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janocchio-users — Questions and suggestions from Janocchio users
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From: bdrakuli <bdr...@ch...> - 2013-10-03 18:40:20
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Dear Janocchio developers, I have relatively simple system Ph-CH=CH-Py-CH=CH-Ph, Ph rings are para-substituted and Py state for pyridine (2,6-disubstituted with the rest of molecules). When I input set of conformers and ascribe coupling constants, 'red light' appeared when coupling constant of ~ 16 Hz is ascribed to -CH=CH- moiety, which are in all conformers in trans configuration. I used Janocchio in past for different systems, but does not observe such artifacts. Any comment is highly appreciated. Kind regards Branko |
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From: Oliver G. <o.g...@nu...> - 2011-07-04 13:54:42
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Hi all, Would it be possible to use this software to predict STD-NMR data? Oliver |
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From: Yael B. <ba...@te...> - 2009-09-16 06:46:50
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Thank you for the suggestion! I reinstalled java and its now working great! Sincerely, Yael Quoting jan...@da...: > Hi, > > Thanks for the messages and trying Janocchio. > I'm currently running Janocchio on RedHat enterprise 4 (kernel > 2.6.9-42.ELsmp) on a x86_64 machine, > with Sun Java 1.6.0_03, without the issues you mention. I have > previously used more recent Ubuntu installs > and other Java versions, but don't have a full list of 'suppported' set > ups. > Would suggest upgrading/reinstalling Java, although if the applet is > working I'm not sure what effect that will have. > Sorry can't be more help. > > Dave > > > > On Tue, 08 Sep 2009 14:40 +0300, "Yael Balazs" > <ba...@te...> wrote: > > Thank you David Evans and Gary Sharman for making this tool available. > > Janocchio.jar as a stand alone is running nicely on our windows PC. > > > > I would also like to have it run on a PC with a red hat enterprise OS. > > The installation overall seems fine - but it is running ridiculously slow > > (not computer hardware, core duo). Display of a structure is fine. Atom > > selection is bogging down, both graphics and for NOE display (several > > minutes > > the one time it displayed at all, it usually just hangs). > > > > Any tips/tricks/suggestions what to try? > > I tried changing install directories and changing permissions, but I'm > > just shooting in the dark. > > > > For the installation I unzipped the janocchio-1.1-bin_dep.zip and either > > double-clicked on the Janocchio.jar icon or tried from the command line > > using java -jar /opt/janocchio-1.1/Janocchio.jar > > Janocchio opens. I can open an .sd or a .mol file and rotate. > > Any operation involving atom selection is problematic (including adding > > labels). > > > > I don't see any graphical highlighting of a selected atom, like I do when > > working with Janocchio on the Windows PCs. > > > > I hope there's an obvious mistake I've made which is easily corrected. > > > > Sincerely, > > Yael > > > > -- > > Yael S. Balazs, Ph.D. > > http://schulich.technion.ac.il/mrc > > NMR Facility Manager phone: +972-4-829-3748 > > Schulich Faculty of Chemistry fax: +972-4-829-5703 > > Technion - Israel Institute of Technology > > Haifa, Israel 32000 email: ba...@te... > > > > > ------------------------------------------------------------------------------ > > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > > 30-Day > > trial. Simplify your report design, integration and deployment - and > > focus on > > what you do best, core application coding. Discover what's new with > > Crystal Reports now. http://p.sf.net/sfu/bobj-july > > _______________________________________________ > > Janocchio-users mailing list > > Jan...@li... > > https://lists.sourceforge.net/lists/listinfo/janocchio-users > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Janocchio-users mailing list > Jan...@li... > https://lists.sourceforge.net/lists/listinfo/janocchio-users > -- Yael S. Balazs, Ph.D. http://schulich.technion.ac.il/mrc NMR Facility Manager phone: +972-4-829-3748 Schulich Faculty of Chemistry fax: +972-4-829-5703 Technion - Israel Institute of Technology Haifa, Israel 32000 email: ba...@te... |
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From: <jan...@da...> - 2009-09-08 15:41:16
