Re: [Jmol-users] Jmol on PDA
Hi, I am not aware of someone trying to run Jmol with J9. The Jmol applet may be able to run on it, but you would have to try. The Jmol application probably won't work since it requires Java 1.4 or +. Tell us what you find if you try Jmol with J9. Nico De: [EMAIL PROTECTED] Is it possible to run Jmol using IBM's J9 virtual machine. We would like to use Jmol on PDAs as a visualisation tool for high school chemistry students. Any assistance would be appreciated. - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] emails into sourceforge archive
De: Annemarie Rom-Weisenbach Hello. I could find no explanation about this on the web site. If I have missed something, please point me there. How long does it take the emails from this list to make it into the SourceForge jmol-users archive? Right now, the latest in the archive date from Oct 2. I am wondering how long I'll need to keep personal copies of interesting topics before they will be available in the archive. Hi, Thanks for pointing this out. it's probably a bug in sourceforge. I will check the mailing list configuration, and if there's no reason there for the mails not being, I will open a support request on sourceforge. Nico - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmol
De: Rzepa, Henry [EMAIL PROTECTED] In the mediawiki invocation of Jmol, how might one address different instances of a jmol. Might it be eg jmol name=first or jmol id=first? Would either of these be supported by your code? The following should work jmol jmolApplet namefirst/name /jmolApplet /jmol See http://wiki.jmol.org/index.php/MediaWiki#Reference Nico - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol 10.9.84
Jmol 10.9.84 is available at http://www.jmol.org/files/ Changes: - set labelPointerBackground - set labelPointerBox - set labelPointerNoBox - polyhedra restrict fix There's still a bug concerning translations (i18n) in this release (the messages classes are compiled as JDK 1.5). I am trying to find a fix. Currently, the archives available on Bob's site should work correctly. Nico - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol prerelease 10.9.80
De: Paul Pillot [EMAIL PROTECTED] I get the following error message with this version (downloaded from sourceforge) : Ignore java.lang.UnsupportedClassVersionError: org/jmol/translation/JmolApplet/Messages_fr (Unsupported major.minor version 49.0) at java.lang.ClassLoader.defineClass0(Native Method) Strange, it seems that some classes have been compiled with Java 1.5 instead of 1.4. Will check this evening. Nico - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] issue with message callbacks and in ternationalization
De: Bob Hanson [EMAIL PROTECTED] ooh, you're not the only one. I've done the same thing in the past and never ever thought about translation. We could IN PRINCIPLE offer a no translation option, but that seems to me rather rude. You are right that this could very well break some pages -- mine included. For example, I have a page that says: if(what.indexOf(Script completed)=0)return Oh, oh! I don't know what the solution for this is. We could: 1) back off and not translate so much -- but what to choose? The limit could be that everything output to the console is not translated, but I don't like this idea much. 2) promote using jmolScriptWait() more, which returns the number of selected atoms directly with no need for callbacks. (If that is what you are doing.) We should promote using methods (like jmolScriptWait()) for pages wanting to have feedback from Jmol. The problem with parsing textual output from Jmol is not limited to i18n, but can also occur with pure English: - between two versions of Jmol we can change some strings. - the user can already choose to display the level (DEBUG, INFO, ...) associated with the textual output, or even to suppress some output levels Be that as it may, you are right, Paul, pages using this hack will be broken for non-English speakers. Yieks. Bob Paul Pillot wrote: Hello, I have a simple page with a messagecallback function which extracts the number of atoms selected in the expression n atoms selected I've just realized that it's not working anymore because, using a french browser I get the message n atomes séléctionnés instead. Internationalization in Jmol is great, but I think that in this case it may break lots of parsers, without their authors knowing the bug (imagine someone writing a script, and doing intensive debugging in english browsers, how can he guess that the message won't be the same if an user as different language settings ?). How can we adress this important issue ? Paul - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] surfaces and JVXL files
De: Bob Hanson [EMAIL PROTECTED] One problem I see is that, at least on a PC, the menu doesn't seem to smartly scroll. Is this a Swing option I'm missing? No, this is a Swing limitation, very frustrating. AFAIK, Only way to overcome this is to handle it manually: if you have more than X elements in the menu then you have to divide you menu in submenus. That's something I had to do for a menu containing 600 elements. If you need, I can send a sample code. Nico - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] new command-line options; jmol writes JVXL files directly
A little Jmol window opened and closed itself after a while. The output file afterwards contained the measurement list. that is the correct behavior. I don't know how to hide that window, and I'm not sure I want to. Is that OK? If someone can figure out how to make this totally no display, I'm all for it. That's past my ability. I will take a look at it if I find some time this evening (still at the office :( ) Nico - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Two questions concerning the Jmol Applet
De: Angel Herraez [EMAIL PROTECTED] Welcome, Christian 1) is it possible to display simultaneously two proteins in the applet? If yes how? As Bob has pointed out, you can only load one file, so two proteins must be in the same file --can do it by hand or with some software. Not entirely true. There's an *experimental* feature in Jmol to read several files. IIRC: load name file 1 file 2 ... file n It's not finished but you can always try it. Nico --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid0709bid3057dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol.js prototype: Jmol-new.js and jmolScriptWait
