Re: [Jmol-users] installation
Hi Kris I'm no expert in Linux, but it seems that your system doesn't know how to open jar files. So, you must invoke Java for that file: java -jar Jmol.jar adding the proper paths to java and Jmol.jar, if needed Another option is to try the script file included in the distribution, which for your system should be jmol or jmol.sh that is supposed to have the proper parameters, but you probably have to tweak it a bit Let us know if you find the solution (or not) - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] installation
Hi, Try: java -jar Jmol.jar or double-click on Jmol.jar (will start with Java if Java is setup that way) Otherwise: is there a .sh file in the archive ? Nico On Tue, Nov 18, 2008 at 9:03 AM, Van Alsenoy Kris <[EMAIL PROTECTED]>wrote: > Dear All, > > I've downloaded jmol-11.6.4-binary.tar.gz. In the resulting directory > jmol-11.6.4 I now have a file > -rwxr-xr-x 1 alsenoy users 4238127 2008-11-09 23:26 Jmol.jar > > >From the README.txt file I understood that I should be able to run this > program, if I do, I get the message : > bash: ./Jmol.jar: cannot execute binary file > > What should I do ? > > Many thanks in advance, > sincerely, > kris > > -- > -- > Kris Van Alsenoy, > Structural Chemistry Group, Department of Chemistry, > University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium > [EMAIL PROTECTED] /Phone:+32(3)8202366/Fax:+32(3)8202310 > visit us at: http://www.ua.ac.be/structuurchemie > -- > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] installation
Dear All, I've downloaded jmol-11.6.4-binary.tar.gz. In the resulting directory jmol-11.6.4 I now have a file -rwxr-xr-x 1 alsenoy users 4238127 2008-11-09 23:26 Jmol.jar >From the README.txt file I understood that I should be able to run this program, if I do, I get the message : bash: ./Jmol.jar: cannot execute binary file What should I do ? Many thanks in advance, sincerely, kris -- -- Kris Van Alsenoy, Structural Chemistry Group, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium [EMAIL PROTECTED] /Phone:+32(3)8202366/Fax:+32(3)8202310 visit us at: http://www.ua.ac.be/structuurchemie -- - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Installation help request
Rchard: I am going through the same transition and I am not a programmer. Look at the source here http://classes.yale.edu/chem225b/studyaids/MOVIES/instrJmol.html I place all .mol files in the jmol folder that contains jmol.js etc. .mol files can be in folders if you wish. My jmol folder is at the level (shell) of index.html. My html files can be in any shell as long as I reference properly. If the html is two levels deeper than the jmol folder then ../../jmol/caffeine.mol. Fred Hello JMolsters, Installation help request I have been experimenting with jmol as an alternative to Chime. It seems almost impossible to get Chime loaded on networked computers used in UK secondary education. Like others in this forum, I took some of the code for displaying caffeine and other molecules from other sites, but seemed to have problems with accessing files in different directories. I have almost got it sorted out ( see http://www.biotopics.co.uk/jmol/JmolApplet/JMolmenu.html ), but I get a disturbing yellow error page (twice?) as each molecule loads. My server error log repeatedly shows that I am missing the following files: jmol/ui/JmolPopupWords.class jmol/ui/JmolPopupWords_en.properties jmol/ui/JmolPopupWords_en.class jmol/ui/JmolPopupWords_en_GB.properties jmol/ui/JmolPopupWords_en_GB.class Conceivably I have done something wrong when unpacking Jmol-10.00, possibly resulting in a messy directory hierarchy. Can anyone tell me what should be where? Alternatively: Can I turn off the messages? A possibly related question: what should be the location of Jmol.js and under what circumstances is a codebase definition necessary? Thanks in advance. Richard Dr. Richard G Steane Near Guildford Surrey UK Website: http://www.biotopics.co.uk dedicated to Biology teaching and learning --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Professor Frederick E. Ziegler Sterling Chemistry Laboratory 225 Prospect Street Yale University P.O. Box 208107 New Haven, Connecticut 06520-8107 E-mail: [EMAIL PROTECTED] Telephone: (203) 432-3959 Fax: (203) 432-6144 --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_idv37&alloc_id865&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Installation help request
