[Jmol-users] Jmol 13.0.1 connect_atoms error
Is this structure not longer valid? We have several scripts using it in the past and things were Ok. Today, running on Jmol 13.0.1 it returns parsing error. Does it works Ok on previous versions of Jmol? On newer versions? Jaim data connect; connect_atoms 91 198040960.4 -2.501 hbond; 1705187240960.4 -2.974 hbond; 1722185340960.4 -2.543 hbond; end connect_atoms; -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with Jmol export to web?
Unfortunately it looks like even if the model is loaded from disk (rather than database) that E2W does not work. No error message shows up, and right-clicking in the applet window gives the message 0.0: in the model 1/1 submenu. I think this indicates that no model was loaded. Too bad. It was a nice, easy way to get students started making web pages without html or javascript. Thanks -Art -Original Message- From: Angel Herráez [mailto:angel.herr...@uah.es] Sent: Wednesday, September 11, 2013 3:58 AM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] Problem with Jmol export to web? Export to web should work fine, it uses Java Jmol and Jmol.js I hav had no problems with it in a couple of courses with several people. Although using a sample page is an option, it requires users to know a bit about html and javascript to modify. I have found that E2W is an easy starting point for general users. So I advise do not get away from it -- just find out the one or two situations where the user does not get a working page: 1- Using Jmol.jar extracted from the distribution zip without having extracted all the other files too. 2- Loading a structure from database. 3- Providing incorrect paths for Jmol files in the dialog. · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- 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 https://urldefense.proofpoint.com/v1/url?u=http://pubads.g.doubleclick.net/gampad/clk?id%3D5127%26iu%3D/4140/ostg.clktrkk=DAg7EJlu1K0Rh3TtbXoISg%3D%3D%0Ar=fjW3YEaX7L6b5Qr8M6KoEajTOc8b2Al40L8KZaVTlmM%3D%0Am=%2FekaOOb9To3ww5aqUfVXN6KmQ8lUpim%2F5KpW68aUneE%3D%0As=d47410ea646a20dc4c48162bb1c6a9113e7fee939db8091f72b32f2a0d73b361 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/jmol-usersk=DAg7EJlu1K0Rh3TtbXoISg%3D%3D%0Ar=fjW3YEaX7L6b5Qr8M6KoEajTOc8b2Al40L8KZaVTlmM%3D%0Am=%2FekaOOb9To3ww5aqUfVXN6KmQ8lUpim%2F5KpW68aUneE%3D%0As=ecaff76c1d0e8ec911d7904ceef086baf78a1c78f5db3e1a1eb43eadc9361454 -- CONFIDENTIALITY NOTICE: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to which they are addressed. If you are not the intended recipient, you may not review, copy or distribute this message. If you have received this email in error, please notify the sender immediately and delete the original message. Neither the sender nor the company for which he or she works accepts any liability for any damage caused by any virus transmitted by this email. -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] (no subject)
Hi Friends, i am trying to format the page http://pinostriccoli.altervista.org/? p=6434 and i want the molecule floating to the left so that written text gos to its right. I found jmol.setAppletCss. Where should I insert the script and what can be the exat sintax? thanks Pino -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] (no subject)
The jQuery way to do that would be somethng like this:
$(#jmolApplet0_appletinfotablediv).css({top:5px,left:400px})
where jmolApplet0 is the name of my applet.
Bob
On Mon, Sep 16, 2013 at 4:12 PM, pino.stricc...@libero.it
pino.stricc...@libero.it wrote:
Hi Friends, i am trying to format the page
http://pinostriccoli.altervista.org/?
p=6434
and i want the molecule floating to the left so that written text gos to
its
right.