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Re: [Jmol-users] Jmol applets in MediaWiki and Wikipedia
Could someone please explain how to achieve the following code result uploadedFileContentsEthanol.xyz/uploadedFileContents When I try to upload a file, mediawiki tells me its not a recognised image file, and refuses it. I guess a setting has to be tweaked somewhere (perhaps even setting a chemical/x-xyz MIME type?) to allow this? Is it on the Jmol wiki ? I have authorized uploading .cml, .pdb and .xyz files. I don't see you in the users list, maybe it's just a problem of permissions. Try registering. I have only tested it from my user access with sysop privileges. Nico --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid0709bid3057dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol applets in MediaWiki and Wikipedia
De: Angel Herraez [EMAIL PROTECTED] Just from reading the doc, this looks wonderful functionality. Congratulations, Nico! Thanks :) --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid0709bid3057dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: Re: [Jmol-users] Jmol prerelease 10.00.60 (latest before official release)
1p84.pdb: What a monster! Actually, this bug was never fixed. It's fixed now and will appear corrected in the next release. It was fixed by me, but under an other number (1450367) because the report was made twice. But I made the fix directly in the PDB reader, not elsewhere. Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: [Jmol-users] Re: Jmol-Übersetzung
De: Daniel Leidert [EMAIL PROTECTED] Attached is what I have been able to do with the translation so far. I simply edited the files with Notepad under Windows, there seemed to be need to install poedit (or would that give me more insight into anything?). poedit is - the name already says it - an editor, which is intended to be used for gettext po files. It is a very special editor for such files. But every other editor is also fine. There is just one requirement: The editor _MUST NOT_ add any control characters except for e.g. newline. MS Word is definitely an editor, which CANNOT be used for this work. poEdit really helps editing the translation by clearly showing what needs to be translated. But Notepad should work also. and b) definitely a test setup so the messages can be seen in the context of the application. Don't you have an environment to build Jmol on Windows? I have basic Eclipse experience so I'll work through the steps tonight. You will further need gettext for Windows (and if you run the default target, you will probably also need the applications mentioned at http://wiki.jmol.org/index.php/Internationalisation#Translating_the_Applet-.2C_User-_and_Developers-Guide). I have update the Eclipse page, it should be self sufficient: http://wiki.jmol.org/index.php/Eclipse * What happens if I think an English message might need slight changes? Tell it the list. I still think that e.g. AtomSetChooser is a real bad string. So if you find more such strings, write it to the list. Yes, the Java source code needs to be changed. It won't be changed for 10.2 because it will require to modify all translations after that, but suggestions are welcome for next versions. I assume msgids coincide with the text displayed in English, No. The coincide with the text found in the source. (x)gettext parses the Java source and extracts all translatable strings. It does not know, what strings it extracts nor in which language they are written. Yes to both in fact: - msgid is the english text - msgid is the key to find the translation but I don't suppose I can just go ahead and change ids in the German PO file. No, never change the msgid or the translation won't be used (or the msgid will be reverted to it's original value by gettext tools) The attachment is forwarded to the list too. Do I include it in the source or do I wait for the next version ? Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: [Jmol-users] Jmol-Übersetzung
No, never change the msgid or the translation won't be used (or the msgid will be reverted to it's original value by gettext tools) gettext AFAIR uses a hash-table. It gets the original string and then searches the table in the given catalog for the corresponding translations. It does AFAIR not revert a string from the hash-table. It does. For example, if you fix a simple thing in an English string, gettext tools will be able to see that it's probably the same string, and the msgid will be changed and the translation marked as fuzzy (that's what happened when we added the to the menu items) Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] zoom/centering changes
Although I see plenty of blank space at the bottom of the page, the divs (table cells?) are short (each with a scroll bar) such that I cannot view the whole applet and the messaging beneath it at the same time. I can take a screen shot and post it if this is not clear. The bottom line is, if the divs went to the bottom of the page, I would not need to scroll every single time to see the information you are displaying beneath the applet (which takes the top half of the applet out of view, as well). I have the same problem on XP/2k with Firefox/IE Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: [Jmol-users] Jmol prerelease 10.00.60 (latest before o fficial release)
If release date gets nearer and I still missed to update the German translation (if nobody else wants to do the update), please give me a short hint. ATM I have a lot of work, but I don't want to miss the translation update/translation preparation for 10.2.x. 10.2.0 is scheduled for Friday 04/14 but Sebastian (see other post in mailing list) already proposed himself to update the German translation. Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol prerelease 10.00.60 (latest before official release)
