Re: [Jmol-users] Installing jmol as extention to mediawiki
On Wed, Sep 14, 2011 at 12:44:11AM +0200, Angel Herr?ez wrote: Hi, Henry https://wiki.ch.ic.ac.uk/wiki/index.php?title=User_talk:Rzepa1 All applets in there work for me: #2, 3 and 4 open a popup with Jmol applet correctly displayed #5 displays the applet and the vibrating BF3 model That's in Fiirefox 6.0.2, WinXP, Java 1.6.0_27 Don't you see it? Works for me also on Ubuntu with Firefox. Brian. -- Brian Salter-Duke (Brian Duke) brian.salter-d...@monash.edu Honorary Researcher Fellow Monash Institute of Pharmaceutical Sciences, Monash University Parkville Campus, VIC 3052, Australia. -- BlackBerryreg; DevCon Americas, Oct. 18-20, San Francisco, CA Learn about the latest advances in developing for the BlackBerryreg; mobile platform with sessions, labs more. See new tools and technologies. Register for BlackBerryreg; DevCon today! http://p.sf.net/sfu/rim-devcon-copy1 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JMOL and Wikipedia
On Tue, Jun 02, 2009 at 12:43:34PM +0200, Egon Willighagen wrote: On Tue, Jun 2, 2009 at 1:15 AM, Brian Salter-Duke b_d...@bigpond.net.au wrote: On quality, I think that is a different and general concern. We try to not use poor quality images, so we would try to use only good quality Jmol data files. I am happy that we restrict the type of jmol files to a small number, perhaps initially only *.pdb files. Of course we would have to add file extensions for jmol files to the upload process anyway, so we would not need to add all possible file extensions. PDB is not a good format for small molecules; CML would be much better, e.g. by allowing embedding of important information regarding identification of the structure, or adding info on who added that image. Please be specific when you suggest file formats: there are two main areas of interest here: protein (PDB is the de facto standard), small molecules. In both cases, there are many alternative, and PDB as format has, at least, lesser quality than other offerings. I also really don't get the security concerns brought up... sorry, for dropping in on this, but have been involved in talk several years ago too, and if you want Jmol without JavaScript, that is no problem. JavaScript as security problem regarding a Jmol extension for WP is a non-issue. People have been using plain HTML for embedding Jmol in various website for more than 10 years, and I have no clue why this would not be a problem for WP. Please explain. I do not get the security concerns either, but Tim Starling was very concerned a couple of years ago. I e-mailed him 2 weeks ago and he has not replied. I suspect that the WMF techs have put Jmol into the too hard basket. Also, much as I would love to have Jmol on WP, I do not see a lot of support. I raised it in two places on the English WP. The response was rather thin. See these two discussions:- http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry#Jmol_on_wikipedia http://en.wikipedia.org/wiki/Wikipedia_talk:Using_Jmol_to_display_molecular_models#Is_this_the_time.3F I am really not sure where we take it now. It just is not getting anywhere. Maybe the wikimedia technical email list is worth a try. What do you think? Brian. Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- -- On two occasions I have been asked [by members of Parliament], Pray, Mr. Babbage, if you put into the machine wrong figures, will the right answers come out?. I am not able rightly to comprehend the kind of confusion of ideas that could provoke such a question. -- Charles Babbage Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JMOL and Wikipedia
On Fri, May 29, 2009 at 12:21:32PM +0200, Ralf Stephan wrote: I think we should stick to uploaded files as these could go on Commons and be available to all wikimedia projects. Separate files, I presume as sub-pages of the page using the 3D jmol image, will be less general, but also more susceptable to vandals editing them and possibly adding dangerous code there. How will you maintain quality if that is your concern? I'm maintaining proteins at the german language WP and I'll delete any 3D model that doesn't refer to PDB data. I'm interested in your solution to the more general problem of small molecules. Sorry, but I am not entirely understanding you. First, this is not really my concern. It would however, I am quite sure, be the concern of the WMF technical people. I discussed Jmol severel years ago with Tim Starling before he moved to Sydney from here in Melbourne. He was very concerned about security for use of the Jmol extension on wikipedia. Second, I think that the more we make Jmol files just like other files such as images, the easier and better it will be. On quality, I think that is a different and general concern. We try to not use poor quality images, so we would try to use only good quality Jmol data files. I am happy that we restrict the type of jmol files to a small number, perhaps initially only *.pdb files. Of course we would have to add file extensions for jmol files to the upload process anyway, so we would not need to add all possible file extensions. Am I missing your point? If so I apologise. Regards, Brian. Regards, ralf -- -- Microsoft is not the answer. It is the question. The answer is 'No'. -- Unknown Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JMOL and Wikipedia
On Thu, May 21, 2009 at 05:51:46PM +0200, Angel Herr?ez wrote:
Chris Foley wrote:
I think this has great potential but I don't like applets appearing
in my web pages if I don't want/expect it
Right. The discussion has always being on the idea that the applet
should load only when the user chooses so. One option is an image (if
we could manage to have it generated by the server, which is
unlikely), another is a link or button.