Hello Richard I think you are safe using Jmol 10.00 (I have pages that use it), but you need to take one of two courses of action: 1) If you want to write your tags, as you are doing now, you need to follow Jmol's request for a full set of instructions, which is what the yellow pane is telling you (namely, add a http://jmol.sourceforge.net/jslibrary/ to know how exactly to use it. I can help you if you need. > My server error log repeatedly shows that I am missing the following files: > jmol/ui/JmolPopupWords.class > jmol/ui/JmolPopupWords_en.properties > jmol/ui/JmolPopupWords_en.class > jmol/ui/JmolPopupWords_en_GB.properties > jmol/ui/JmolPopupWords_en_GB.class I cannot help about these. > Conceivably I have done something wrong when unpacking Jmol-10.00, possibly > resulting in a messy directory hierarchy. Can anyone tell me what should be > where? I don't think you have done anything wrong in this respect. > A possibly related question: what should be the location of Jmol.js and > under what circumstances is a codebase definition necessary? As advised by Nico, Jmol.js can be anywhere as long as you refer to it. Regarding the jar file(s), if you run pages form a web server they can be anywhere too, but if you want to use local files (such as hard disk or a CD), jmolapplet.jar(s) must be above the molecular model files in the folder hierarchy --or in the same folder--. I get good results putting both the jar(s) and Jmol.js in the top-level (or root) folder of the pages' folder structure. You are welcome to write me off-list if you want some more help. --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Installation help request
Hi, welcome in the Jmol world Richard Steane wrote: Hello JMolsters, Jmol with a 'm', JMol is an other application ;) Installation help request I have been experimenting with jmol as an alternative to Chime. It seems almost impossible to get Chime loaded on networked computers used in UK secondary education. Like others in this forum, I took some of the code for displaying caffeine and other molecules from other sites, but seemed to have problems with accessing files in different directories. I have almost got it sorted out ( see http://www.biotopics.co.uk/jmol/JmolApplet/JMolmenu.html ), but I get a disturbing yellow error page (twice?) as each molecule loads. My server error log repeatedly shows that I am missing the following files: jmol/ui/JmolPopupWords.class jmol/ui/JmolPopupWords_en.properties jmol/ui/JmolPopupWords_en.class jmol/ui/JmolPopupWords_en_GB.properties jmol/ui/JmolPopupWords_en_GB.class Conceivably I have done something wrong when unpacking Jmol-10.00, possibly resulting in a messy directory hierarchy. Can anyone tell me what should be where? Alternatively: Can I turn off the messages? You are using version 10.00.00 So, you have probably done nothing wrong, it's just the way Java checks for Resource for the current language. You should try a prerelease version (v10.00.45) which should fix the problem because the i18n stuff has been completely changed. The prerelease version contains a lot more functions than v10.00, but no translations in other languages (bug in the generation which should be fixed for the next prerelease)) If the prerelease version show also errors in the log (they will be different in they exist), please report it here so we can investigate. A possibly related question: what should be the location of Jmol.js and under what circumstances is a codebase definition necessary? The best place is to put it in the same directory as JmolApplet*.jar. The location is up to you, it should work. The only problem can be if you want to run it in a local environment (file://) instead of with a web server. You can check the Jmol wiki (http://wiki.jmol.org/) for more informations. Nico --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Installation help request