Jmol prerelease 10.00.60 is now available for download from: http://www.jmol.org/files This release includes: * hbonds calculate * changes on Frieda recenter/zoom made in 10.00.59 were reverted This prerelease should be the latest before the official Jmol release 10.2 scheduled for next Friday. Please, test this version as much as you can, since it will become the next stable release. Until the release of Jmol 10.2, work should be focused on : - documentation - tests - updating the translations For translators: if you have time, you can update the translations in your language. Check http://wiki.jmol.org/index.php/Internationalisation The number of untranslated messages for the languages supported by Jmol is : - ca (Catalan) : 4 - de (German) : 74 - es (Spanish) : 2 - et (Estonian) : 5 - fr (French) : done - nl (Dutch) : done - pt (Portuguese) : 15 The release of 10.2 will be the opportunity to change our version releasing scheme. There will be 2 versions maintained at the same time : - 10.2.x will be the stable release branch (only bugfixes) - 10.3.x will be the development release branch (bugfixes, new features, ...) We also intend to make stable releases more often. Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New Jmol Wiki: No MouseManual
De: Eric Martz [EMAIL PROTECTED] To the new Wiki developers: Please restore the former http://wiki.jmol.org/MouseManual into the new wiki. I did some page renaming when I exported the Wiki to the new format. So there are two solutions : - use the new names (Mouse_Manual) in the application. I will do it for it the next release of Jmol, is it possible to do it also for FirstGlance ? - add a MouseManual redirect page in the Wiki. I think I will do both, so that old versions still access a valid URL, but that would be better if new versions were accessing the new page directly FirstGlance in Jmol (in use by Nature Structural and Molecular Biology) has a link to this document, as does Jmol's menu itself (About Jmol, Mouse Manual). Thanks for pointing this out Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New Jmol Wiki: No MouseManual
To the new Wiki developers: Please restore the former http://wiki.jmol.org/MouseManual into the new wiki. I did some page renaming when I exported the Wiki to the new format. So there are two solutions : - use the new names (Mouse_Manual) in the application. I will do it for it the next release of Jmol, is it possible to do it also for FirstGlance ? Renaming is needed because the wiki uses a different URL formating. You will have to replace: http://wiki.jmol.org/MouseManual by http://wiki.jmol.org/index.php/Mouse_Manual - add a MouseManual redirect page in the Wiki. Done, but it's probably not enough Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol prerelease 10.00.59
Jmol prerelease 10.00.59 is now available for download from: http://www.jmol.org/files This release includes: * Fixed links to the new Wiki * Updated translations * Changes in Frieda recenter/zoom * Many changes in Eval * Max zoom increase Note: some changes may not be in the next official release, I have to see with Egon. --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol prerelease 10.00.57
Miguel wrote: Jmol prerelease 10.00.57 is now available for download from: http://www.jmol.org/files This release: * reintroduces the connect() expression (see below) select connect(2) invalid expression token:connect : select connect(2) as all other connect(min,max,selection) forms in 10.00.57 I thought it was connected() not connect() Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] New Jmol Wiki
Hi everyone, The Jmol Wiki is now using a totally new version under MediaWiki instead of MoinMoin Wiki. The URL is still the same: http://wiki.jmol.org/ It may take a few days for the DNS changes to propagate correctly through the internet, so don't worry if you still get the previous wiki, everything should be resolved by itself in 1 or 2 days. Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New Jmol Wiki
De: Daniel Leidert [EMAIL PROTECTED] Be sure to patch and/or update it in realtime. MediaWiki often had security issues. Ok, it's the last current version. It seems, that everyone is allowed to change content. I highly recommend to change this so only registered users are allowed to change content, or spam will destroy your work. I prefer to let it that way for the moment and see what happens. If spam becomes a problem, then I will require registration. Note that there are already 2 anti-spam mechanisms in place : - open-proxy blocking - blacklist If they are not enough, I will make registration necessary for edition. Another question: Since when the GFDL is used as license for the Wiki content? Did the old Wiki also use the GFDL? AFAIR not and so I do not agree to use the GFDL license, especially for the parts I wrote - mainly internationalisation stuff. The information written there should be free to all - with an all-permissive license or a simple two-liner, which gives unlimited permission to copy, distribute and modify it. Ok, I can remove the GFDL license. Will see this evening. Regards, Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New Jmol Wiki
De: Rzepa, Henry [EMAIL PROTECTED] Re MediaWiki and Jmol. This seems likely to be a FAQ, but I am not up on the totality of the postings to this list. We have enabled JMol within MediaWiki using eg http://fahwiki.net/index.php/Jmol_MediaWiki_Extension Check rather the page on the new wiki : http://wiki.jmol.org/index.php/MediaWiki I have updated it yesterday, but it's still a development version only. I intend to work on it in the next days/weeks to have a fully working extension. but it seems a very restricted solution, supporting only .xyz files. It also mandates the use of hard line breaks to delineate atoms etc. It was tested only on .xyz files, but it should work with other file formats. Check Bduke user's page on the Jmol wiki, I think it's not .xyz file. What is the problem with the hard line breaks ? They correspond to the line breaks in the files. Is there perchance a solution that supports other formats, ideally CML, but at a pinch MDL Molfiles? Try the current version of the extension on the Jmol Wiki, hopefully it will work. If it doesn't work, tell me, I will see what can be done about it. Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] prerelease 10.00.50
De: Miguel [EMAIL PROTECTED] It looks like the 'color' command bug from 10.00.48 that was fixed in 10.00.49 is not fixed in 10.00.50. If I load a PDB structure with my interface Jmol gets stuck and shows the error message below. Regards, Rolf Rolf, I cannot reproduce this problem ... it seems to work OK for me. I checked Dots.java: it's different from what's in Bob's branch. A test is missing in the trunk. I have committed the change, I think Rolf can try with it. Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Relative against absolute addresses