I personally like the idea of Jmol being part of the ChemBox (I guess
it is called something like that). Some chemicals have links to
PubChem, or expansible boxes with formulas, details, etc. There could
be a link like see in 3D that would open the Jmol applet either
inline or in a separate page as Chris proposes.
For example, the Toluene page has this, using Template:Chembox
{{chembox
| Name = Toluene
| ImageFileL1 = Toluol.svg
| ImageSizeL1 = 80px
| ImageFileR1 = Toluene-from-xtal-3D-balls.png
| ImageSizeR1 = 150px
| OtherNames = phenylmethanebr/toluolbr/methylbenzene
| Section1 = {{Chembox Identifiers
| SMILES = Cc1c1
| CASNo = 108-88-3
| ChemSpiderID = 1108
| RTECS = XS525
}}
| Section2 = {{Chembox Properties
| Formula = Csub7/subHsub8/sub
(Csub6/subHsub5/subCHsub3/sub)
| MolarMass = 92.14 g/mol
| Appearance = Clear colorless, liquid
| Density = 0.8669 g/mL, liquid
| Solubility = 0.47 g/l (20-25?C)
| MeltingPt = -93 ?C
| BoilingPt = 110.6 ?C
| Viscosity = 0.590 c[[Poise|P]] at 20?C
}}
| Section3 = {{Chembox Structure
| Dipole = 0.36 [[Debye|D]]
}}
| Section7 = {{Chembox Hazards
| ExternalMSDS = [http://www.sciencelab.com/xMSDS-Toluene-9927301
ScienceLab.com]
| MainHazards = highly flammable
| NFPA-H = 2
| NFPA-F = 3
| NFPA-R =
| FlashPt = 4 ?C/ 39.2 ?F
| RPhrases = {{R11}}, {{R38}}, {{R48/20}}, {{R63}}, {{R65}},
{{R67}}
| SPhrases = {{S2}}, {{S36/37}}, {{S29}}, {{S46}}, {{S62}}
}}
| Section8 = {{Chembox Related
| Function = [[aromatic hydrocarbon]]
| OtherFunctn = [[benzene]]br/[[xylene]]br/[[naphthalene]]
| OtherCpds = [[methylcyclohexane]]}}
}}
How about a new parameter for Jmol inside {{Chembox Structure ?
I think this is a brilliant idea.
I come at this from the wikipedia side as I certainly spend more time
there than with jmol. The difference between the English wikipedia and
all other wikis is that it is massively larger. This makes the technical
people, like Tim Starling, rather conservative about what they allow. I
think we have to start small. Doing as you suggest pretty well leaves
the jmol insertions to the people in WikiProject Chemicals (I am not
active there, only on its parent project WikiProject Chemistry) who will
know what to do. They will iron out initial bugs. Then we should
restrict the use to file upload. Images are now called File:.., not
Image:.., so this makes it easy to add more file extensions to handle
pdb files etc. Such files could be uploaded to Commons to be available
on all WMF projects. That would involve working with the Commons
community. I suggest we limit the number of file extensions initially.
