[Jmol-users] Jmol.script() not returning
We used to have a call to javascript as part of the script text, but that is not longer working: Jmol.script(jmol0,'load data/123.pdb; javascript alert(“Back”);’); On the following example, the alert() happens before the script gets executed. The threading mechanism plays here against us. Jmol.script(jmol0,'load data/123.pdb; select all; color blue;'); alert(“Back”); Suggestions? The set (callback) mechanism doesn’t seem to be the right choice. Jaim -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol.script() not returning
It's not that the alert is coming first; it's that there is no REFRESH before the alert. If you had that command prior to the javascript command, then the structure will appear before the alert. I would argue that this is proper behavior. There is no particular reason to demand an automatic refresh prior to a javascript command, and the behavior is the same for both Java and HTML5 modes. Bob On Mon, Jan 13, 2014 at 5:12 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: We used to have a call to javascript as part of the script text, but that is not longer working: Jmol.script(jmol0,'load data/123.pdb; javascript alert(“Back”);’); On the following example, the alert() happens before the script gets executed. The threading mechanism plays here against us. Jmol.script(jmol0,'load data/123.pdb; select all; color blue;'); alert(“Back”); Suggestions? The set (callback) mechanism doesn’t seem to be the right choice. Jaim -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol.script() not returning
I agree that the use of refresh is often needed; that's my experience, in many occasions it's been key. However, the doc says otherwise: http://chemapps.stolaf.edu/jmol/docs/#refresh (Unnecessary, and thus deprecated.) I would remove that phrase, Bob :) -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol.script() not returning
Dear Bob, Can you please give me an example on how to call a javascript function after the Jmol.script() is done? Thank you in advance, Jaim On Jan 13, 2014, at 1:55 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: It's not that the alert is coming first; it's that there is no REFRESH before the alert. If you had that command prior to the javascript command, then the structure will appear before the alert. I would argue that this is proper behavior. There is no particular reason to demand an automatic refresh prior to a javascript command, and the behavior is the same for both Java and HTML5 modes. Bob On Mon, Jan 13, 2014 at 5:12 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: We used to have a call to javascript as part of the script text, but that is not longer working: Jmol.script(jmol0,'load data/123.pdb; javascript alert(“Back”);’); On the following example, the alert() happens before the script gets executed. The threading mechanism plays here against us. Jmol.script(jmol0,'load data/123.pdb; select all; color blue;'); alert(“Back”); Suggestions? The set (callback) mechanism doesn’t seem to be the right choice. Jaim -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol.script() not returning
Even if adding refresh to Jmol.script, the alert happens before the model gets loaded: Jmol.script(jmol0,'load data/123.pdb; select all; color blue; refresh;'); alert(“Back”); Jaim On Jan 13, 2014, at 2:03 PM, Angel Herráez angel.herr...@uah.es wrote: I agree that the use of refresh is often needed; that's my experience, in many occasions it's been key. However, the doc says otherwise: http://chemapps.stolaf.edu/jmol/docs/#refresh (Unnecessary, and thus deprecated.) I would remove that phrase, Bob :) -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol.script() not returning
I use the javascript command frequently. From past experience, arguments in
functions can cause issues. At a minimum, I would put quotes around the
javascript itself. I think this has to be rigged so that these are double
quotes - i.e. javascript alert('Hey there!') This means changing your quote
structure in the whole Jmol script.
One thing that made issues go away for me completely is to simply use a
function without an argument. That function, when called, can do anything you
need done after the Jmol script executes.
Otis
--
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o...@chemagic.com
http://chemagic.com
On Jan 13, 2014, at 7:03 AM, Angel Herráez angel.herr...@uah.es wrote:
I agree that the use of refresh is often needed; that's my
experience, in many occasions it's been key.
However, the doc says otherwise:
http://chemapps.stolaf.edu/jmol/docs/#refresh
(Unnecessary, and thus deprecated.)
I would remove that phrase, Bob :)
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Re: [Jmol-users] Jmol.script() not returning
Have you tried it on 14.0.5 with HTML5?
Jaim
On Jan 13, 2014, at 2:26 PM, Otis Rothenberger
osrot...@chemagic.commailto:osrot...@chemagic.com wrote:
I use the javascript command frequently. From past experience, arguments in
functions can cause issues. At a minimum, I would put quotes around the
javascript itself. I think this has to be rigged so that these are double
quotes - i.e. javascript alert('Hey there!') This means changing your quote
structure in the whole Jmol script.
One thing that made issues go away for me completely is to simply use a
function without an argument. That function, when called, can do anything you
need done after the Jmol script executes.
Otis
--
Otis Rothenberger
o...@chemagic.commailto:o...@chemagic.com
http://chemagic.com
On Jan 13, 2014, at 7:03 AM, Angel Herráez
angel.herr...@uah.esmailto:angel.herr...@uah.es wrote:
I agree that the use of refresh is often needed; that's my
experience, in many occasions it's been key.