De: Brian Salter-Duke [EMAIL PROTECTED] I raised this once before, and I may be out of date, but I'd like to raise it again. It seems necessasry to use relative addresses for jmol.js and the jmol directory in web pages. I can the see the principle i here but it causes serious problems in two respects:- 1. When trying to incorporate jmol in wiki pages. One user doing this reports that ../extensions/jmol is needed for it to work in preview and ./extensions/jmol when the article is saved (I could have these the wrong way round). An absolute address would fix this. I can not even get it to work like that user reports. I'm still struggling. I will work again on Jmol extension for MediaWiki in April, after the Jmol wiki is moved to MediaWiki. If you can wait until then, I will see what can be done to install easily the Jmol extension. Otherwise, you can easily modify Jmol.js to remove the test on absolute addresses. Miguel: would it be ok to add a function like jmolAuthorizeAbsoluteAddress() in Jmol.js so that people can desactivate the test on absolute addresses ? Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol in Molecular Endocrinology
De: [EMAIL PROTECTED] My paper describing a database system for glycoprotein-hormone receptors (GRIS) is finally accepted and published online by Molecular Endocrinology! The system makes extensive use of Jmol to visualize the receptor structures and for structure analysis tools. If it's not already done, you can add a description of your website in the Jmol Wiki. http://wiki.jmol.org/WebsitesUsingJmol Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] running scripts
I've been trying to debug this, but the script() does not return any feedback... null in all cases, even if I make the script invalid. Also tried evalScript()... all nulls... What am I doing wrong? Are you sure that the command is completed when you script() returns ? I thought that script() was asynchronous. Try adding some delay between each command to see if something is different. Or better, use scriptWait() instead of script() --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] running scripts
Try adding some delay between each command to see if something is different. but I don't see any cartoons even after some time... :( The problem is that commands are not queued up at all, so I think that if you issue a command when the previous one is still running, then the command is just lost Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol macros: scripting in the application
De: Egon Willighagen [EMAIL PROTECTED] I'm not what you mean here... yes, hardcoding it in the application is always possible... but the nice thing about macros is, is that you don't have to recompile Jmol... but maybe I did not understand you. I was talking about a menu item to an help page on the Macro feature, not a macro itself ;) Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Broken color command - V.10.00.48
De: [EMAIL PROTECTED]
When I analyzed the problem it showed up that at least the 'color dots'
command seems to be broken.
When I type for example 'color dots red' in the Jmol console window
Jmol freezes and I get the following error message in the Java console:
Dots.setProperty('color')
Dots.setProperty('colorConvex')
java.lang.NullPointerException
at org.jmol.viewer.Dots.setProperty(Dots.java:199)
at org.jmol.viewer.Dots.setProperty(Dots.java:189)
at org.jmol.viewer.Frame.setShapeProperty(Frame.java:757)
at org.jmol.viewer.ModelManager.setShapeProperty(ModelManager.java:347)
at org.jmol.viewer.Viewer.setShapeProperty(Viewer.java:1838)
at org.jmol.viewer.Eval.colorObject(Eval.java:1621)
at org.jmol.viewer.Eval.color(Eval.java:1565)
at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:336)
at org.jmol.viewer.Eval.run(Eval.java:294)
at java.lang.Thread.run(Unknown Source)
The error occurs independant of the PDB file that is loaded.
I have tried with the SVN version and I didn't get any problem with a few PDB
files from the Jmol-datafiles directory.
Nico
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Re: [Jmol-users] Jmol and MediaWiki
Message d'origine De: Miguel [EMAIL PROTECTED] There was some progress about mid 2005 in getting the Jmol applet working under Wikis. I am particularly interested in wikis running under MediaWiki. I want to be able to display Jmol molecular images on a regular basis on a wiki. Does anyone know whether there has been any progress since last July? I can not find anything. Not much progress has been made. Nico has done some work for MediaWiki. I am very interested in making things work well with MediaWiki ... but I am currently swamped with other things. I haven't work on it for a few months. The latest version can be found at http://fahwiki.net/ I will probably work on it in a near future, but we need to decide a few things with Miguel before. If you have suggestions on the MediaWiki extension for Jmol, please send them to me or to the list. Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] My protein dipole moment server now uses jmol
De: Clifford Felder [EMAIL PROTECTED] Dear Miguel and the jmol user and developer community. More and more sites are looking to use your wonderful program. I am pleased to announce that my protein dipole moment server at http://bioinfo.weizmann.ac.il/dipol/indexj.html now uses jmol to display both the protein as a backbone ribbon and the dipole vector in jmol. I am grateful to Dr. Jaime Prilusky for his tremendous help to make this happen. Feel free to add a reference to your website in the Jmol Wiki: http://wiki.jmol.org/WebsitesUsingJmol Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [Fwd: [Bug 269973] Java applet causes all typing in browser to
De: Bob Hanson [EMAIL PROTECTED] PLEASE take a moment and VOTE FOR THIS BUG! https://bugzilla.mozilla.org/show_bug.cgi?id=269973 It's a known bug; we need it FIXED! Agreed and done. I suggest also to vote for this one which depends on a fix to the bug above to be fixed: https://bugzilla.mozilla.org/show_bug.cgi?id=256763 Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid0944bid$1720dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] applet/JavaScript interface possibilities
