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From: LANCASHIRE,Robert <rob...@uw...> - 2020-09-16 00:36:11
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Bob, this was an issue with some versions of ACD/Labs as well where they had not started using the 3.01 NMR release after Y2K If you comment it out altogether in the file it might work was my suggestion since I have had to do 50+ files over the last 2 days for our Organic Lab and without it everything was at the correct position. Robert From: Robert Hanson [mailto:ha...@st...] Sent: Tuesday, 15 September 2020 7:30 PM To: LANCASHIRE,Robert <rob...@uw...> Cc: Jennifer L. Muzyka <jen...@ce...>; jsp...@li... Subject: Re: Jmol / JSpecView Definitely this line: ##.SHIFT REFERENCE= INTERNAL, NONE, 26214, 5 On Tue, Sep 15, 2020 at 7:22 PM Robert Hanson <ha...@st...<mailto:ha...@st...>> wrote: Oh, that is really too bad, Jennifer. What a pain for you! And I suppose JEOL is not putting something like this very high on their TODO list -- or are they? I have a bit of time tonight. I will take a quick look. Robert, just use the JSpecView menu File...Save As...Original :) -- Robert M. Hanson 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 We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place. |
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From: LANCASHIRE,Robert <rob...@uw...> - 2020-09-15 18:09:51
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Hi Jennifer,
looking at the ABOUT (right click and bottom of menu) I see a date of 2014.
MUCH has changed since then!
The Directory listing does not seem to allow me to download a file to check with the latest version.
One thing that is worth looking at though is the
##.SHIFT REFERENCE= (STRING, TEXT, AFFN, AFFN)
this was often wrong in some ACD/Labs exports such that commenting or deleting that line gave the correct display.
Not sure what we had to do with JEOL and if that is the cause?
Robert
-----Original Message-----
From: Jennifer L. Muzyka [mailto:jen...@ce...]
Sent: Tuesday, 15 September 2020 12:40 PM
To: jsp...@li...
Cc: LANCASHIRE,Robert <rob...@uw...>
Subject: FW: Jmol / JSpecView
My question relates to JSpecView as implemented within the JSmol interface.
The JEOL Delta software isn't compatible with the Catalina version of the Mac OS. It turns out that most of our students are Mac users and they have dutifully upgraded to the latest OS. Which means we needed a different way to display spectra to our students. So the spectra are saved in JCAMP format in a shared directory that allows students to access the files with a web browser.
Some of the spectra have strange numbers for chemical shifts. So the chemical shifts for proton NMR spectra have numerical values around 2000 (maybe Hz instead of ppm?). These spectra look fine when I open the JCAMP files using iNMR. So it seems like there's some incompatibility between the JCAMP file exported by JEOL or the display of that file with JSpecView. You can see an example at https://chemserv.centre.edu/listing5.php?dir=JDX/&sort=date&order=asc&cat=nmr/#
I would appreciate advice that would allow my students to see their spectra directly instead of having to save the file and open it in iNMR. Thanks.
Jennifer
Jennifer L. Muzyka [she/her/hers]
Stodghill Professor of Chemistry
Centre College
Danville, KY. 40422
https://sites.centre.edu/muzyka
https://organicers.org
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From: Eelco v. D. <Eel...@Pe...> - 2013-03-25 13:22:14
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Hi Robert, Thanks for, again, the quick response. That's great news and a wonderful initiative. Please keep me informed of the development plans, development start, developments. Maybe we can be of assistance somehow. The project for our next, ongoing, development is in the preparation phase and will hopefully start within short notice. This could mean that our developments could run in parallel. Regards, Eelco -----Oorspronkelijk bericht----- Van: LANCASHIRE,Robert J [mailto:rob...@uw...] Verzonden: maandag 25 maart 2013 13:13 Aan: Eelco van Dam; jsp...@li... Onderwerp: RE: [Jspecview-users] JSpecView to JSSpecView? HI, Yes, we do plan to convert but timing is not settled and it may well be closer to October before you see anything. Robert -----Original Message----- From: Eelco van Dam [mailto:Eel...@Pe...] Sent: Monday, March 25, 2013 06:15 AM To: jsp...