I*f you decide to print this...*
> >
> > **
> >
> > * then you'll need to find a place to file it...!*
> >
> >
> >
> ------------------------------------------------------------------------------
> > How ServiceNow helps IT people transform IT departments:
> > 1. Consolidate legacy IT systems to a single system of record for IT
> > 2. Standardize and globalize service processes across IT
> > 3. Implement zero-touch automation to replace manual, redundant tasks
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
> > _______________________________________________
> > Jmol-users mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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 --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 3
> Date: Tue, 10 Sep 2013 19:44:45 -0400
> From: Robert Hanson <[email protected]>
> Subject: Re: [Jmol-users] JSmol in wordpress
> To: "[email protected]" <[email protected]>,
> "[email protected]" <
> [email protected]>
> Message-ID:
> <CAF_YUvU5XLZ=
> [email protected]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> worked but took a long time to load with all the other stuff going on on
> that page as well.
>
>
> On Tue, Sep 10, 2013 at 4:29 PM, [email protected] <
> [email protected]> wrote:
>
> > Dear friends, finally i succeded to put JSmol inside Wordpress. It works.
> >
> > What happened before, i dont know. It remain to be seen until what grade
> > it works.
> >
> > The url is this http://pinostriccoli.altervista.org/?p=6434
> >
> >
> > If you can check the page it would be nice ...
> >
> > Pino
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > How ServiceNow helps IT people transform IT departments:
> > 1. Consolidate legacy IT systems to a single system of record for IT
> > 2. Standardize and globalize service processes across IT
> > 3. Implement zero-touch automation to replace manual, redundant tasks
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
> > _______________________________________________
> > Jmol-users mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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 --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
>
> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. Consolidate legacy IT systems to a single system of record for IT
> 2. Standardize and globalize service processes across IT
> 3. Implement zero-touch automation to replace manual, redundant tasks
> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
>
> ------------------------------
>
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> End of Jmol-users Digest, Vol 88, Issue 22
> ******************************************
>
--
Aiden/Jiayi Zhou
Office Tel: 709-864-4891
Master Candidate
Dept. of Computer Science
Memorial University of Newfoundland
St. John's, NL, Canada, A1B 3X5
P I*f you decide to print this...*
**
* then you'll need to find a place to file it...!*
------------------------------------------------------------------------------
How ServiceNow helps IT people transform IT departments:
1. Consolidate legacy IT systems to a single system of record for IT
2. Standardize and globalize service processes across IT
3. Implement zero-touch automation to replace manual, redundant tasks
http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
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