De: Bob Hanson [EMAIL PROTECTED] OK, now this is just an idea I'm working with. What I'm interested in is others' ideas of what to implement here. Obviously anything that can be currently shown should be implemented this way -- orientation, for example. What else? The JSON part seems interesting in the situation of Applet + Javascript, but is there an easy way to use it in the situation of Java (for example, when integrating Jmol in an other application, or even inside Jmol for the povray export) ? Will we need to code a parser for the JSON String ? 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://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] java error help
De: Frieda Reichsman [EMAIL PROTECTED] Hi, I am getting the following error message in the Java console, on Mac OSX10.4, can someone tell me what it means? I suspect I am doing something simple wrong, but cannot seem to find my error. error opening file:/Users/friedar/Sites/minm/scitech/boyer/animations/ enzyme/cox2.pdb java.lang.StringIndexOutOfBoundsException: String index out of range: 37 openFile(cox2.pdb) 18 ms Could you send the pdb files so that we can try to open it and see where the exception happens ? 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://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Re: compressed PDB
De: Egon Willighagen [EMAIL PROTECTED] A: jmol-users@lists.sourceforge.net Sujet: Re: [Jmol-users] Re: compressed PDB Date: Thu, 2 Feb 2006 17:01:37 +0100 On Thursday 02 February 2006 16:56, Tamas Horvath wrote: or gzipped of course On 2/2/06, Tamas Horvath [EMAIL PROTECTED] wrote: Can Jmol read a zipped/jar-ed pdb file? Yes, just like an unziped/unjared PDF file. Jmol detects this on the fly. Are you sure ? I thought only gzipped files were working, which would make sense: - gzip is a single file compression format - zip/jar is compression format for a directory structure: how do you what file you should read in it ? 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://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] README.txt file in the distribution
De: [EMAIL PROTECTED] I'd like to see this file expanded to have, even a brief, description of each of the files in the distribution. Would you be willing to write the descriptions ? 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://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] README.txt file in the distribution
De: [EMAIL PROTECTED] Oh, I would have already if I knew what they all were. :-) But other than Jmol.js and Jmol.jar and Jmol.sh I haven't very much of a clue :-) Ok, I have done a first version. I am committing it under CVS. It's not complete, I hope someone else will modify it 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://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] distinguish some hydrogen atoms
Hi, De: Kevin Dunn [EMAIL PROTECTED] I would like to use a different color for hydrogen atoms attached to N or O than those attached to C. What is the easiest way to do this using a pdb file? I tried just lying in the pdb, calling some hydrogens Li, but this seems ugly and the van der Waals radii are wrong. If I call some atomd HA and some HB is there a way to give them different colors? Simply loads your file, select the atoms you want to change color and change their color. Use commands like that: select substructure([H][N]) and substructure([H]); color atoms blue; The substructure command is only available in the pre-release version of Jmol (you can use it), but there's probably an other way to select only the atoms you are interested in. 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://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] CML visualization in Jmol
De: Miguel [EMAIL PROTECTED] Francois indicated that his CML files have no connectivity information. If he uses 'set autobond off' then he will have only atoms, with no bonds at all. In fact, his example contains bond informations: bondArray bond atomRefs2=1 2 order=1/ bond atomRefs2=1 11 order=1/ Apparently, Jmol doesn't understand them. For what I understand from the code of CMLReader, the reader expects to have the atom ids in the atomRefs attribute, not the atom numbers. 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://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Loading an pdb file from a url
De: Tjaart de Beer [EMAIL PROTECTED] Hi I am a newbie tryinh to developing pages with javascript. I am trying to enable a user to load any pdb file (from the PDB) into Jmol from a webpage. I have tried using the following: jmolApplet(600, load http://www.pdb.org/pdb/files/1tx2.pdb;); without any success. It gives me an error saying bad URL but if I open up the link in Firefox I see the physical pdb file. The idea is to allow the user to type in a pdb file code which will then be automatically loaded. Any ideas? I think this is a security problem, the Applet probably doesn't have the right to access an other webserver than the one it was downloaded from. You should check the archives of the mailing lists (or wait for someone to help), there are probably examples on how to do this. 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_idv37alloc_id865op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol prerelease 10.00.43
De: Angel Herraez [EMAIL PROTECTED] Angel and Nicolas wrote: The pop-up About Mouse Manual and About Translations do nothing in the app. Should that be so? (Haven´t tested the applet yet) Does the About www.jmol.org do something ? Was it working with previous prereleases ? All 3 links work in the applet 10.00.43, opening a new browser window (Firefox 1.0.6 and IE 6 WIndows) Good :) In the app they do nothing. Quite normal for the moment, there's absolutely no code at all to handle this. Something to put on the TODO list. Nicolas --- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today * Register for a JBoss Training Course Free Certification Exam for All Training Attendees Through End of 2005 Visit http://www.jboss.com/services/certification for more information ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] PFAAT uses Jmol
De: Timothy Driscoll [EMAIL PROTECTED] hi all, in case anyone is interested: I just came across a protein sequence alignment tool called PFAAT (http://pfaat.sourceforge.net/). this software uses Jmol as an inline structure visualization module. it looks pretty cool, and I can see great possibilities in the combination. (displaying aligned 3D structures, coloring 3D structure by alignment score, etc.) Thanks for the link :) You should add it in the Jmol wiki at http://wiki.jmol.org/ApplicationsEmbeddingJmol Nico --- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Flow control/timing and Jmol?