@li... Subject: [Jspecview-users] JSpecView to JSSpecView? L.S., Last year we started a new development to realize an educational platform to teach spectroscopy to students. For this, we used Jmol and JSpecView with the combination of the two (i.e. the interaction between the two applets). For anyone interested in this development, it is based on Drupal. We created a module for it, see http://drupal.org/project/molecule. In this module both Jmol and JSpecView are combined. When you combine this module with the module Closed Question (http://drupal.org/project/closedquestion) you can create questions in combination with the visualization and interaction of Jmol and/or JSpecView. It works great. For those who want to learn more, we are setting up a website that will contain more information and some demonstration, www.eduspec.org. Meanwhile, Java started to have some problems with their support in the browser world, what was a bit of a setback. Now Jmol has started the initiative of developing JSmol. This could be a major improvement for us in our ongoing development of the learning environment, but we don't want to lose the interaction with JSpecView. So, is there any plan of developing "JSSpecView" that will maintain the interaction like with Jmol and JSpecView within the JavaScript world? Kind regards, Eelco van Dam <http://www.Peacs.nl> www.Peacs.nl ---------------------------------------------------------------------------- -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar _______________________________________________ Jspecview-users mailing list Jsp...@li... https://lists.sourceforge.net/lists/listinfo/jspecview-users |
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From: LANCASHIRE,Robert J <rob...@uw...> - 2013-03-25 12:33:04
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HI, Yes, we do plan to convert but timing is not settled and it may well be closer to October before you see anything. Robert -----Original Message----- From: Eelco van Dam [mailto:Eel...@Pe...] Sent: Monday, March 25, 2013 06:15 AM To: jsp...@li... Subject: [Jspecview-users] JSpecView to JSSpecView? L.S., Last year we started a new development to realize an educational platform to teach spectroscopy to students. For this, we used Jmol and JSpecView with the combination of the two (i.e. the interaction between the two applets). For anyone interested in this development, it is based on Drupal. We created a module for it, see http://drupal.org/project/molecule. In this module both Jmol and JSpecView are combined. When you combine this module with the module Closed Question (http://drupal.org/project/closedquestion) you can create questions in combination with the visualization and interaction of Jmol and/or JSpecView. It works great. For those who want to learn more, we are setting up a website that will contain more information and some demonstration, www.eduspec.org. Meanwhile, Java started to have some problems with their support in the browser world, what was a bit of a setback. Now Jmol has started the initiative of developing JSmol. This could be a major improvement for us in our ongoing development of the learning environment, but we don't want to lose the interaction with JSpecView. So, is there any plan of developing "JSSpecView" that will maintain the interaction like with Jmol and JSpecView within the JavaScript world? Kind regards, Eelco van Dam <http://www.Peacs.nl> www.Peacs.nl ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar _______________________________________________ Jspecview-users mailing list Jsp...@li... https://lists.sourceforge.net/lists/listinfo/jspecview-users |
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From: Eelco v. D. <Eel...@Pe...> - 2013-03-25 11:34:16
|
L.S., Last year we started a new development to realize an educational platform to teach spectroscopy to students. For this, we used Jmol and JSpecView with the combination of the two (i.e. the interaction between the two applets). For anyone interested in this development, it is based on Drupal. We created a module for it, see http://drupal.org/project/molecule. In this module both Jmol and JSpecView are combined. When you combine this module with the module Closed Question (http://drupal.org/project/closedquestion) you can create questions in combination with the visualization and interaction of Jmol and/or JSpecView. It works great. For those who want to learn more, we are setting up a website that will contain more information and some demonstration, www.eduspec.org. Meanwhile, Java started to have some problems with their support in the browser world, what was a bit of a setback. Now Jmol has started the initiative of developing JSmol. This could be a major improvement for us in our ongoing development of the learning environment, but we don't want to lose the interaction with JSpecView. So, is there any plan of developing "JSSpecView" that will maintain the interaction like with Jmol and JSpecView within the JavaScript world? Kind regards, Eelco van Dam <http://www.Peacs.nl> www.Peacs.nl |
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From: LANCASHIRE,Robert J <rob...@uw...> - 2012-12-15 22:40:47
|