I will look at proteopedia over the weekend and then e-mail Tim
Starling, who I know and who is in Australia. It is a few years since I
last discussed it with him. I'll try to find out what he thinks needs to
be done. Has Gerard approached anyone?
Earlier, I suggested a trial on wikiversity. I started putting up some
web course materials there on computational chemistry over a year ago,
but have been distracted by other things. I have one module that uses
Jmol (or Rasmol, or Chime earlier) extensively. I am prepared to put all
that up as a trial of Jmol on wikiversity if the WMF techs allow it.
Nevertheless, the quicker we get it on wikipedia the better. There will
however be issues about adding it to all language wikipedia. Maybe only
the english wikipedia and perhaps a few others such as the German and
French wikipedias have the chemistry editor base to use Jmol well and
not create trouble for the techs.
I am happy to act as a facilitor between the Jmol community and the
English Wikipedia community (and perhaps the Commons community),
particularly the WikiProject Chemistry
(http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Chemistry).
Take a look at:-
http://en.wikipedia.org/wiki/Wikipedia:Using_Jmol_to_display_molecular_models
It has had few edits since May 2007. Leap in and add your ideas there.
Some of the WikiProject Chemistry folks will have it on their watchlist
and notice the new activity.
Brian.
--
The problem with defending the purity of the English language is that
English is about as pure as a cribhouse whore. We don't just borrow words;
on occasion, English has pursued other languages down alleyways to beat
them unconscious and riffle [sic] their pockets for new vocabulary
-- James D. Nicoll
Brian Salter
Re: [Jmol-users] Jmol mediawiki extension
On Tue, Dec 09, 2008 at 01:21:01PM +0100, Angel Herraez wrote: I'd like to keep this discussion going, so here is a little bit more, picking up on the possibilities to have Jmol supported in Wikipedia and other Wikis: [Nico's message snipped] And on 1 Dec 2008 9:49, Brian Salter-Duke wrote: I am just thinking aloud here. I think there could be a solution to add a chaneg to medciawiki itself to have some specific Jmol tags, something like: jmolimage ... /jmolimage We already have the jmol tag added by the extension. Is there any difference intended? avoiding all calls to Jmol itself. I don't quite understand. There is no call to Jmol until the extension inserts the Jmol code. And by using jmolAppletButton or jmolAppletLink one avoids Jmol to be loaded until the visitor requests it. This is an example of an image inserted on wikipedia:- [[Image:Meissner effect zoom.jpg|thumb|200px|right|A [[magnet]] levitating above a [[high-temperature superconductor]] demonstrates the [[Meissner effect]].]] Everything is together. I presume the bits are handled by mediawiki. In contrast, a simple Jmol call is full of html/javascript like stuff. jmoljmolAppletscriptset spin X 10; spin on/script nameethane_s1/namecolorpalegreen/colorsize250/size uploadedFileContentsethane_s.pdb/uploadedFileContents /jmolApplet jmolButtonscriptspin on/scriptnameethane_s1/nametextStart spinning/text/jmolButton jmolButtonscriptspin off/scriptnameethane_s1/nametextStop spinning/text/jmolButton /jmol What if it was like this:- [[Jmolimage:ethane_s.pdb|color=palegreen|script=spin X 10|script=spin on|size=250|button=(spin on,Start spinning)|button=(spin off,Stop spining)]] Jmolimage:ethane_s.pdb starts it all off and includes:- uploadedFileContentsethane_s.pdb/uploadedFileContents color=palegreen includes colorpalegreen/color size=250 includes colorpalegreen/color script=spin X 10| script=spin on would generate:- scriptset spin X 10; spin on/script button=(spin on,Start spinning) is interpreted as:- jmolButtonscriptspin on/scriptnameethane_s1/nametextStart spinning/text/jmolButton button=(spin off,Stop spining) is interpreted as:- jmolButtonscriptspin off/scriptnameethane_s1/nametextStop spinning/text/jmolButton I suspect this would be easier for users and could likely be made more secure. However, I have no idea how this would be implemented. The mediawiki language seems to aim to remove as much direct html use as possible. The parameters for jmolimage would give everything that was needed, method, file names, etc. Mediawiki itself would then be doing any chaecks that were needed. It would also be easier for wikipedia editors and I suspect the wikipedia techs would prefer this solution. Is this worth following up? I do noptset spin X 10; spin on/scriptt know mediawiki and could be just talking nonsense. I think it is the JmolMediaWiki Extension that must do all this anyway, not the generic MediaWiki software. And it is doing so already, by using the different sub-tags of the jmol tag. Do you envisage any differences, Brian? Please ellaborate on that. The configuration in the server (LocalSettings.php) may block the use of external URLs for models, or of uploaded files, may block or impose the use of signed applet. The rest of the task in inside the Extension. Another