De: Rzepa, Henry [EMAIL PROTECTED] As I have mentioned in the past, testimonials to the use of Jmol in eg Journal pages could perhaps be collected by some volunteer on the sf pages.I have about 10 examples sprinkled around various journals, including my favorite, http://www.ch.ic.ac.uk/rzepa/bpr/ which will appear in J Chem Ed. Why not adding them in the Jmol wiki ? Everyone can add its own contribution. For example, on the JmolLiterature page ? http://wiki.jmol.org/JmolLiterature Nicolas --- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] error building latest CVS version of JMol
Hi, I did several modifications in build-i18n.xml very recently but I don't have a Unix system to test it, only Windows. I may have done something wrong. Could you run ant in a more verbose mode and send me the resulting output ? Thanks for reporting the problem, Nicolas De: Rajarshi Guha [EMAIL PROTECTED] create-application-pot: [echo] Generating Jmol.pot (gettext PO-template) file in src/org/jmol/translation/Jmol ... [apply] /usr/bin/xgettext: no input file given [apply] Try `/usr/bin/xgettext --help' for more information. [apply] Result: 1 [apply] Applied xgettext to 0 files and 0 directories. BUILD FAILED /home/rajarshi/src/java/jmol/build-i18n.xml:95: Warning: Could not find file /home/rajarshi/src/java/jmol/src/org/jmol/translation/Jmol/tmp/Jmol.pot to copy. Am I missing something from my build environment? xgettext is present. --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] error building latest CVS version of JMol
De: Rajarshi Guha [EMAIL PROTECTED] The output of running ant -v is attached. It's strange, the apply task doesn't seem to find the Java source files ! Are you running ant from the jmol directory ? Nicolas --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: Re: [Jmol-users] atomic and ionic radii in Jmol: demonstration page
De: timothy driscoll [EMAIL PROTECTED] Technical: the page is written completely via javascript to allow for easy translation/localization --now in English and Spanish--. localization does not require javascript: http://www.w3.org/TR/1999/REC-html401-19991224/struct/dirlang.html it's not required, but it helps a lot to clearly separate what needs to be translated and what doesn't need to be translated : - the javascript is not translated and is the same for all languages - the html (in fact xml for the source code) is of minimal size, so it's easy to maintain the translations when the english page changes. The same principle was applied for the colors page, the xml source code (the file that needs translations) is only 5k (~100 lines), the javascript is about 35k. Easier for translators --- SF.Net email is Sponsored by the Better Software Conference EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile Plan-Driven Development * Managing Projects Teams * Testing QA Security * Process Improvement Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: Re: [Jmol-users] Re: [Jmol-developers] DOC - stereo
De: Bob Hanson [EMAIL PROTECTED] Do you suggest we add this to the documentation? Maybe at least a health warning? I vote for adding this to the online doc :) both the recipe and the health warning Nicolas Egon Willighagen wrote: the recipe to look at these stereo images is like this: ... --- SF.Net email is Sponsored by the Better Software Conference EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile Plan-Driven Development * Managing Projects Teams * Testing QA Security * Process Improvement Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] (no subject)
A: jmol-users@lists.sourceforge.net Is ver 10 of jmol available for WinXP Pro? If so where? If not what ver is? And, where can I dwnld that ver? Jmol v10 is available for all platforms with Java 1.4 (maybe with older versions). You can download it from the main page http://sourceforge.net/projects/jmol/ Nicolas --- SF.Net email is Sponsored by the Better Software Conference EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile Plan-Driven Development * Managing Projects Teams * Testing QA Security * Process Improvement Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] more documentation examples
De: Sebastian Lisken [EMAIL PROTECTED] I would have thought that more Jmol-Users subscribers were disturbed by that huge file that Nicolas Vervelle posted to the list (by mistake, I assume). Yep, that was a mistake, sorry for that. I didn't check the file size before sending it. The mail was blocked and I asked Egon and Miguel to eventually remove it, but it was accepted before my second mail reached them. I would have removed it myself, but I don't have admin rights for the mailing lists. Nicolas --- SF.Net email is Sponsored by the Better Software Conference EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile Plan-Driven Development * Managing Projects Teams * Testing QA Security * Process Improvement Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Ligand selection blues
Hi, De: David Leader [EMAIL PROTECTED] I am refering to specific ligands in the pdb file which I have in my database. I can turn them on with commands of the type: param name=script value=set hetero off; select LLP; spacefill; color cpk; set hydrogen off Initially I turned these off with the simple command that works in rasmol/chime: param name=altscript value=restrict protein However in the particular case cited (LLP in 1a8i.pdb) there are amino acids in the ligand and Jmol treats the ligand as protein. It would be nice if I could specifically turn LLP off, but the best I can do to get back to where I was is: param name=altscript value=restrict 0;cpk off;restrict protein;wireframe off; backbone 0.3 Does anyone know a more elegant way of doing this? I think you can do the following : If you're using one of the prerelease version, you can specify selection using SMILES patterns. Something like : restrict not substructure(your smiles pattern); Hope this helps Nicolas --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77alloc_id492op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] drums on jmol colors page