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Hi, Tested multi-conformer formats are .sdf and .xyz. Concantenating two .mol files will only work in general if there is a $$$$ line after each conformer (this converts from mol format to sdf format), if you tried this and it still didn't work I'm not sure. Dave On Tue, 08 Sep 2009 15:18 +0300, "Yael Balazs" <ba...@te...> wrote: > Does someone have a demo multi-conformer file available that I could look > at and > try out? > I'd like to see the format of a file that allows me to step through > frames. > I tried a .mol file with two conformers and it loads as one frame > with two conformers on display. > I'm guessing I need a different format for Janocchio to recognize that > I want each conformer displayed in a different frame. > (It seemed like using the shift to to open multiple files should put > them into different frames, but that didn't work). > > Pax, > Yael > > -- > Yael S. Balazs, Ph.D. > http://schulich.technion.ac.il/mrc > NMR Facility Manager phone: +972-4-829-3748 > Schulich Faculty of Chemistry fax: +972-4-829-5703 > Technion - Israel Institute of Technology > Haifa, Israel 32000 email: ba...@te... > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Janocchio-users mailing list > Jan...@li... > https://lists.sourceforge.net/lists/listinfo/janocchio-users |
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From: <jan...@da...> - 2009-09-08 15:34:09
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Hi, Thanks for the messages and trying Janocchio. I'm currently running Janocchio on RedHat enterprise 4 (kernel 2.6.9-42.ELsmp) on a x86_64 machine, with Sun Java 1.6.0_03, without the issues you mention. I have previously used more recent Ubuntu installs and other Java versions, but don't have a full list of 'suppported' set ups. Would suggest upgrading/reinstalling Java, although if the applet is working I'm not sure what effect that will have. Sorry can't be more help. Dave On Tue, 08 Sep 2009 14:40 +0300, "Yael Balazs" <ba...@te...> wrote: > Thank you David Evans and Gary Sharman for making this tool available. > Janocchio.jar as a stand alone is running nicely on our windows PC. > > I would also like to have it run on a PC with a red hat enterprise OS. > The installation overall seems fine - but it is running ridiculously slow > (not computer hardware, core duo). Display of a structure is fine. Atom > selection is bogging down, both graphics and for NOE display (several > minutes > the one time it displayed at all, it usually just hangs). > > Any tips/tricks/suggestions what to try? > I tried changing install directories and changing permissions, but I'm > just shooting in the dark. > > For the installation I unzipped the janocchio-1.1-bin_dep.zip and either > double-clicked on the Janocchio.jar icon or tried from the command line > using java -jar /opt/janocchio-1.1/Janocchio.jar > Janocchio opens. I can open an .sd or a .mol file and rotate. > Any operation involving atom selection is problematic (including adding > labels). > > I don't see any graphical highlighting of a selected atom, like I do when > working with Janocchio on the Windows PCs. > > I hope there's an obvious mistake I've made which is easily corrected. > > Sincerely, > Yael > > -- > Yael S. Balazs, Ph.D. > http://schulich.technion.ac.il/mrc > NMR Facility Manager phone: +972-4-829-3748 > Schulich Faculty of Chemistry fax: +972-4-829-5703 > Technion - Israel Institute of Technology > Haifa, Israel 32000 email: ba...@te... > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Janocchio-users mailing list > Jan...@li... > https://lists.sourceforge.net/lists/listinfo/janocchio-users |
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From: Rzepa, H. <h....@im...> - 2009-09-08 13:03:59
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At 13:37 +0100 8/9/09, Yael Balazs wrote: >Using Henry Rzepa's Janocchio applet >http://www.ch.ic.ac.uk/local/organic/janocchio/index.html >takes a while to open, and the digital signature cannot be verified, >but it allows me to run Janocchio excellently on the Linux box. > >What are the drawbacks to running this way? (And what does Henry think about >this!?) Janocchio is certainly not my applet! But what one can do is take any applet, and sign it with an application certificate, for local use. Such a signing does not imply ownership, merely that someone has certified its use outside of the regular Java sandbox. The reason for signing is normal to ensure that the applet can save to a local file store (not possible with an unsigned applet). A similar approach is adopted for the Jmol applet. -- Professor Henry S Rzepa. +44 (020) 7594 5774 (Voice); http://www.ch.ic.ac.uk/rzepa/ & /rzepa/blog Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). |
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From: Yael B. <ba...@te...> - 2009-09-08 12:43:51