However, the doc says otherwise:
http://chemapps.stolaf.edu/jmol/docs/#refresh
(Unnecessary, and thus deprecated.)
I would remove that phrase, Bob :)
--
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Re: [Jmol-users] Jmol.script() not returning
On 01/13/2014 01:21 PM, Jaime Prilusky wrote:
Even if adding refresh to Jmol.script, the alert happens before the model
gets loaded:
Jmol.script(jmol0,'load data/123.pdb; select all; color blue; refresh;');
alert(“Back”);
If you take the 'alert' out of the 'Jmol.script' command set it is
expected that the 'alert' is processed immediately after the Jmol script
commands are put into the Jmol scripting command cue.
It should be sufficient to add 'refresh;' into your initial version:
Jmol.script(jmol0,'load data/123.pdb; select all; color blue; refresh;
javascript alert(“Back”);’);
Maybe you need to allow javascript commands first, e.g. add it to your
Info settings:
Info = {...
allowjavascript: true
};
Regards,
Rolf
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Re: [Jmol-users] Jmol.script() not returning
I'm using 14.0.2. I can check out 14.0.5 later this morning.
I should have mentioned in the previous note that the function without an
argument no longer needs the quotes around the javascript.
The javascript command has been fussy for me for years. Keeping quotes out of
the javascript itself made my problems go away - hence the function with no
argument.
Otis
--
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o...@chemagic.com
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On Jan 13, 2014, at 7:36 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.il
wrote:
Have you tried it on 14.0.5 with HTML5?
Jaim
On Jan 13, 2014, at 2:26 PM, Otis Rothenberger osrot...@chemagic.com wrote:
I use the javascript command frequently. From past experience, arguments in
functions can cause issues. At a minimum, I would put quotes around the
javascript itself. I think this has to be rigged so that these are double
quotes - i.e. javascript alert('Hey there!') This means changing your
quote structure in the whole Jmol script.
One thing that made issues go away for me completely is to simply use a
function without an argument. That function, when called, can do anything
you need done after the Jmol script executes.
Otis
--
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Re: [Jmol-users] Jmol.script() not returning
Jaim,
Quick test on your side: Does alert(1234) work. No quotes - just alert(1234)?
Otis
--
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o...@chemagic.com
http://chemagic.com
On Jan 13, 2014, at 7:49 AM, Otis Rothenberger osrot...@chemagic.com wrote:
I'm using 14.0.2. I can check out 14.0.5 later this morning.
I should have mentioned in the previous note that the function without an
argument no longer needs the quotes around the javascript.
The javascript command has been fussy for me for years. Keeping quotes out of
the javascript itself made my problems go away - hence the function with no
argument.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jan 13, 2014, at 7:36 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.il
wrote:
Have you tried it on 14.0.5 with HTML5?
Jaim
On Jan 13, 2014, at 2:26 PM, Otis Rothenberger osrot...@chemagic.com wrote:
I use the javascript command frequently. From past experience, arguments in
functions can cause issues. At a minimum, I would put quotes around the
javascript itself. I think this has to be rigged so that these are double
quotes - i.e. javascript alert('Hey there!') This means changing your
quote structure in the whole Jmol script.
One thing that made issues go away for me completely is to simply use a
function without an argument. That function, when called, can do anything
you need done after the Jmol script executes.
Otis
--
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Re: [Jmol-users] Jmol.script() not returning
so noted. Changing that to: refresh * Forces a screen repaint during script execution. Usually unnecessary, this command is useful during selected looping operations or in conjunction with such commands as javascript that otherwise might not initiate a screen repaint. Refreshing is automatically carried out after a script completes unless set refreshing FALSE has been invoked. Commands that automatically invoke refresh include delay, move, moveto, navigate, write, and zap.* On Mon, Jan 13, 2014 at 6:03 AM, Angel Herráez angel.herr...@uah.es wrote: I agree that the use of refresh is often needed; that's my experience, in many occasions it's been key. However, the doc says otherwise: http://chemapps.stolaf.edu/jmol/docs/#refresh (Unnecessary, and thus deprecated.) I would remove that phrase, Bob :) -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol.script() not returning
That's right, too. In this case you are putting a script into the queue and then immediately and independently firing the alert message. Your initial way is correct; just add a REFRESH command prior to that if you want the model to be displayed during the alert. On Mon, Jan 13, 2014 at 6:21 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Even if adding refresh to Jmol.script, the alert happens before the model gets loaded: Jmol.script(jmol0,'load data/123.pdb; select all; color blue; refresh;'); alert(“Back”); Jaim On Jan 13, 2014, at 2:03 PM, Angel Herráez angel.herr...@uah.es wrote: I agree that the use of refresh is often needed; that's my experience, in many occasions it's been key. However, the doc says otherwise: http://chemapps.stolaf.edu/jmol/docs/#refresh (Unnecessary, and thus deprecated.) I would remove that phrase, Bob :) -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