advantage of this approach is that wikipedia could limit the mehtods available and perhaps limit them to file upload only. Already possible (see above). I understand this. When the extension was first written, it was understandable that a number of different approaches were tried. Maybe it is time to limit these choices and make it simpler. Particularly on wikipedia, which has a large number of editors who are likely to be less familiar with Jmol than users on say the Jmol wiki, I think we have to decide. The choice is I think really between an uploaded file (on either wikipedia or Commons) and inline data. The latter will be seen as clumsy, but it makes it all self contained and does not mean that the whole upload business has to be altered - see below. The former would be better, but changes would be needed. The mediawiki code would need changing anyway to allow use of Jmol files on Commons as well as wikipedia. This needs further work, but is related to the above config. settings. Whether Commons or the home wiki (say wikipedia or wikiversity) many changes would be needed. First, upload is restricted to files with certain extensions. We would have to decide which file types we wanted and allow those extensions to the upload. Second, we need to think about copyright issues on uploaded files and how these are going to be added. If you click on an image, it brings up the image page that displays both the image and all the upload, copyright, etc. details. How would this work for say a pdb file. So, third, we have a different image page. Adding an new prefix Jmolimage may
Re: [Jmol-users] Jmol mediawiki extension
On Tue, Dec 09, 2008 at 02:03:17PM +0100, Nicolas Vervelle wrote: Hi, On Tue, Dec 9, 2008 at 1:21 PM, Angel Herraez [EMAIL PROTECTED] wrote: I'd like to keep this discussion going, so here is a little bit more, picking up on the possibilities to have Jmol supported in Wikipedia and other Wikis: On 30 Nov 2008 22:53, Nicolas Vervelle wrote: On the matter of security issues, there are at least 2 things to do : * Being able to entirely deactivate the possibility to let arbitrary Javascript being called by Jmol. I don't know if there's a way in Jmol to disable this. There's a need to completely disable the 'javascript' command in Jmol scripts. The problem is demonstrated by http://wiki.jmol.org:81/index.php/User:Ilmari_Karonen/JS_injection_dem o Do we still need this? (see below) * Ensuring that the extension doesn't allow for true Javascript injection (whatever text is entered by someone in the jmoltags, this only creates Jmol applet and Jmol scripts, nothing else). I think this means ensuring that in the generated page, the text is always correctly escaped to prevent Javascript injection. This is implemented in the last update. The second problem nees to be treated in the extension. My knowledge on PHP and the security issues is limited (and I don't have much time avaiable), so some help from someone knowing how to deal with the script injection would be very useful. The way I've implemented it, any script passed to the Extension (inside the extension's script tag) containing the word javascript (case-insensitive) will be completely ignored. I gues it can be done so that only the javascript part is removed and the remaining script is preserved, but I don't know so much PHP as to do so. And the idea is that users-editors of wiki pages should not try at all to use javascript in the wiki pages. This approach is interesting but I am not sure it covers all the possibilities. For example, I think you can still run Javascript with scripts calling other scripts : - Create a wiki page with contents corresponding to a Jmol script with Javascript in it. - Add a jmol tag in a page with a script calling the other script As a side effect, the text, title, name... tags of the extension cannot contain the forbidden word either (they are all parsed via the same function as script is). Not a big sacrifice. Not a problem :) And on 1 Dec 2008 9:49, Brian Salter-Duke wrote: The mediawiki code would need changing anyway to allow use of Jmol files on Commons as well as wikipedia. This needs further work, but is related to the above config. settings. I am not sure using Jmol files on Commons needs any change. I thought that files in the Image namespace in Commons are simply exported to other wikis and kept up to date. I am fairly sure that this is not right. The code looks at Commons first for the image, and then on the local wiki. I could however be mistaken. Wikipedia images confuse me. Brian. Nico -- next part -- An HTML attachment was scrubbed... -- -- The PROPER way to handle HTML postings is to cancel the article, then hire a hitman to kill the poster, his wife and kids, and fuck his dog and smash his computer into little bits. Anything more is just extremism. -- Paul Tomblin Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
Take a look at this blog:- http://ultimategerardm.blogspot.com/2008/12/jmol.html More publicity to get Jmol properly working on wikis. Brian. -- First they ignore you, then they laugh at you, then they fight you, then you win. -- Gandhi, being prophetic about Linux. Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
