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 [Jmol-users] (no subject) From: pieremanuele canepa - 2010-11-11 16:44 Attachments: Message as HTML Dear All, Can you show me the Jmol command to add a new atom knowing its fractional or Cartesian coordinates? Thanks a lot, Piero -- *Please consider the environment before printing this e-mail.* ** Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- 

 [Jmol-users] (no subject) From: - 2012-09-21 12:25 Attachments: Message as HTML Hi everybody. I have a simple issue. A mistake in rendering cicloexane ring from JME to Jmol. At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure the error. I remember being an old issue with Jmol. It appears in Jmol13, and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr ring for cycloexane. What happens ?Pino 

 Re: [Jmol-users] (no subject) From: Robert Hanson - 2012-09-21 13:40 Attachments: Message as HTML It works at http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolSmilesTest.htm without a problem. I'll take a look at your page to see what is going on there. On Fri, Sep 21, 2012 at 7:25 AM, pino.striccoli@... < pino.striccoli@...> wrote: > Hi everybody. I have a simple issue. A mistake in rendering cicloexane > ring from JME to Jmol. > > At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure > the error. I remember being an old issue with Jmol. It appears in Jmol13, > and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr > ring for cycloexane. What happens ? > > Pino > > > > ------------------------------------------------------------------------------ > Got visibility? > Most devs has no idea what their production app looks like. > Find out how fast your code is with AppDynamics Lite. > http://ad.doubleclick.net/clk;262219671;13503038;y? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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] (no subject) From: Robert Hanson - 2012-09-21 13:42 Attachments: Message as HTML Oh, one thing I see is that you are using an older JME applet. Try the one in http://chemapps.stolaf.edu/jmol/docs/examples-12 Although I don't think that is the problem. On Fri, Sep 21, 2012 at 7:25 AM, pino.striccoli@... < pino.striccoli@...> wrote: > Hi everybody. I have a simple issue. A mistake in rendering cicloexane > ring from JME to Jmol. > > At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure > the error. I remember being an old issue with Jmol. It appears in Jmol13, > and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr > ring for cycloexane. What happens ? > > Pino > > > > ------------------------------------------------------------------------------ > Got visibility? > Most devs has no idea what their production app looks like. > Find out how fast your code is with AppDynamics Lite. > http://ad.doubleclick.net/clk;262219671;13503038;y? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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] (no subject) From: Robert Hanson - 2012-09-21 13:45 Attachments: Message as HTML try using the JME output rather than the MOL file output. On Fri, Sep 21, 2012 at 8:40 AM, Robert Hanson wrote: > It works at > http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolSmilesTest.htmwithout a problem. I'll take a look at your page to see what is going on > there. > > On Fri, Sep 21, 2012 at 7:25 AM, pino.striccoli@... < > pino.striccoli@...> wrote: > >> Hi everybody. I have a simple issue. A mistake in rendering cicloexane >> ring from JME to Jmol. >> >> At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure >> the error. I remember being an old issue with Jmol. It appears in Jmol13, >> and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr >> ring for cycloexane. What happens ? >> >> Pino >> >> >> >> ------------------------------------------------------------------------------ >> Got visibility? >> Most devs has no idea what their production app looks like. >> Find out how fast your code is with AppDynamics Lite. >> http://ad.doubleclick.net/clk;262219671;13503038;y? >> http://info.appdynamics.com/FreeJavaPerformanceDownload.html >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > 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 Chair, Chemistry Department 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] (no subject) From: Robert Hanson - 2012-09-21 13:51 Attachments: Message as HTML This worked: jmolLoadInlineScript( gid('editor').jmeFile(),"") On Fri, Sep 21, 2012 at 8:40 AM, Robert Hanson wrote: > It works at > http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolSmilesTest.htmwithout a problem. I'll take a look at your page to see what is going on > there. > > On Fri, Sep 21, 2012 at 7:25 AM, pino.striccoli@... < > pino.striccoli@...> wrote: > >> Hi everybody. I have a simple issue. A mistake in rendering cicloexane >> ring from JME to Jmol. >> >> At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure >> the error. I remember being an old issue with Jmol. It appears in Jmol13, >> and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr >> ring for cycloexane. What happens ? >> >> Pino >> >> >> >> ------------------------------------------------------------------------------ >> Got visibility? >> Most devs has no idea what their production app looks like. >> Find out how fast your code is with AppDynamics Lite. >> http://ad.doubleclick.net/clk;262219671;13503038;y? >> http://info.appdynamics.com/FreeJavaPerformanceDownload.html >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > 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 Chair, Chemistry Department 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] (no subject) From: Angel Herráez - 2012-09-21 15:21 Hi Pino Yes, this problem has been there always with reading MOLfile data. As Bob says, using the JME format for the transfer fixes it. You can see both demonstrated in my page (compare the 2 buttons) http://biomodel.uah.es/en/DIY/JME/JME.htm If you still need to use MOL (as I do in my pages that do not use JME but other editors), the problem only affects a few very symmetrical molecules like cyclohexane and tert-butane. I just had the idea of changing the Z coord of one of the atoms (to break the symmetry) and it works for cyclohexane, see http://biomodel.uah.es/en/DIY/JME/JME2.htm but not for tert-butane as Jmol wrongly interprets tertiary carbons as planar (there was discussion about this some time ago and I guess some conclusion that I cannot remember, but I could not find a solution to apply to my page --but this is another issue.) PS: Could you please ammend my name in your page? Thanks 