I found jmol.setAppletCss. Where should I insert the script and what can be
the exat sintax?
thanks
Pino
--
LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
1,500+ hours of tutorials including VisualStudio 2012, Windows 8,
SharePoint
2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack
includes
Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/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
--
LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint
2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] jsmol -- local file reading/drag drop and local file writing
OK. I have uploaded changes to Jmol that allow JSmol/HTML5 to read and write files to a local drive. Whew! That was tricky -- text, binary, zip, gzip, pngj, xml -- I checked as many as I could find. Please test on a variety of platforms: http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.6_2013.09.16.zip top center column -- local file read write Bob ___JmolVersion=13.3.6_dev_2013.09.16 bug fix: chains improperly selected in JSmol/HTML5 bug fix: JSmol/HTML5 not allowing drag-drop or file loading from a local drive. bug fix: JSmol/HTML5 not allowing WRITE FILE ? bug fix: platformSpeed persists but appears unreadable after loading a state bug fix: JavaScript version InputStreamReader not processing non-UTF data correctly bug fix: second reading of older PNG files with embedded script fails due to improper png file caching new feature: set drawFontSize // defaults to 14.0 -- 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jsmol -- local file reading/drag drop and local file writing
That's also now in place at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm If you have trouble, clear your cache and try again. I had to do that to get Firefox to move to the latest upload. Uploading of local files: load ? # displays a dialog over the applet x = load(?) # allows moving file data straight into a variable instead of loading it as a model. Downloading to the local drive: write FILE ? # the original file data Still to get working: write MOL ? write XYZ ? write PDB ? Bob On Mon, Sep 16, 2013 at 5:54 PM, Robert Hanson hans...@stolaf.edu wrote: OK. I have uploaded changes to Jmol that allow JSmol/HTML5 to read and write files to a local drive. Whew! That was tricky -- text, binary, zip, gzip, pngj, xml -- I checked as many as I could find. Please test on a variety of platforms: http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.6_2013.09.16.zip top center column -- local file read write Bob ___JmolVersion=13.3.6_dev_2013.09.16 bug fix: chains improperly selected in JSmol/HTML5 bug fix: JSmol/HTML5 not allowing drag-drop or file loading from a local drive. bug fix: JSmol/HTML5 not allowing WRITE FILE ? bug fix: platformSpeed persists but appears unreadable after loading a state bug fix: JavaScript version InputStreamReader not processing non-UTF data correctly bug fix: second reading of older PNG files with embedded script fails due to improper png file caching new feature: set drawFontSize // defaults to 14.0 -- 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 -- 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with Jmol export to web?
I'll take a look. On Mon, Sep 16, 2013 at 3:27 PM, Cox, Arthur G. a...@southuniversity.eduwrote: Unfortunately it looks like even if the model is loaded from disk (rather than database) that E2W does not work. No error message shows up, and right-clicking in the applet window gives the message 0.0: in the model 1/1 submenu. I think this indicates that no model was loaded. Too bad. It was a nice, easy way to get students started making web pages without html or javascript. Thanks -Art -Original Message- From: Angel Herráez [mailto:angel.herr...@uah.es] Sent: Wednesday, September 11, 2013 3:58 AM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] Problem with Jmol export to web? Export to web should work fine, it uses Java Jmol and Jmol.js I hav had no problems with it in a couple of courses with several people. Although using a sample page is an option, it requires users to know a bit about html and javascript to modify. I have found that E2W is an easy starting point for general users. So I advise do not get away from it -- just find out the one or two situations where the user does not get a working page: 1- Using Jmol.jar extracted from the distribution zip without having extracted all the other files too. 2- Loading a structure from database. 3- Providing incorrect paths for Jmol files in the dialog. · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- 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 https://urldefense.proofpoint.com/v1/url?u=http://pubads.g.doubleclick.net/gampad/clk?id%3D5127%26iu%3D/4140/ostg.clktrkk=DAg7EJlu1K0Rh3TtbXoISg%3D%3D%0Ar=fjW3YEaX7L6b5Qr8M6KoEajTOc8b2Al40L8KZaVTlmM%3D%0Am=%2FekaOOb9To3ww5aqUfVXN6KmQ8lUpim%2F5KpW68aUneE%3D%0As=d47410ea646a20dc4c48162bb1c6a9113e7fee939db8091f72b32f2a0d73b361 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/jmol-usersk=DAg7EJlu1K0Rh3TtbXoISg%3D%3D%0Ar=fjW3YEaX7L6b5Qr8M6KoEajTOc8b2Al40L8KZaVTlmM%3D%0Am=%2FekaOOb9To3ww5aqUfVXN6KmQ8lUpim%2F5KpW68aUneE%3D%0As=ecaff76c1d0e8ec911d7904ceef086baf78a1c78f5db3e1a1eb43eadc9361454 -- CONFIDENTIALITY NOTICE: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to which they are addressed. If you are not the intended recipient, you may not review, copy or distribute this message. If you have received this email in error, please notify the sender immediately and delete the original message. Neither the sender nor the company for which he or she works accepts any liability for any damage caused by any virus transmitted by this email. -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with Jmol export to web?