On Sun, Nov 30, 2008 at 10:53:29PM +0100, Nicolas Vervelle wrote: Hi everyone, I have been quite busy for several months on other matters than Jmol, so I haven't worked at all on the extension. I am happy to see people interested in making it work, and bringing it to Wikipedia. On the matter of security issues, there are at least 2 things to do : - Being able to entirely deactivate the possibility to let arbitrary Javascript being called by Jmol. I don't know if there's a way in Jmol to disable this. There's a need to completely disable the 'javascript' command in Jmol scripts. The problem is demonstrated by http://wiki.jmol.org:81/index.php/User:Ilmari_Karonen/JS_injection_demo - Ensuring that the extension doesn't allow for true Javascript injection (whatever text is entered by someone in the jmol tags, this only creates Jmol applet and Jmol scripts, nothing else). I think this means ensuring that in the generated page, the text is always correctly escaped to prevent Javascript injection. Both things clearly need to be done in order to hope to see Jmol on Wikipedia : having every editor being able to add arbitrary Javascript that will be run by everyone viewing a page is a security issue. The first problem needs first to be answered in the Jmol applet itself. Is there a way to add an option in the applet construction to remove the 'javascript' command in Jmol scripts ? Bob ? The second problem nees to be treated in the extension. My knowledge on PHP and the security issues is limited (and I don't have much time avaiable), so some help from someone knowing how to deal with the script injection would be very useful. Nico I am just thinking aloud here. I think there could be a solution to add a chaneg to medciawiki itself to have some specific Jmol tags, something like: jmolimage ... /jmolimage avoiding all calls to Jmol itself. The parameters for jmolimage would give everything that was needed, method, file names, etc. Mediawiki itself would then be doing any chaecks that were needed. It would also be easier for wikipedia editors and I suspect the wikipedia techs would prefer this solution. Is this worth following up? I do not know mediawiki and could be just talking nonsense. Another advantage of this approach is that wikipedia could limit the mehtods available and perhaps limit them to file upload only. The mediawiki code would need changing anyway to allow use of Jmol files on Commons as well as wikipedia. Some mediawiki changes are going to be needed anyway. Brian. -- Real Programmers can write FORTRAN in any language. -- unknown Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
Hi folks, Gerard Meijssen [EMAIL PROTECTED] has asked me to pass this on to the Jmol list. I responded to this discussion on the Commons-l list:- [Commons-l] Support for Chemical Markup Language - followup -- Hoi, If you want to get the JMOL software internationalised and localised, you may want to consider talking to the Betawiki people. We do the localisation of MediaWiki and we do the localisation of many of its extensions. We would be interested in working on JMOL as it is a lively and relevant software / community. I am also involved in a testing envirionment for MediaWiki extensions, if you are interested in using this environment, let me know.. I take it that you will convey my message to the JMOL mailing list ? Thanks, Gerard -- This does seem to be a useful idea. I'll have a look at betawiki but I'm very busy this week and early next week. Cheers, Brian. -- Brian Salter-Duke (Brian Duke) 626 Melbourne Rd, Spotswood, VIC, 3015, Australia. Email: [EMAIL PROTECTED]Phone: 03-93992847 Web: http://www.salter-duke.bigpondhosting.com/brian/index.htm - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
On Sat, Nov 29, 2008 at 02:53:18PM +, Rzepa, Henry wrote: On 29 Nov 2008, at 01:41, Brian Salter-Duke wrote: The question of having Jmol used on wikipedia has again been raised on the commons email list. On contributor to the discussion says that the jmol mediawiki extension now only works with an older version of mediawiki. Certainly my examples at:- http://wiki.jmol.org:81/index.php/User:Bduke I have gotten things to work myself (Thanks Angel for the remark that gave the clue). In the distribution http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-extensions/wiki/MediaWiki/ edit the file Jmol.php to make the change from $wgJmolExtensionPath = /extensions/Jmol; to $wgJmolExtensionPath = $wgScriptPath./extensions/Jmol; That is great news. Thanks, Henry. My page on the Jmol wiki is now working and I have something I can point the wikipedia tech folks to so that they can look at Jmol. The question of security still remains. Has this been addresed by anyone? Does anyone on this list think it is an issue? It is quite clear that Kmol will never be added to wikipedia until the tech folks are totally convinced that there are no security issues. I just do not know much about security and I do not speak php. Regards, Brian. -- On two occasions I have been asked [by members of Parliament], Pray, Mr. Babbage, if you put into the machine wrong figures, will the right answers come out?. I am not able rightly to comprehend the kind of confusion of ideas that could provoke such a question. -- Charles Babbage Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