Alex, Earlier this year, the JSpecView code and Jmol code was merged thanks to Bob Hanson. I suspect all of this is possible in the stand-alone application and much of that code is exposed when using the signed applet. I'm not sure if any examples have been placed on-line to do what you ask but it is doesn't sound like it would be difficult to test. Maybe try a quick sample page and then send a note to Bob if things don't work might be the easiest way forward Robert From: Alex Henderson [mailto:ale...@ge...] Sent: Saturday, December 15, 2012 11:48 AM To: LANCASHIRE,Robert J Cc: jsp...@li...; Robert Hanson Subject: Re: [Jspecview-users] Load file outside website or using JSON Robert, Thanks for the suggestions I'll try it out. I suspect, however, this might only allow me to access files on the client drive. I'd like to be able to access files on the server that are not in the directory structure that is web served (or via the server from another location through php or JSONP). I'd also like to view files that are extracted from a database or generated on the fly. This is where I see JSON(P) coming in. Are any of these possible? Does anyone have an example they could share? Thanks again, Alex On 14/12/2012 19:24, LANCASHIRE,Robert J wrote: Alex, You would probably be advised to use the SIGNED applet to avoid JAVA security issues What version are you running? Robert -----Original Message----- From: Alex Henderson [mailto:ale...@ge...] Sent: Friday, December 14, 2012 10:50 AM To: jsp...@li...<mailto:jsp...@li...> Subject: [Jspecview-users] Load file outside website or using JSON Hi, Is it possible to load a file from outside the host website? I think that as an applet that might not be possible. If not, is it possible to load a file using JSON? Thanks, Alex ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ Jspecview-users mailing list Jsp...@li...<mailto:Jsp...@li...> https://lists.sourceforge.net/lists/listinfo/jspecview-users |
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From: Alex H. <ale...@ge...> - 2012-12-15 16:47:37
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Robert, Thanks for the suggestions I'll try it out. I suspect, however, this might only allow me to access files on the client drive. I'd like to be able to access files on the server that are not in the directory structure that is web served (or via the server from another location through php or JSONP). I'd also like to view files that are extracted from a database or generated on the fly. This is where I see JSON(P) coming in. Are any of these possible? Does anyone have an example they could share? Thanks again, Alex On 14/12/2012 19:24, LANCASHIRE,Robert J wrote: > Alex, > > You would probably be advised to use the SIGNED applet to avoid JAVA security issues > What version are you running? > > > Robert > > -----Original Message----- > From: Alex Henderson [mailto:ale...@ge...] > Sent: Friday, December 14, 2012 10:50 AM > To: jsp...@li... > Subject: [Jspecview-users] Load file outside website or using JSON > > Hi, > > Is it possible to load a file from outside the host website? > I think that as an applet that might not be possible. > > If not, is it possible to load a file using JSON? > > Thanks, > Alex > > > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d > _______________________________________________ > Jspecview-users mailing list > Jsp...@li... > https://lists.sourceforge.net/lists/listinfo/jspecview-users |
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From: LANCASHIRE,Robert J <rob...@uw...> - 2012-12-14 19:44:57
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Alex, You would probably be advised to use the SIGNED applet to avoid JAVA security issues What version are you running? Robert -----Original Message----- From: Alex Henderson [mailto:ale...@ge...] Sent: Friday, December 14, 2012 10:50 AM To: jsp...@li... Subject: [Jspecview-users] Load file outside website or using JSON Hi, Is it possible to load a file from outside the host website? I think that as an applet that might not be possible. If not, is it possible to load a file using JSON? Thanks, Alex ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ Jspecview-users mailing list Jsp...@li... https://lists.sourceforge.net/lists/listinfo/jspecview-users |
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From: Alex H. <ale...@ge...> - 2012-12-14 16:13:17
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Hi, Is it possible to load a file from outside the host website? I think that as an applet that might not be possible. If not, is it possible to load a file using JSON? Thanks, Alex |
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From: Tim te B. <tim...@nb...> - 2012-10-29 15:17:11
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Thanks for the quick reply. I have been able to get both applets to load spectra that are available with files, so getting the applets to load is not part of the issue. I'm both generating spectra on the server, and loading spectra from a database, so I'd like to load the spectra inline through JavaScript instead of writing them to files and loading those. This inline loading is what throws the NullPointerException from my initial report, and none of the online examples appear to use inline loading. I suspect that the inline loading might therefore be broken, but am still too unfamiliar to state definitely that it is. Is this something that could be looked at and possibly fixed? Or perhaps there is an alternative example somewhere that does successfully use inline loading that I could take a look at... Best, Tim |
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From: LANCASHIRE,Robert J <rob...@uw...> - 2012-10-29 14:41:43
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Tim,
I think Bob suggested that the problem was ensuring that BOTH applets had properly loaded before making calls to load files etc.