 [Jmol-users] Display only a single protein chain From: Andreas Truszkowski - 2012-09-25 13:04 Hi, I can't find any script snippets on how to display only a single chain of an entire protein. E.g. Insulin (PDB: 4INS) has two compounds with each having 2 chains. How can I hide/display the chains independently. Kind regards, Andreas 

 Re: [Jmol-users] Display only a single protein chain From: Angel Herráez - 2012-09-25 13:18 Hi Andreas You need to find out the chain IDs (usually A, B ... but not always) Then display *:A; // will also hide all the others display add *:A; // makes A visible without hiding others etc. Check the DISPLAY and HIDE commands in the documentation 

 Re: [Jmol-users] Display only a single protein chain From: Andreas Truszkowski - 2012-09-25 13:29 Thank you very much. But hiding/displaying of protein chains is not documented. Kind regards, Andreas Am 25.09.2012 15:18, schrieb Angel Herráez: > Hi Andreas > > You need to find out the chain IDs (usually A, B ... but not always) > Then > > display *:A; // will also hide all the others > display add *:A; // makes A visible without hiding others > > etc. > Check the DISPLAY and HIDE commands in the documentation > > > > ------------------------------------------------------------------------------ > 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/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > 

 Re: [Jmol-users] Display only a single protein chain From: Angel Herráez - 2012-09-25 13:35 Sorry, hiding and displaying of ANYTHING is documented. You just combine display command with atom expressions, which are described in the doc (and used by most commands). Good luck! 

 [Jmol-users] ion sizes From: Pshemak Maslak - 2012-09-25 13:46 Displaying NaCl (from a cif file) shows Na+ sphere bigger than that of Cl-. I am assuming that atomic radii are use. Is there ionic radii info in Jmol? If so, how can one display it? PM 

 Re: [Jmol-users] ion sizes From: Phillip Barak - 2012-09-25 14:06 spacefill ionic --pb On 09/25/12, Pshemak Maslak wrote: > Displaying NaCl (from a cif file) shows Na+ sphere bigger than that of > Cl-. I am assuming that atomic radii are use. Is there ionic radii info > in Jmol? If so, how can one display it? > > PM > > > > > ------------------------------------------------------------------------------ > 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/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users 

 Re: [Jmol-users] ion sizes From: Otis Rothenberger - 2012-09-25 14:29 I'm playing with CIF files for the first time myself. The radii are VdW, and the following script components may be useful to you: connect delete;spacefill IONIC 30%;label "" Edit features in or out per your needs. Otis -- Otis Rothenberger otis@... http://chemagic.com On Sep 25, 2012, at 9:46 AM, Pshemak Maslak wrote: > Displaying NaCl (from a cif file) shows Na+ sphere bigger than that of > Cl-. I am assuming that atomic radii are use. Is there ionic radii info > in Jmol? If so, how can one display it? > > PM > > > > > ------------------------------------------------------------------------------ > 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/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users 

 [Jmol-users] (no subject) From: - 2013-08-27 16:56 Attachments: Message as HTML After a long break from JSmol, i decided to upload the last version of JSmol and continue working on my pages, but i found some problems with these pages http://pinostriccoli.altervista.org/html5/index.htmlwhen trying to load molecoles in pdb. It seems loading just mol and xyz files.I have the error file reader not found .... Any suggestion?did i do some mistake in uploading? Thanks a lotPino 