On Sun, Nov 30, 2008 at 01:16:21AM +0100, Angel Herráez wrote: On 30 Nov 2008 at 9:48, Brian Salter-Duke wrote: That is great news. Thanks, Henry. My page on the Jmol wiki is now working and I have something I can point the wikipedia tech folks to so that they can look at Jmol. Brian, I'm quite surprised that your page has started to work NOW. Unless Nico has updated the Wiki without saying a word, what I updated earlier this evening was the php file in the Jmol SVN pages. I would not expect that to affect the Wiki automatically. The question of security still remains. Has this been addresed by anyone? Does anyone on this list think it is an issue? A recent addition to the Wiki questions security on the basis that any javascript can be run from Jmol script. I'm not sure, though, what security issues that raises. See http://wiki.jmol.org:81/index.php/User:Ilmari_Karonen/JS_injection_demo The latest post in the Talk page http://wiki.jmol.org:81/index.php/User_talk:Ilmari_Karonen/JS_injection_demo sounds very threatening, but I don't understand it fully. It may, however, be a big obstacle for Wikipedia adoption. Discussion has been going on at both:- Wikimedia Commons Discussion List [EMAIL PROTECTED] and Wikimedia developers [EMAIL PROTECTED] This discussion may illustrate the problem:- [Post to commons list] See https://bugzilla.wikimedia.org/show_bug.cgi?id=16491 That users can embed javascript is not acceptable to run it on Wikipedia. Other parameters, like urlContents or signed wouldn't be used but at least they can be disabled. [Me] I am afraid this is all beyond my expertise. Are you saying that there is no way Jmol can ever be used on WMF projects? [Reply from someone else] There is, as soon as the Javascript embedding possibility gets disabled and the extension gets a proper review (TM). This link:- https://bugzilla.wikimedia.org/show_bug.cgi?id=16491 mentioned there is interesting but the question of the CML extension is getting confused with the Jmol extension as both were mentioned in the original post on the Commons list. While Jmol on wikipedia would be great, I would really like it on wikiversity to illustrate some teeaching materials I have started to put there. Brian. -- If people are good only because they fear punishment, and hope for reward, then we are a sorry lot indeed. -- Albert Einstein Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol mediawiki extension
The question of having Jmol used on wikipedia has again been raised on the commons email list. On contributor to the discussion says that the jmol mediawiki extension now only works with an older version of mediawiki. Certainly my examples at:- http://wiki.jmol.org:81/index.php/User:Bduke are not working. I still very much want to get jmol working on wikipedia and would like to also get it on wikiversity for some teaching materials I have started to add there. However, I have been very much out of touch recently. Could someone please update me on what the situation is with the jmol mediawiki extension and point me to an example of it working, so I can point the wikipedia technical folks to have a look at the examples? Also, last time I tried to get jmol on wikipedia I was told there were security issues with the extension. Have these been addressed? Regards, Brian. -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Honorary Researcher Fellow Department of Medicinal Chemistry, Parkville Campus, Monash University, VIC 3052, Australia - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Delaying loading the web applet - re Jmol on Wikipedia
On Sun, Jul 16, 2006 at 03:44:36PM +0200, Nicolas Vervelle wrote: Really great Angel, I like option 5 a lot. I will try to add it to the MediaWiki extension (with a few fixes also to the extension) as soon as I manage to find some time. That would be great, Nico. I hope you can find the time. I replied to Angel privately but my message was included in one from him to the list. However let me add to that publically on the list to thank Angel for this excellent and rapid response to my question. I am sure that this will be a great help to establishing use of Jmol in Wikipedia. I too like option 5, but I am not sure what the constraints on the pdb image shown are. We might want a choice of image here including the chemdraw like images that are currently widely used in chemistry articles on wikipedia. In some cases we might want just a specific paragraph of text rather than an image. Are these possible? I agree that option 1 popups are annoying but some people like them. If we implement option 1 for wikis, I think we need to allow n popups at once if there are n Jmol images from the page. As Angel wrote