Hi, De: Angel Herraez [EMAIL PROTECTED] I have started to compile a page describing colors used by Jmol. For now, it will be linked from the Wiki http://wiki.jmol.org/JmolColors Your draft is really nice :) The suggestion for a tooltip seems also good to me, or at least reorganizing the matrix to be less vertical (page has a lot of empty space on a big screen). If you're interested, you can modify the source pages of Jmol website to have something similar on the colors page. Otherwise, I will try to do it in August. Nicolas --- SF.Net email is Sponsored by the Better Software Conference EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile Plan-Driven Development * Managing Projects Teams * Testing QA Security * Process Improvement Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Script loops
De: Richard Spinney [EMAIL PROTECTED] 1) spin this seems to default to a rotation about the Y axis. Is there a way to change the rotation to the X or Z axis? spin set X speed 2) Loop command: I understand this causes the entire script to repeat (after a delay). Is there a way to get only part of the script to loop? i.e. A possible way of doing it is to put the part that will repeat in a separate script that is called from the main script (script scriptName Hope this helps Nicolas --- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Script loops
De: Richard Spinney [EMAIL PROTECTED] Hi Nicolas, Thanks for the info on the spin command. I tried your idea about a separate script: var script1 =move 0 0 51.43 0 0 0 0 0 1; loop 1; jmolCheckbox(spin off; reset; script1, reset; rotate X 90; spin on, Animation on/off); But this does not work, I get a message of command expected : script1. Is it just a syntax error on my part? You have to create a separate file the script. For example, create a text file name script1.txt with the content: move 0 0 51.43 0 0 0 0 0 1; loop 1; then in your page : jmolCheckbox(spin off; reset; script script1.txt, reset; rotate X 90; spin on, Animation on/off); It should work I think. Nicolas --- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Povray and backbone visualization
Hi, De: Chris Weichenberger [EMAIL PROTECTED] Dear all, I have tried unsuccessfully to render a backbone drawing with povray. I am using the standalone jmol.sh script on a Debian linux (kernel version 2.6.11.10) with the Java Runtime Environment version 1.4.2-01. I start jmol (version 10.00 and 10.00.12) from the shell issuing 'jmol.sh 1phz.gz' where 1phz is a standard PDB file. The script select *; cpk off; wireframe off; backbone 100 then shows the backbone as a CA trace in Jmol. Running povray from the toolbar only displays a background color picture. However, if I go on to select the backbone nitrogen and carbons via backbone off; select *.N or *.CA or *.C; wireframe 100 to feed this to povray via the toolbar button, it nicely renders a trace as also seen on the Jmol screen. Comparing the two *.pov Jmol output files, I see in the first case an empty '#if (showBonds)' section whereas the in the latter I have it filled with bond data. Looks like Jmol does not output backbone CA trace by some reason. Does anybody have a solution to this problem? I have already checked the archives and bug tracker - without results. I worked on the povray output some time ago (january maybe) to add other things than just atoms and bonds, but I left it unfinished because the JmolViewer interface needs a lot of work to give access to informations on how every element is rendered. This part must be thought with care. Maybe Miguel remembers the discussions we had at this time. Otherwise, the current version outputs only : - atoms - bonds (if you don't set wireframe to off) - and one of the structure (don't remember which) but you have to manually edit the .pov: set to true a #declare showXXX. The showBonds section is empty in the first case because of wireframe off. Nicolas --- This SF.Net email is sponsored by: NEC IT Guy Games. How far can you shotput a projector? How fast can you ride your desk chair down the office luge track? If you want to score the big prize, get to know the little guy. Play to win an NEC 61 plasma display: http://www.necitguy.com/?r ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [EMAIL PROTECTED]
De: Egon Willighagen [EMAIL PROTECTED] On Tuesday 10 May 2005 01:23 pm, Egon Willighagen wrote: I'll setup a team; it could be good advertisement for Jmol. I've been trying for about a day now, with no success... I get this error all the time: The database did not respond. . . Please try again in several minutes Sorry for the inconvenience! Ok, I just tried and it worked :) Team number is 44383, named Jmol --- This SF.Net email is sponsored by Oracle Space Sweepstakes Want to be the first software developer in space? Enter now for the Oracle Space Sweepstakes! http://ads.osdn.com/?ad_ids93alloc_id281op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: Re: [Jmol-users] [EMAIL PROTECTED]
De: [EMAIL PROTECTED] De: Egon Willighagen [EMAIL PROTECTED] On Tuesday 10 May 2005 01:23 pm, Egon Willighagen wrote: I'll setup a team; it could be good advertisement for Jmol. I've been trying for about a day now, with no success... I get this error all the time: The database did not respond. . . Please try again in several minutes Sorry for the inconvenience! Ok, I just tried and it worked :) Team number is 44383, named Jmol I have just returned the first points for Jmol team :) I have switched 8 of my fah clients to Jmol team, the rest will follow later. Nicolas --- This SF.Net email is sponsored by Oracle Space Sweepstakes Want to be the first software developer in space? Enter now for the Oracle Space Sweepstakes! http://ads.osdn.com/?ad_ids93alloc_id281op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [EMAIL PROTECTED]