I think it works, but we have the added security features now that the
unsigned applet can't access local files. So you have to go into the HTML
and change this bit:
if (jmoljarpath ==.){
jmoljarfile=JmolApplet.jar; //use the unitary applet instead of
incremental
}
to
if (jmoljarpath ==.){
jmoljarfile=JmolAppletSigned.jar; //use the unitary applet
instead of incremental
}
I realize that that is not obvious.
Bob
On Mon, Sep 16, 2013 at 6:31 PM, Robert Hanson hans...@stolaf.edu wrote:
I'll take a look.
On Mon, Sep 16, 2013 at 3:27 PM, Cox, Arthur G.
a...@southuniversity.eduwrote:
Unfortunately it looks like even if the model is loaded from disk (rather
than database) that E2W does not work. No error message shows up, and
right-clicking in the applet window gives the message 0.0: in the model 1/1
submenu. I think this indicates that no model was loaded.
Too bad. It was a nice, easy way to get students started making web pages
without html or javascript.
Thanks
-Art
-Original Message-
From: Angel Herráez [mailto:angel.herr...@uah.es]
Sent: Wednesday, September 11, 2013 3:58 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Problem with Jmol export to web?
Export to web should work fine, it uses Java Jmol and Jmol.js I hav had
no problems with it in a couple of courses with several people.
Although using a sample page is an option, it requires users to know a
bit about html and javascript to modify. I have found that E2W is an easy
starting point for general users. So I advise do not get away from it --
just find out the one or two situations where the user does not get a
working page:
1- Using Jmol.jar extracted from the distribution zip without having
extracted all the other files too.
2- Loading a structure from database.
3- Providing incorrect paths for Jmol files in the dialog.
·
Dr. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-28871 Alcalá de Henares (Madrid), Spain
--
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
https://urldefense.proofpoint.com/v1/url?u=http://pubads.g.doubleclick.net/gampad/clk?id%3D5127%26iu%3D/4140/ostg.clktrkk=DAg7EJlu1K0Rh3TtbXoISg%3D%3D%0Ar=fjW3YEaX7L6b5Qr8M6KoEajTOc8b2Al40L8KZaVTlmM%3D%0Am=%2FekaOOb9To3ww5aqUfVXN6KmQ8lUpim%2F5KpW68aUneE%3D%0As=d47410ea646a20dc4c48162bb1c6a9113e7fee939db8091f72b32f2a0d73b361
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/jmol-usersk=DAg7EJlu1K0Rh3TtbXoISg%3D%3D%0Ar=fjW3YEaX7L6b5Qr8M6KoEajTOc8b2Al40L8KZaVTlmM%3D%0Am=%2FekaOOb9To3ww5aqUfVXN6KmQ8lUpim%2F5KpW68aUneE%3D%0As=ecaff76c1d0e8ec911d7904ceef086baf78a1c78f5db3e1a1eb43eadc9361454
--
CONFIDENTIALITY NOTICE: This email and any files transmitted with it are
confidential and intended solely for the use of the individual or entity to
which they are addressed. If you are not the intended recipient, you may
not review, copy or distribute this message. If you have received this
email in error, please notify the sender immediately and delete the
original message. Neither the sender nor the company for which he or she
works accepts any liability for any damage caused by any virus transmitted
by this email.