it, option 1 shows a page with two molecules but clicking the second replaces the image in the first popup. In practice we would want to have 2 popups side by side for comparision. Personally I would allow just option 5 - allowing image - and option 4 - replace box with no image with Jmol object. Cheers, Brian. Nico Angel Herraez wrote: Brian, I have written a small prototype of how this could be done. The files, including Jmol files, sum up 845 kb, so I am not sending it to the list You can test it at http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/pop-up_Jmol.htm If you prefer, you can get it all zipped at http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/pop-up_Jmol.zip It can be polished; tell me what you miss - 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 End of Jmol-users Digest, Vol 2, Issue 12 * -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] - NB New! Old still works Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://www.salter-duke.bigpondhosting.com/brian/index.htm Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. - 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] Delaying loading the web applet - re Jmol on Wikipedia
As I have mentioned before I am trying to get Jmol up and running on Wikipedia. It seems that my Wikipedia technical admin friend raised this on IRC and asked people to look at how it all worked on, I guess, the Jmol wiki. They concluded that WP users expect pages to come up immediately and that WP users would be put off by the slowness of loading the Jmol applet. He suggested to me that what was needed was something like this:- When the page comes up, it has a large box that says Clicking here will bring up a 3-dimensional image of the molecule that you can manipulate. It uses the Jmol applet. This may take quite a time to download if you do not already have it in cache. If you want to use the Jmol image, click here or rather better words expressing this. The box could perhaps give a clue about the Jmol image by have a 2-dimensional jpg or whatever image. Clicking on that box would bring up Jmol replacing the box on the page. Is this possible, perhaps using javascript? If so, can anybody smarter than I at javascript write something, so we can test it on the Jmol wiki? I am sure that this or something like it will make the introduction of Jmol to Wikipedia more acceptable to the Wikipedia administrators. However, it is not holding back a test of Jmol on Wikipedia. That is being delayed for other reasons - good reasons. While this delay is going on, we could perhaps improve the way Jmol might be used on Wikipedia pages. I welcome comment and assistance. Brian. -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] - NB New! Old still works Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://www.salter-duke.bigpondhosting.com/brian/index.htm Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. - 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 applets in MediaWiki and Wikipedia
On Wed, Apr 26, 2006 at 11:37:51PM +0200, Egon Willighagen wrote: On Wednesday 26 April 2006 22:26, Nicolas Vervelle wrote: I have finished a first version of a fully functional version of a MediaWiki extension to add Jmol applets in MediaWiki wikis (like the well-known Wikipedia). Looks good! Anyone who knows where to start lobbying to get this included in WikiPedia? I have been discussing this with one of the senior Wikipedia developers but waiting until Nico had completed his extension. I will follow up on this today. I have only just seen the news this morning here in Australia. See:- http://en.wikipedia.org/wiki/Wikipedia:Using_Jmol_to_display_molecular_models and its talk page, where is information from Nico and others. I hope we can get a trial on Wikipedia soon. Cheers, Brian. Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ --- 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 -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. --- 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] 10.2.0 application
On Mon, Apr 17, 2006 at 02:43:49PM -0400, Jules Moskowitz wrote: I have been able to use jmol-10.00.45 as both and applet with a browser and as an application to look at some molecules from terminal (imacg5, OS 10.4). I have been able to use jmol-10.2.0 with the browser but not as an application. When I go from the terminal to the jmol-10.2.0 folder and attempt to use the command jmol, I get: tcsh: jmol: Command not found. I had a similar problem on linux. dos2unix jmol ttt mv ttt jmol fixed it. Brian. Both jmol and jmol.sh are executables as in 10.00.45. Anybody know what I am doing wrong or is there a bug in jmol? Professor Jules W. Moskowitz Chemistry Department New York University 100 Washington Square East New York, NY 10003-6688 Phone: (212)998-8437 Fax: (212) 260-7905 Email: [EMAIL PROTECTED] -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. --- 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=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Google map fun: where are those Jmol users/developers?