De: Egon Willighagen [EMAIL PROTECTED] Nicolas, is there a Jmol team for FAH? I don't think so, but it can be a good idea ;) If you create one, that will be a difficult decision for me to switch team (letting my 300.000 points to the old team and starting again at 0). Nicolas --- This SF.Net email is sponsored by Oracle Space Sweepstakes Want to be the first software developer in space? Enter now for the Oracle Space Sweepstakes! http://ads.osdn.com/?ad_ids93alloc_id281op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Java Embedding Plugin 0.9.1, supports Mac OS X Tiger
Might interest some of you : The Java Embedding Plugin is a utility that allows other web browsers than Apple's Safari to use the most recent available versions of Java on Mac OS X (Java 1.4.X and, on Tiger, Java 1.5).When used together with an updated version of Mozilla's MRJ Plugin Carbon (included in this distribution), the Java Embedding Plugin's functionality is currently available to recent versions of Mozilla, Firefox and Camino. But in principle any web browser could use one of the Java Embedding Plugin's two APIs to add support for Java 1.4.X and (where available) Java 1.5. --- This SF.Net email is sponsored by Oracle Space Sweepstakes Want to be the first software developer in space? Enter now for the Oracle Space Sweepstakes! http://ads.osdn.com/?ad_ids93alloc_id281op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmol
I have added a Smiles parser in Jmol recently (development version only) but currently it is only used to do pattern matching. I thought of adding a Smiles reader also but I don't know how to give coordinates to the atoms so I didn't look deeper into it. Nicolas De: Karol Kozak [EMAIL PROTECTED] Dear Jmol users, I am going to use jmol as applet. Is any chance to read smiles as input parameter? --- 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_ide95alloc_id396op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: Re: [Jmol-users] atom colours
De: [EMAIL PROTECTED] Thanks Tim! Unfortunately I'm behind a corporate fire-wall that won't permit CVS access so I'm not able to just grab the source anytime I want to :-( You can still use the viewCVS interface of sourceforge (it is browser based) --- 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_ide95alloc_id396op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: Re: Re: [Jmol-users] atom colours
You can still use the viewCVS interface of sourceforge (it is browser based) Thanks for the suggestion and I just spent some time poking about a bit with it. I don't think this type of access would have helped in this case because unless you already know your way around all the sources I don't see any way of finding something when you don't know where to look. But maybe I am just so unfamiliar with sourceforge's CVS presentation that I'm missing the obvious. No, you're right, I was thinking that you knew were to look. My mistake. Ycan use CVSGrab (found at sourceforge) which is a CVS client that uses viewCVS. I have never used it but it seems its goal is exactly to checkout from CVS bypassing firewalls. Let me know if you try it. Nicolas --- 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_ide95alloc_id396op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] two consoles
Hi, The first one is here essentially for debugging purposes, it is where the logs are printed. Usually a normal user has not much interest in this one. It is mainly for developers. System.out and System.err are redirected there. The second one if for the scripting language: input commands and get commands results. I thought it was possible to access both consoles from the top menu. I don't have access right now to a Jmol app so I can't check it. Nicolas De: Herraez Sanchez Angel [EMAIL PROTECTED] Hi I have just found out that there are two different Jmol consoles in the app. One opens under the top menu, 'Help' 'Jmol console', the other opens from the pop-up menu 'Console' 'Open/Close' (and it's the one where ore can type commands). Can someone clarify what is the purpose of each? To me it is a little misleading; they should have different names. Also, it could be interesting to have access to both from the top menu. --- 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_ide95alloc_id396op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: Re: [Jmol-users] two consoles
De: [EMAIL PROTECTED] I thought it was possible to access both consoles from the top menu. I don't have access right now to a Jmol app so I can't check it. I was able to check : the second console is accessible with File / Script --- 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_ide95alloc_id396op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: Select hydrogens bonded to nitrogens
Hi, a month ago someone asked about selecting hydrogens bonded to nitrogens. The only solution found at this time was to work with distance. A new command substructure() has been added to the development version of Jmol that should work for this : select hydrogen and substructure([NH]) To try it, you will have to checkout the latest version of the source code from CVS and build Jmol. Nicolas --- This SF.net email is sponsored by: 2005 Windows Mobile Application Contest Submit applications for Windows Mobile(tm)-based Pocket PCs or Smartphones for the chance to win $25,000 and application distribution. Enter today at http://ads.osdn.com/?ad_idh82alloc_id148op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: Re: [Jmol-users] drag'n'drop
Hi,De: "Miguel" <[EMAIL PROTECTED]>A: jmol-users@lists.sourceforge.net Date: Tue, 15 Feb 2005 08:05:25 -0500 (EST)Hi All, may be this is a very stupid question, but is the drag and drop functionality non working at all in Jmol, or is it just a problem in MacOSX, or is it just a problem on my mac? Many thanks Adriano, There is no support for drag-n-drop in Jmol. Miguel, it has been added to Jmol very recently, thansk to Simon Tyrrel. It's the FileDropper class in the org.openscience.jmol.app package. It would only work in the Jmol application, not in the unsigned Jmol applet. Yes, it works only with the application and JVM 1.5 (not for 1.4) It is only present in the prerelease version of Jmol (version 10.00.07) Nicolas --- 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_ide95_id396=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