--
LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
1,500+ hours of tutorials including VisualStudio 2012, Windows 8,
SharePoint
2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack
includes
Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/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
--
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
Re: [Jmol-users] jsmol -- local file reading/drag drop and local file writing
Bob, Beautiful! What can I say? You are awesome, man. So, on my side, I tested the following commands that you just enabled on Firefox and Chrome: load ?.pdb write FILE ?.pdb write JPG ?.jpg write PNG ?.png They all work on both browsers. I did not have much luck on IE. But, do we care? Only dummies use IE. Do not waste your time on configuring these features for IE. Anyone who uses IE is most probably not going to work with JSmol. So, my advice, would be to focus your energy and add new features that work in Firefox and Chrome. IE is just a different beast and it is only going to bug you down and cause other issues. You can always add an in-built warning sign (like java reminds users that no java is installed!) that warns IE users that JSmol is not configured for IE and that it only works with Firefox and Chrome. That way you can focus your energy on adding additional features to JSmol in lieu of IE taking your valuable time. Just some thoughts. Thanks very much, Bob! You made my day (I am in the process of moving to JSmol and do away with Jmol altogether on my webpage). Amjad On Mon, Sep 16, 2013 at 7:27 PM, Robert Hanson hans...@stolaf.edu wrote: That's also now in place at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm If you have trouble, clear your cache and try again. I had to do that to get Firefox to move to the latest upload. Uploading of local files: load ? # displays a dialog over the applet x = load(?) # allows moving file data straight into a variable instead of loading it as a model. Downloading to the local drive: write FILE ? # the original file data Still to get working: write MOL ? write XYZ ? write PDB ? Bob On Mon, Sep 16, 2013 at 5:54 PM, Robert Hanson hans...@stolaf.edu wrote: OK. I have uploaded changes to Jmol that allow JSmol/HTML5 to read and write files to a local drive. Whew! That was tricky -- text, binary, zip, gzip, pngj, xml -- I checked as many as I could find. Please test on a variety of platforms: http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.6_2013.09.16.zip top center column -- local file read write Bob ___JmolVersion=13.3.6_dev_2013.09.16 bug fix: chains improperly selected in JSmol/HTML5 bug fix: JSmol/HTML5 not allowing drag-drop or file loading from a local drive. bug fix: JSmol/HTML5 not allowing WRITE FILE ? bug fix: platformSpeed persists but appears unreadable after loading a state bug fix: JavaScript version InputStreamReader not processing non-UTF data correctly bug fix: second reading of older PNG files with embedded script fails due to improper png file caching new feature: set drawFontSize // defaults to 14.0 -- 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 -- 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.0.1 connect_atoms error
what version did that work in? Should be: data connect_atoms 91 198040960.4 -2.501 hbond; 1705187240960.4 -2.974 hbond; 1722185340960.4 -2.543 hbond; end connect_atoms; This format is not documented; it was intended only for definition of the state. For reference, the columns are: 1 and 2 are the 0-based atom indices 3 is the coded bond type. 4 is the diameter of the connector 5 is the energy calculated for this bond (only relevant for hydrogen bonds) 6 is the human-readable meaning of the coded bond type (ignored) Bob On Mon, Sep 16, 2013 at 1:45 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Is this structure not longer valid? We have several scripts using it in the past and things were Ok. Today, running on Jmol 13.0.1 it returns parsing error. Does it works Ok on previous versions of Jmol? On newer versions? Jaim data connect; connect_atoms 91 198040960.4 -2.501 hbond; 1705187240960.4 -2.974 hbond; 1722185340960.4 -2.543 hbond; end connect_atoms; -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jsmol -- local file reading/drag drop and local file writing