The best method of moving forward is to copy the web pages from Stolaf or UWI and ensure that they work under your system.
Then modify to what you want....
Good luck
Robert
-----Original Message-----
From: Tim te Beek [mailto:tim...@nb...]
Sent: Monday, October 29, 2012 08:57 AM
To: jsp...@li...
Subject: [Jspecview-users] NPE when loading JDX Spectrum inline through JavaScript in JmolJSV.js / Jmol.jsvLoadInline
Hi all,
I'm having difficulty integrating JspecView and Jmol together on a webpage using the new Jmol Javascript files. Specifically, when I try to load a spectrum inline using the following JavaScript snippet:
Jmol.jsvLoadInline(jsvApplet, "##TITLE = Predicted 1H NMR spectrum in metanol (CD3OD)\n##JCAMP-DX= 5.00.....
I get the following stacktrace in my browser console:
>>>
JSVGraphSet 1 nSpectra = 1
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at
sun.applet.PluginAppletSecurityContext$4.run(PluginAppletSecurityContext.java:670)
at java.security.AccessController.doPrivileged(Native Method) at
sun.applet.PluginAppletSecurityContext.handleMessage(PluginAppletSecurityContext.java:667)
at
sun.applet.AppletSecurityContextManager.handleMessage(AppletSecurityContextManager.java:70)
at
sun.applet.PluginStreamHandler.handleMessage(PluginStreamHandler.java:235)
at
sun.applet.PluginMessageHandlerWorker.run(PluginMessageHandlerWorker.java:78)
Caused by: java.lang.NullPointerException at jspecview.util.FileManager.isURL(FileManager.java:123)
at jspecview.util.FileManager.getName(FileManager.java:239)
at jspecview.common.JSVTree.createTree(JSVTree.java:183)
at jspecview.common.JSVTree.splitSpectra(JSVTree.java:377)
at jspecview.common.JSVTree.openDataOrFile(JSVTree.java:338)
at
jspecview.applet.JSVAppletPrivate.openDataOrFile(JSVAppletPrivate.java:774)
at jspecview.applet.JSVAppletPrivate.loadInline(JSVAppletPrivate.java:303)
at jspecview.applet.JSVApplet.loadInline(JSVApplet.java:163)
... 10 more
JSVPanel NMR Predicted 1H NMR spectrum in metanol (CD3OD) finalized Error on Java side: null
Browsing the JspecView code I can't pinpoint exactly what's happening, but it starts with this call in JSVAppletPrivate#loadInline:
openDataOrFile(data, null, null, null, -1, -1, true);
Can someone help me setup the inline loading of JDX files from JavaScript using the new Jmol JavaScript files to tie Jmol and JSpecView together?
Best,
Tim
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From: Tim te B. <tim...@nb...> - 2012-10-29 13:57:10
|
Hi all,
I'm having difficulty integrating JspecView and Jmol together on a webpage
using the new Jmol Javascript files. Specifically, when I try to load a
spectrum inline using the following JavaScript snippet:
Jmol.jsvLoadInline(jsvApplet, "##TITLE = Predicted 1H NMR spectrum in
metanol (CD3OD)\n##JCAMP-DX= 5.00.....
I get the following stacktrace in my browser console:
>>>
JSVGraphSet 1 nSpectra = 1
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at
sun.applet.PluginAppletSecurityContext$4.run(PluginAppletSecurityContext.java:670)
at java.security.AccessController.doPrivileged(Native Method)
at
sun.applet.PluginAppletSecurityContext.handleMessage(PluginAppletSecurityContext.java:667)
at
sun.applet.AppletSecurityContextManager.handleMessage(AppletSecurityContextManager.java:70)
at
sun.applet.PluginStreamHandler.handleMessage(PluginStreamHandler.java:235)
at
sun.applet.PluginMessageHandlerWorker.run(PluginMessageHandlerWorker.java:78)
Caused by: java.lang.NullPointerException
at jspecview.util.FileManager.isURL(FileManager.java:123)
at jspecview.util.FileManager.getName(FileManager.java:239)
at jspecview.common.JSVTree.createTree(JSVTree.java:183)
at jspecview.common.JSVTree.splitSpectra(JSVTree.java:377)
at jspecview.common.JSVTree.openDataOrFile(JSVTree.java:338)
at
jspecview.applet.JSVAppletPrivate.openDataOrFile(JSVAppletPrivate.java:774)
at jspecview.applet.JSVAppletPrivate.loadInline(JSVAppletPrivate.java:303)
at jspecview.applet.JSVApplet.loadInline(JSVApplet.java:163)
... 10 more
JSVPanel NMR Predicted 1H NMR spectrum in metanol (CD3OD) finalized
Error on Java side: null
Browsing the JspecView code I can't pinpoint exactly what's happening, but
it starts with this call in JSVAppletPrivate#loadInline:
openDataOrFile(data, null, null, null, -1, -1, true);
Can someone help me setup the inline loading of JDX files from JavaScript
using the new Jmol JavaScript files to tie Jmol and JSpecView together?