 Re: [Jmol-users] (no subject) From: Rolf Huehne - 2013-08-27 17:21 On 08/27/2013 06:56 PM, pino.striccoli@... wrote: > After a long break from JSmol, i decided to upload the last version of JSmol and continue working on my pages, but i found some problems with these pages http://pinostriccoli.altervista.org/html5/index.htmlwhen trying to load molecoles in pdb. It seems loading just mol and xyz files.I have the error file reader not found .... Any suggestion?did i do some mistake in uploading? > Thanks a lotPino > Your update didn't work correctly. The JSmol version that is shown in the JSmol menu on your page is '13.1.12_dev' but the latest is at least 13.3.4. You should try updating again. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhuehne@... Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 

 Re: [Jmol-users] (no subject) From: Angel Herráez - 2013-08-27 17:26 Hello Pino I looked at your source code. Some things have changed, particularly integration with jQuery (and that deals with the AJAX methods for loading files from remote servers, as fas as I understand). Instead of calling several JS files, you should just call jsmol.min.js See the Wiki > JSmol page for more details 

 [Jmol-users] (no subject) From: - 2013-09-16 21:13 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 

 Re: [Jmol-users] (no subject) From: Robert Hanson - 2013-09-16 22:40 Attachments: Message as HTML 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.striccoli@... < pino.striccoli@...> 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=58041151&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > 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 

 Re: [Jmol-users] (no subject) From: Angel Herráez - 2013-09-17 07:43 Ciao Pino http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Functions_that_s et_CSS_rules explains it. > I found jmol.setAppletCss. Where should I insert the script and what can be > the exat sintax? Not exact, but something like this: Before the call to getJmolApplet: Jmol.setAppletCss(".toLeft") as long as you have defined the css code for class "toLeft" or Jmol.setAppletCss("style='float:left'") 

 [Jmol-users] (no subject) From: Carl McBride - 2013-11-14 11:18 This is not really a bug, I am just looking for an idiots guide to running both JSmol (jmol-13.2.8) in conjunction with MathJax (release branch v2.2) on a MediaWiki (1.21.2) site without getting a red [Math Processing Error]. All the best, carl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dr. Carl McBride Departamento de Ciencias y Técnicas Fisicoquímicas Facultad de Ciencias Universidad Nacional de Educación a Distancia (UNED) 28040 Madrid Spain friedel.uned.es/carlmcbride.html http://www.SklogWiki.org >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 

 Re: [Jmol-users] (no subject) From: Robert Hanson - 2013-11-14 18:42 Attachments: Message as HTML Do we have that on the wiki yet, Angel? If not, we need to add it. Since MathJax actually rewrites the entire page after loading, you have to make sure your Jmol applet is added within a script that runs only after MathJax is complete. Not sure if MathJax has a callback on that, but there is a div on the page that is hidden and is reporting MathJax progress. Here is a rendition of that prior message on this list, updated a bit for newer JSmol.min.js versions. It's a pretty simple solution. Really what the problem is is that both Jmol and MathJax are competing for the AJAX processing. For compatibility with MathJax, make sure: 1) you are using dynamic loading of the applet -- no

 Re: [Jmol-users] (no subject) From: Angel Herráez - 2013-11-14 19:05 No, we don't have it in the Wiki. I remember some former thread about MathJax but did not take note. I will try to do it some day I think there is a page on compatibility with other frameworks/libraries, it could go there 

 [Jmol-users] (no subject) From: - 2013-11-26 17:14 Can anybody explain to me this error i find on this page http://pinostriccoli. altervista.org/?p=5589? On firefox (windows or linux) it works ok. In Chrome (windows or Linux) gives me unrecognised format error. What happens? any idea? Pino 

 Re: [Jmol-users] (no subject) From: Jaime Prilusky - 2013-11-26 17:54 Chrome 31.0.1650.57 and Safari Version 7.0 (9537.71) on Mac 10.9 also gave format error, most probably the same you got. Simply Javascript on Firefox (Gecko engine) runs under different rules than on Chrome/Safari (WebKit engine). Jaim On Nov 26, 2013, at 7:14 PM, pino.striccoli@... wrote: > Can anybody explain to me this error i find on this page http://pinostriccoli. > altervista.org/?p=5589? > On firefox (windows or linux) it works ok. In Chrome (windows or Linux) gives > me unrecognised format error. > What happens? any idea? > Pino > > ------------------------------------------------------------------------------ > Rapidly troubleshoot problems before they affect your business. Most IT > organizations don't have a clear picture of how application performance > affects their revenue. With AppDynamics, you get 100% visibility into your > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users `