Hello JMolsters, Installation help request I have been experimenting with jmol as an alternative to Chime. It seems almost impossible to get Chime loaded on networked computers used in UK secondary education. Like others in this forum, I took some of the code for displaying caffeine and other molecules from other sites, but seemed to have problems with accessing files in different directories. I have almost got it sorted out ( see http://www.biotopics.co.uk/jmol/JmolApplet/JMolmenu.html ), but I get a disturbing yellow error page (twice?) as each molecule loads. My server error log repeatedly shows that I am missing the following files: jmol/ui/JmolPopupWords.class jmol/ui/JmolPopupWords_en.properties jmol/ui/JmolPopupWords_en.class jmol/ui/JmolPopupWords_en_GB.properties jmol/ui/JmolPopupWords_en_GB.class Conceivably I have done something wrong when unpacking Jmol-10.00, possibly resulting in a messy directory hierarchy. Can anyone tell me what should be where? Alternatively: Can I turn off the messages? A possibly related question: what should be the location of Jmol.js and under what circumstances is a codebase definition necessary? Thanks in advance. Richard Dr. Richard G Steane Near Guildford Surrey UK Website: http://www.biotopics.co.uk dedicated to Biology teaching and learning --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
RE:[Jmol-users] Installation Jmol 10
Bonjour, Quelle est l'utilisation envisagée de Jmol ? S'il s'agit de consulter des pages aucune installation ou stockage n'est nécessaire. Il suffit de lancer ces pages. S'il s'agit de créer des pages utilisant Jmol, il suffit de définir un répertoire de travail sur sa machine et de stocker en attendant tout le dossier dans ce répertoire. Seuls quelques fichiers seront utiles et nécessaires au fonctionnement des pages. Le reste correspont à des documents, des échantillons ... Toutes une série de bricoles utiles ou pas selon le cas. S'il s'agit de participer au développement de Jmol, cela dépasse mes compétences ... ;-) J'espère que ces infos seront utiles. Hervé Furstoss --- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Installation Jmol 10
Title: Installation Jmol 10 Bonjour, Je ne sais pas ou mettre tous les dossiers téléchargés, cela ne se met pas tout seul. Dans quels fichiers du disque dur pour Mac OS X ? Je vous envoie une capture d'écran Merci Hello, I do not know or to put all the downloaded files, that is not put all alone. In which files of the hard disk for Mac OS X? I send a capture of Merci screen to you -- Viviane Guillaume biological Professor biochemistry-engineering ENCPB Paris <>
Re: [Jmol-users] Installation problem
What happens when you run "java -version"? Or when you run "java -Djmol.home=c:\jmol-2 -cp c:\jmol-2\jars\jmol.jar org.openscience.jmol.Jmol"? Thanks, Bradley - Original Message - From: "kerrell chia" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Tuesday, April 30, 2002 1:13 AM Subject: [Jmol-users] Installation problem > Hi, I've problem install jmol. > > I'm using an AMD (32bit) machine in the windows 98 > environment and I the file I download was jmol-2.zip > I extract it to c:\ and get a directory c:\jmol-2 > > Then after, I click on the jmol.bat but it gave me a > "bad command or file name" error. Then go to the > command prompt and type > set JMOL_HOME=h:\jmol-2 > and > jmol.bat > but this time the error was > "Out of environment space" > "Bad command or file name" > > Please help, anyone. > > Cheers, > BK > > __ > Do You Yahoo!? > Everything you'll ever need on one web page > from News and Sport to Email and Music Charts > http://uk.my.yahoo.com > > ___ > Jmol-users mailing list > [EMAIL PROTECTED] > https://lists.sourceforge.net/lists/listinfo/jmol-users >
[Jmol-users] Installation problem
Hi, I've problem install jmol. I'm using an AMD (32bit) machine in the windows 98 environment and I the file I download was jmol-2.zip I extract it to c:\ and get a directory c:\jmol-2 Then after, I click on the jmol.bat but it gave me a "bad command or file name" error. Then go to the command prompt and type > set JMOL_HOME=h:\jmol-2 and > jmol.bat but this time the error was "Out of environment space" "Bad command or file name" Please help, anyone. Cheers, BK __ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