Best,
Tim
|
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From: LANCASHIRE,Robert J <rob...@uw...> - 2012-08-23 16:09:06
|
Tim, Bob Hanson <ha...@st...> suggests --------------- The answer is that you should be able to do this with a script command to JSpecView to select the specific peak. PEAK HNMR "ortho" or PEAK HNMR n where "n" is the index of the peak in the set of peaks of that type. ------------------ Robert -----Original Message----- From: Tim Cooijmans [mailto:t.c...@si...] Sent: Thursday, August 23, 2012 06:37 AM To: jsp...@li... Subject: [Jspecview-users] [JSpecview-users] Selecting peak from JDX file using javascript? Hi, I'm developing an integration of JSpecView and Jmol in Drupal together with Eelco van Dam for an educational environment. We're using the direct applet to applet JSpecView-JMol interaction to show vibrations and the associated peaks using JDX files. Of course when we click on a peak defined in the file this peak will be highlighted. However we didn't find a way to have a peak highlighted on load. Is there a way to do this using either parameters or javascript? (Javascript would be even nicer as this would mean it could be done dynamically). Regards, Tim Cooijmans ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Jspecview-users mailing list Jsp...@li... https://lists.sourceforge.net/lists/listinfo/jspecview-users |
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From: LANCASHIRE,Robert J <rob...@uw...> - 2012-08-23 11:58:13
|
Tim I wonder whether you should send this to the Jmol List since that is more likely to get broader coverage. Jmol now incorporates JSpecView and Bob Hanson has been doing all the major code development since January. Simple answer is it should all be possible now with the new features Bob has introduced. You'll need to get the latest version of Jmol/JSpecView though Regards Robert -----Original Message----- From: Tim Cooijmans [mailto:t.c...@si...] Sent: Thursday, August 23, 2012 06:37 AM To: jsp...@li... Subject: [Jspecview-users] [JSpecview-users] Selecting peak from JDX file using javascript? Hi, I'm developing an integration of JSpecView and Jmol in Drupal together with Eelco van Dam for an educational environment. We're using the direct applet to applet JSpecView-JMol interaction to show vibrations and the associated peaks using JDX files. Of course when we click on a peak defined in the file this peak will be highlighted. However we didn't find a way to have a peak highlighted on load. Is there a way to do this using either parameters or javascript? (Javascript would be even nicer as this would mean it could be done dynamically). Regards, Tim Cooijmans ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Jspecview-users mailing list Jsp...@li... https://lists.sourceforge.net/lists/listinfo/jspecview-users |
|
From: Tim C. <t.c...@si...> - 2012-08-23 11:36:52
|
Hi, I'm developing an integration of JSpecView and Jmol in Drupal together with Eelco van Dam for an educational environment. We're using the direct applet to applet JSpecView-JMol interaction to show vibrations and the associated peaks using JDX files. Of course when we click on a peak defined in the file this peak will be highlighted. However we didn't find a way to have a peak highlighted on load. Is there a way to do this using either parameters or javascript? (Javascript would be even nicer as this would mean it could be done dynamically). Regards, Tim Cooijmans |
|
From: LANCASHIRE,Robert J <rob...@uw...> - 2012-05-03 10:48:01
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HI, I'm currently traveling and email access not guaranteed to be good. Please look at examples from http://wwwchem.uwimona.edu.jm/spectra/JSpecView2/samples and http://chemapps.stolaf.edu/jmol/docs/examples-12/jspecview/ The URL you mention is for the old call-back methods and not for the direct applet to applet JCAMP-JMOL interaction. For IR the procedure is as you explained. You can obtain experimental data from a spectrometer or off the web and the vibrational information is calculated based on QM etc. In general the agreement is not wonderful and so there is a large amount of input needed by the person developing the links to try to match the two together. If you use the simulated IR from the same package that calculated the vibrational info you would of course get a good match and I have some examples showing this and then comparing the real spectrum recorded. Similarly for Raman. The Jmol display of XYZVib can be tweaked a little in terms of size of the perturbation but is clearly simplistic. I'm not sure whether any software packages give the sort of display you are thinking of directly. There are some interpolation arrangements I have seen that might do that. Are you going to BCCE in July? Bob and I will both be there. Regards Robert -----Original Message----- From: Eelco van Dam [mailto:Eel...