Great. My pleasure. (Actually not, because I really hate to dig into the data stream code.) Thanks for the advice. It should require MSIE 10, which is what I tested it on. MSIE 9 doesn't have the FileLoader interface, I think. But except for this, we support back to MSIE 9 at least. Bob ps - Please don't disparage those who for whatever reason want to/need to use MSIE. On Mon, Sep 16, 2013 at 6:56 PM, Amjad Farooq am...@farooqlab.net wrote: Bob, -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jsmol -- local file reading/drag drop and local file writing
Thanks Bob! My apologies for being so negative about IE. I have always had a terrible time with it. But, of course, good luck to others. Amjad *AMJAD FAROOQ PhD DIC | Associate Professor Dept of Biochemistry Molecular Biology | Miller School of Medicine | University of Miami | Miami | FL 33136 Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami , FL 33136 am...@farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax 305-243-3955 | www.farooqlab.net* On Mon, Sep 16, 2013 at 8:08 PM, Robert Hanson hans...@stolaf.edu wrote: Great. My pleasure. (Actually not, because I really hate to dig into the data stream code.) Thanks for the advice. It should require MSIE 10, which is what I tested it on. MSIE 9 doesn't have the FileLoader interface, I think. But except for this, we support back to MSIE 9 at least. Bob ps - Please don't disparage those who for whatever reason want to/need to use MSIE. On Mon, Sep 16, 2013 at 6:56 PM, Amjad Farooq am...@farooqlab.net wrote: Bob, -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with Jmol export to web?
We really should fix this. My hope is to find some time to update export to
web to generate pages that can us JSmol as well before next Spring.
Unfortunately, my time is booked pretty solid, so I cannot make promises to do
this. Maybe we should make this patch to the templates as a temporary fix.
Jonathan
On Sep 16, 2013, at 6:57 PM, jmol-users-requ...@lists.sourceforge.net wrote:
Message: 1
Date: Mon, 16 Sep 2013 18:45:58 -0500
From: Robert Hanson hans...@stolaf.edu
Subject: Re: [Jmol-users] Problem with Jmol export to web?
To: jmol-users@lists.sourceforge.net
jmol-users@lists.sourceforge.net
Message-ID:
caf_yuvuge3yrk8oh6o9cdnfz0wyihno-qo9x4pbu0z5yeug...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
I think it works, but we have the added security features now that the
unsigned applet can't access local files. So you have to go into the HTML
and change this bit:
if (jmoljarpath ==.){
jmoljarfile=JmolApplet.jar; //use the unitary applet instead of
incremental
}
to
if (jmoljarpath ==.){
jmoljarfile=JmolAppletSigned.jar; //use the unitary applet
instead of incremental
}
I realize that that is not obvious.
Bob
Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow
--
LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint
2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.0.1 connect_atoms error
Thank you for the correct format. Jaim On Sep 17, 2013, at 3:03 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: what version did that work in? Should be: data connect_atoms 91 198040960.4 -2.501 hbond; 1705187240960.4 -2.974 hbond; 1722185340960.4 -2.543 hbond; end connect_atoms; This format is not documented; it was intended only for definition of the state. For reference, the columns are: 1 and 2 are the 0-based atom indices 3 is the coded bond type. 4 is the diameter of the connector 5 is the energy calculated for this bond (only relevant for hydrogen bonds) 6 is the human-readable meaning of the coded bond type (ignored) Bob On Mon, Sep 16, 2013 at 1:45 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Is this structure not longer valid? We have several scripts using it in the past and things were Ok. Today, running on Jmol 13.0.1 it returns parsing error. Does it works Ok on previous versions of Jmol? On newer versions? Jaim data connect; connect_atoms 91 198040960.4 -2.501 hbond; 1705187240960.4 -2.974 hbond; 1722185340960.4 -2.543 hbond; end connect_atoms; -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