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Using Henry Rzepa's Janocchio applet http://www.ch.ic.ac.uk/local/organic/janocchio/index.html takes a while to open, and the digital signature cannot be verified, but it allows me to run Janocchio excellently on the Linux box. What are the drawbacks to running this way? (And what does Henry think about this!?) Sincerely, Yael -- Yael S. Balazs, Ph.D. http://schulich.technion.ac.il/mrc NMR Facility Manager phone: +972-4-829-3748 Schulich Faculty of Chemistry fax: +972-4-829-5703 Technion - Israel Institute of Technology Haifa, Israel 32000 email: ba...@te... |
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From: Yael B. <ba...@te...> - 2009-09-08 12:43:44
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Does someone have a demo multi-conformer file available that I could look at and try out? I'd like to see the format of a file that allows me to step through frames. I tried a .mol file with two conformers and it loads as one frame with two conformers on display. I'm guessing I need a different format for Janocchio to recognize that I want each conformer displayed in a different frame. (It seemed like using the shift to to open multiple files should put them into different frames, but that didn't work). Pax, Yael -- Yael S. Balazs, Ph.D. http://schulich.technion.ac.il/mrc NMR Facility Manager phone: +972-4-829-3748 Schulich Faculty of Chemistry fax: +972-4-829-5703 Technion - Israel Institute of Technology Haifa, Israel 32000 email: ba...@te... |
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From: Yael B. <ba...@te...> - 2009-09-08 12:43:36
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Thank you David Evans and Gary Sharman for making this tool available. Janocchio.jar as a stand alone is running nicely on our windows PC. I would also like to have it run on a PC with a red hat enterprise OS. The installation overall seems fine - but it is running ridiculously slow (not computer hardware, core duo). Display of a structure is fine. Atom selection is bogging down, both graphics and for NOE display (several minutes the one time it displayed at all, it usually just hangs). Any tips/tricks/suggestions what to try? I tried changing install directories and changing permissions, but I'm just shooting in the dark. For the installation I unzipped the janocchio-1.1-bin_dep.zip and either double-clicked on the Janocchio.jar icon or tried from the command line using java -jar /opt/janocchio-1.1/Janocchio.jar Janocchio opens. I can open an .sd or a .mol file and rotate. Any operation involving atom selection is problematic (including adding labels). I don't see any graphical highlighting of a selected atom, like I do when working with Janocchio on the Windows PCs. I hope there's an obvious mistake I've made which is easily corrected. Sincerely, Yael -- Yael S. Balazs, Ph.D. http://schulich.technion.ac.il/mrc NMR Facility Manager phone: +972-4-829-3748 Schulich Faculty of Chemistry fax: +972-4-829-5703 Technion - Israel Institute of Technology Haifa, Israel 32000 email: ba...@te... |
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From: <jan...@da...> - 2007-10-04 21:42:47
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It seems the problem was a simple typo -- the web page was trying to load swing_layout_1.0_Signed.jar, when the new signed jar was actually called swing-layout-1.0_Signed.jar. (Oops :-)) I've amended the installation docs, which I think led both Prof. Rzepa and myself to make the same error in testing the procedure. Dave |
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From: <jan...@da...> - 2007-10-03 21:00:07
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Hi, Thanks for all the posts! I've been trying to fix the applet issue, but it seems to be dependent on which keystore is used to sign the applet. The signed jar files we've been using in house work everywhere I've tried them, included localhost on my home laptop, using the html code copied from your website. But jars signed with a new keystore, generated as I described in the docs with 'keytool -genkey -alias myalias' don't work, and give the java.lang.NoClassDefFoundError: org/jdesktop/layout/GroupLayout$Group error. I did think that I generated my functioning keystore in the same way, but there must be some difference I suppose. Does anyone out there have experience of this kind of problem? In the interim I could distribute signed jar files -- but I'd like to understand this better, obviously. The mailing list should be set up to accept posts from members without moderation, and to allow new members to join without moderation. I get a message as list admin if anyone tries to post without joining first. All the sourceforge archives seem a bit slow to log new messages. With regard to library size, I think that it might be possible to eliminate the cdk dependency altogether and use the Jmol molecule classes directly, but this has not been a priority so far. If I get enough evidence of other users who want smaller downloads, I'll look into it. I'm glad to hear that Janocchio has been noticed in the open-source community. Given that it is based so heavily on Jmol, we wanted to give the code back. We don't have much time or any special drive at the moment to evangelise it's use outside the company, but I am interested in fixing bugs problems and hearing about interesting feature requests. Dave On Wed, 3 Oct 2007 07:03:06 +0100, "Rzepa, Henry" <h....