@pe...] Sent: Wednesday, May 02, 2012 02:45 PM To: jsp...@li... Cc: LANCASHIRE,Robert J; T.B...@sc... Subject: Creating one source file for JSpecView and Jmol with the correct vibration data We are currently exploring the use of both Jmol and JSpecView in our educational environment. The applets will be used both standalone or combined with each other using that new integration dataformat that specifies the molecule, the spectrum and the vibration data in one file. Nice examples can be found showing the use just as we want it. Now the questions. - Are there already any tools available that can produce the needed JDX files with all data present or is there a workflow specified of how to produce them with the correct data? - We have found several examples (e.g. http://wwwchem.uwimona.edu.jm/spectra/JSpecView/iranim/acetophenoneJ/acetoph enone.html ) on the web of JCAMP-DX files containing vibration information that links molecular movements to an IR spectrum. Does anyone have an idea of how the vibration information is usually obtained and linked to what seems to be an experimentally measured IR spectrum? Is it a matter of calculating a molecular structure (either quantum mechanically or semi-empirically), predicting an IR spectrum and manually comparing it with an actual IR spectrum (i.e. manually adapting the frequencies to conform to the somewhat different peak positions in an experimental spectrum as compared to the predicted spectrum)? - The vibrations are included in the JCAMP-DX file as an XYZ (or XYZVIB or XYZ+vib) section. This basically adds difference vectors to the XYZ+equilibrium structure. In principle, the vibration should of course go both ways (e.g. aromatic out-of-plane bending should have the hydrogens bend upwards first, return to equilibrium and then go down), but as far as we can see this is not the case when specifying the vibrations in the XYZ structure (i.e. in aromatic out-of-plane bending the hydrogens bend upwards first, return to equilibrium and then go up again). Is there a way around this? (An obvious way would probably be to specify the one extreme as the equilibrium structure and twice the difference vector to reach the other extreme; is this possible? Any better ideas?) Kind regards, Eelco van Dam +31-6-43107551 www.Peacs.nl |
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From: Eelco v. D. <Eel...@Pe...> - 2012-05-02 19:02:09
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We are currently exploring the use of both Jmol and JSpecView in our educational environment. The applets will be used both standalone or combined with each other using that new integration dataformat that specifies the molecule, the spectrum and the vibration data in one file. Nice examples can be found showing the use just as we want it. Now the questions. - Are there already any tools available that can produce the needed JDX files with all data present or is there a workflow specified of how to produce them with the correct data? - We have found several examples (e.g. http://wwwchem.uwimona.edu.jm/spectra/JSpecView/iranim/acetophenoneJ/acetoph enone.html ) on the web of JCAMP-DX files containing vibration information that links molecular movements to an IR spectrum. Does anyone have an idea of how the vibration information is usually obtained and linked to what seems to be an experimentally measured IR spectrum? Is it a matter of calculating a molecular structure (either quantum mechanically or semi-empirically), predicting an IR spectrum and manually comparing it with an actual IR spectrum (i.e. manually adapting the frequencies to conform to the somewhat different peak positions in an experimental spectrum as compared to the predicted spectrum)? - The vibrations are included in the JCAMP-DX file as an XYZ (or XYZVIB or XYZ+vib) section. This basically adds difference vectors to the equilibrium structure. In principle, the vibration should of course go both ways (e.g. aromatic out-of-plane bending should have the hydrogens bend upwards first, return to equilibrium and then go down), but as far as we can see this is not the case when specifying the vibrations in the XYZ structure (i.e. in aromatic out-of-plane bending the hydrogens bend upwards first, return to equilibrium and then go up again). Is there a way around this? (An obvious way would probably be to specify the one extreme as the equilibrium structure and twice the difference vector to reach the other extreme; is this possible? Any better ideas?) Kind regards, Eelco van Dam +31-6-43107551 www.Peacs.nl |
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From: Eelco v. D. <Eel...@Pe...> - 2012-03-04 10:12:38