@im...> said: > >Hi, > > > >Thanks for posting this. I'm glad we're not completely ignored :) > > > by the way. The post still has not appeared on the forum. I did > subscribe, but > there seems to be an error because my post was flagged as waiting > moderation > as a non-subscriber. Perhaps that might account for the paucity of > posts? > -- > > Henry Rzepa. > +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rz...@ma... > (iChat) > http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, > SW7 2AZ, UK. > > (Voracious anti-spam filter in operation for received email. > If expected reply not received, please phone/fax). > |
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From: <jan...@da...> - 2007-10-02 19:28:23
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Hi, Thanks for posting this. I'm glad we're not completely ignored :) It does seem that the current applet installation instructions are wrong -- I tried to follow them myself on my home laptop using janocchio-1.0.2 and got the same error as below. Sorry about that -- the identical java code is running as an applet at work, so I will try and fix the problem tomorrow. If anyone else is reading this, please do post and let everyone know if you have any suggestions for or problems with Janocchio. Dave Evans Comp. Chemist at Eli Lilly and Janocchio developer .... (Views and opinions my own and not those of my employer) On Tue, 2 Oct 2007 13:36:02 +0100, "Rzepa, Henry" <h....@im...> said: > I see I have the honour of the second post to this list; may there > be many more. > > I have a query; I signed the jars and mounted at > http://www.ch.ic.ac.uk/local/organic/janocchio/ > > but when run (either Windows or OS X, Firefox), > it gives the error > > Initializing Preferences... > Missing i18n menu resource, trying old scheme for: > Prefs.clearConsoleButton > Initializing Recent Files... > Initializing Script Window... > Initializing AtomSetChooser Window... > Initializing Noes... > java.lang.NoClassDefFoundError: org/jdesktop/layout/GroupLayout$Group > at org.openscience.jmol.app.NoeTable.<init>(NoeTable.java:137) > at org.openscience.jmol.app.Nmr.<init>(Nmr.java:225) > at org.openscience.jmol.app.NmrApplet.start(NmrApplet.java:115) > at sun.applet.AppletPanel.run(AppletPanel.java:418) > at java.lang.Thread.run(Thread.java:613) > > Can the developers advise? > -- > > Henry Rzepa. > +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rz...@ma... > (iChat) > http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, > SW7 2AZ, UK. > > (Voracious anti-spam filter in operation for received email. > If expected reply not received, please phone/fax). > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Janocchio-users mailing list > Jan...@li... > https://lists.sourceforge.net/lists/listinfo/janocchio-users |
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From: Rzepa, H. <h....@im...> - 2007-10-02 12:37:03
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I see I have the honour of the second post to this list; may there be many more. I have a query; I signed the jars and mounted at http://www.ch.ic.ac.uk/local/organic/janocchio/ but when run (either Windows or OS X, Firefox), it gives the error Initializing Preferences... Missing i18n menu resource, trying old scheme for: Prefs.clearConsoleButton Initializing Recent Files... Initializing Script Window... Initializing AtomSetChooser Window... Initializing Noes... java.lang.NoClassDefFoundError: org/jdesktop/layout/GroupLayout$Group at org.openscience.jmol.app.NoeTable.<init>(NoeTable.java:137) at org.openscience.jmol.app.Nmr.<init>(Nmr.java:225) at org.openscience.jmol.app.NmrApplet.start(NmrApplet.java:115) at sun.applet.AppletPanel.run(AppletPanel.java:418) at java.lang.Thread.run(Thread.java:613) Can the developers advise? -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rz...@ma... (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). |
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From: <jan...@da...> - 2007-05-10 08:37:59
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First test message |