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Hi Robert, This is just the kind information we need. Thanks for remembering me with my question. I've seen some posts about the integration between Jmol and JSpecView from the Jmol group. We are, at this moment, investigating how to integrate the different applets to our needs. This is a great help to point us in the right directions. I'll keep you informed about our progress. Thanks. Kind regards, Eelco -----Oorspronkelijk bericht----- Van: LANCASHIRE,Robert J [mailto:rob...@uw...] Verzonden: zondag 4 maart 2012 2:55 Aan: Eel...@Pe...; jsp...@li... Onderwerp: RE: [Jspecview-users] Using one source file with JSpecView and Jmol HI, You may be interested to see the new samples JCAMP-DX files that incorporate a MOL and XYZVIB file in private labels. Jmol and JSpecView have undergone a merge so that both now read the JDX file and can be linked via PEAK information. Some examples are at http://wwwchem.uwimona.edu.jm/spectra/JSpecView2/sample and in the sourceforge SVN under data regards Robert -----Original Message----- From: Eelco van Dam (Peacs) [mailto:Eel...@Pe...] Sent: Saturday, October 08, 2011 11:02 AM To: jsp...@li... Subject: [Jspecview-users] Using one ssource file with JSpecView and JChemPaint L.S., Does anybody have any experience with the combination JSpecView and JChemPaint and one single molecule/spectrum source file like CML or perhaps anything different? I would like to use these applets but with as less overhead in all sorts of different source files. Is this doable? I found already that not all CML files (with all needed information contained) can be opened by both applets. Am I using the wrong database or is there a more implementation problem between the two applets? Kind regards, Eelco ---------------------------------------------------------------------------- -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 _______________________________________________ Jspecview-users mailing list Jsp...@li... https://lists.sourceforge.net/lists/listinfo/jspecview-users |
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From: LANCASHIRE,Robert J <rob...@uw...> - 2012-03-04 02:09:19
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HI, You may be interested to see the new samples JCAMP-DX files that incorporate a MOL and XYZVIB file in private labels. Jmol and JSpecView have undergone a merge so that both now read the JDX file and can be linked via PEAK information. Some examples are at http://wwwchem.uwimona.edu.jm/spectra/JSpecView2/sample and in the sourceforge SVN under data regards Robert -----Original Message----- From: Eelco van Dam (Peacs) [mailto:Eel...@Pe...] Sent: Saturday, October 08, 2011 11:02 AM To: jsp...@li... Subject: [Jspecview-users] Using one ssource file with JSpecView and JChemPaint L.S., Does anybody have any experience with the combination JSpecView and JChemPaint and one single molecule/spectrum source file like CML or perhaps anything different? I would like to use these applets but with as less overhead in all sorts of different source files. Is this doable? I found already that not all CML files (with all needed information contained) can be opened by both applets. Am I using the wrong database or is there a more implementation problem between the two applets? Kind regards, Eelco ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 _______________________________________________ Jspecview-users mailing list Jsp...@li... https://lists.sourceforge.net/lists/listinfo/jspecview-users |
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From: LANCASHIRE,Robert J <rob...@uw...> - 2011-10-09 00:32:39
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Eelco, my experience is with using Jmol and JSpecView in web pages and we have sample pages where it is possible to identify the position in the spectrum that was clicked and then for example interact with the Jmol applet or load an audio clip etc. see the JSpecView pages at http://wwwchem.uwimona.edu.jm/spectra/JSpecView Robert Prof. Robert J. Lancashire mailto:rob...@uw... Department of Chemistry Tel (876) 970 6026 University of the West Indies, Kingston 7 Fax (876) 977 1835 Mona Campus, JAMAICA. http://wwwchem.uwimona.edu.jm/chrl.html ________________________________________ From: Eelco van Dam (Peacs) [Eel...@Pe...] Sent: Saturday, October 08, 2011 10:01 AM To: jsp...@li... Subject: [Jspecview-users] Using one ssource file with JSpecView and JChemPaint L.S., Does anybody have any experience with the combination JSpecView and JChemPaint and one single molecule/spectrum source file like CML or perhaps anything different? I would like to use these applets but with as less overhead in all sorts of different source files. Is this doable? I found already that not all CML files (with all needed information contained) can be opened by both applets. Am I using the wrong database or is there a more implementation problem between the two applets? Kind regards, Eelco ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 _______________________________________________ Jspecview-users mailing list Jsp...@li... https://lists.sourceforge.net/lists/listinfo/jspecview-users |
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From: Eelco v. D. \(Peacs\) <Eel...@Pe...> - 2011-10-08 15:02:01
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L.S., Does anybody have any experience with the combination JSpecView and JChemPaint and one single molecule/spectrum source file like CML or perhaps anything different? I would like to use these applets but with as less overhead in all sorts of different source files. Is this doable? I found already that not all CML files (with all needed information contained) can be opened by both applets. Am I using the wrong database or is there a more implementation problem between the two applets? Kind regards, Eelco |
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From: Eelco v. D. \(Peacs\) <Eel...@Pe...> - 2011-10-08 14:43:25
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Hi Robert, Did you use JSpecView only as a viewer or also as a question tool? I mean, to let students pick a part of the spectrum to identify a specific group in the spectrum. We would like to use this kind of functionality. Kind regards. Eelco -----Oorspronkelijk bericht----- Van: LANCASHIRE,Robert J [mailto:rob...@uw...] Verzonden: vrijdag 7 oktober 2011 0:02 Aan: Eel...@Pe...; jsp...@li... Onderwerp: RE: [Jspecview-users] Using for elearning HI, We use Moodle here and we have been able to run it OK inside that. I had a report in 2006 that someone had tested it on punBB, Drupal, and Moodle I don't know anything about any follow ups. Sorry. We have just created an Android version that should be released soon. We can run on smart cell-phones and Tablets. Regards Robert -----Original Message----- From: Eelco van Dam (Peacs) [mailto:Eel...@Pe...] Sent: Thursday, October 06, 2011 03:59 PM To: jsp...@li... Subject: [Jspecview-users] Using for elearning L.S., Does anybody have any experience with this tool in combination/integration with an elearning environment to create an elearning cource? What elearning tools/environments can make a good combination with this tool? Currently I am investigating it in combination with CloseQuestion. Eelco ---------------------------------------------------------------------------- -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 _______________________________________________ Jspecview-users mailing list Jsp...@li... https://lists.sourceforge.net/lists/listinfo/jspecview-users |
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From: LANCASHIRE,Robert J <rob...@uw...> - 2011-10-06 22:18:08
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HI, We use Moodle here and we have been able to run it OK inside that. I had a report in 2006 that someone had tested it on punBB, Drupal, and Moodle I don't know anything about any follow ups. Sorry. We have just created an Android version that should be released soon. We can run on smart cell-phones and Tablets. Regards Robert -----Original Message----- From: Eelco van Dam (Peacs) [mailto:Eel...@Pe...] Sent: Thursday, October 06, 2011 03:59 PM To: jsp...@li... Subject: [Jspecview-users] Using for elearning L.S., Does anybody have any experience with this tool in combination/integration with an elearning environment to create an elearning cource? What elearning tools/environments can make a good combination with this tool? Currently I am investigating it in combination with CloseQuestion. Eelco ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 _______________________________________________ Jspecview-users mailing list Jsp...@li... https://lists.sourceforge.net/lists/listinfo/jspecview-users |
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From: Eelco v. D. \(Peacs\) <Eel...@Pe...> - 2011-10-06 20:12:45
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L.S., Does anybody have any experience with this tool in combination/integration with an elearning environment to create an elearning cource? What elearning tools/environments can make a good combination with this tool? Currently I am investigating it in combination with CloseQuestion. Eelco |
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From: Sean M. <se...@in...> - 2011-09-06 05:01:51
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We're using the excellent JSpecView applet for a web based application for the Analytical Centre of the University of NSW. One group of instruments (Bruker NMR) export JCAMP-DX 6.0. Are there plans to add support for this version? I'd be glad to help with the implementation, and have started looking into it, but I'm struggling to find a *good* reference on the file format. Sean |
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