On Mon, Apr 17, 2006 at 07:51:47PM +0200, Egon Willighagen wrote: Hi all, I learned this weekend that setting up a Google map is very easy, so set up one for Jmol too: http://jmol.sourceforge.net/maps/people/ If you would like to be added to this map, please send your name, URL (e.g. you page in the Jmol wiki [1]) and longtitude and latitude, with four digits, like 50.0563, to this mailing list. Developers will have a red marker, users a yellow marker. Great fun. I'm a user, -37.8283, 144.8811 (I think I have the sign convention right) Melbourne Australia. Jmol wiki [[User:Bduke]] Cheers, Brian. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 --- 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=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. --- 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=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol and alchemy files
Does Jmol work with Alchemy format data files? Rasmol did and there is a file in the RasMol/data directory called asprin.alc. Jmol seems to not work with it, but I may just be missing something. I think it worked with Chime also. Regards, Brian. -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. --- 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=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New Jmol Wiki
On Tue, Apr 04, 2006 at 01:36:19PM +0100, Rzepa, Henry wrote: 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 but it seems a very restricted solution, supporting only .xyz files. It also mandates the use of hard line breaks to delineate atoms etc. Is there perchance a solution that supports other formats, ideally CML, but at a pinch MDL Molfiles? -- Henry, as Nico says, see my user page [[User:Bduke]] on both the Jmol and i the [EMAIL PROTECTED] wiki. They are pdb files. Brian. Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); [EMAIL PROTECTED] (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). --- This SF.Net email is sponsored by 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=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. --- 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=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Relative against absolute addresses
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. 2. When using a cgi script in the cgi space to write a html page on the fly containing a jmol call. I did find a way to do this but it is messy and I still do not understand why what I have works, but it does. Again, an absolute address would fix things. Can it be done? If not why not? Regards, Brian. -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. --- 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=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Relative against absolute addresses
On Sun, Mar 26, 2006 at 09:33:06PM -0500, Timothy Driscoll wrote:
On Mar 26, 2006, at 8:29 p, Brian Salter-Duke wrote:
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.
hi Brian,
do you mean adding something like this to your applet tag:
codebase=http://www.molvisions.com/jmol/;
Well the instructions say that anything that starts with http is
bevil/b! I have never used codebase. My problem right now is working
within a wiki and that is quite different from normal html. See:-
http://meta.wikimedia.org/wiki/User:NicoV/Jmol_Extension
and:-
http://fahwiki.net/index.php?title=Jmol_MediaWiki_Extension
I am trying to repeat the latter on another wiki. It is these lines in
the php script that are the problem:-
script src='/extensions/jmol/Jmol.js' type='text/javascript'/script\n.
script\n .
jmolInitialize('/extensions/jmol');\n.
It is not clear these should be /extension/.. or ../extension/.. or even
./extension/... All seem to have been used and one guy claims that with
the second it works with the wiki preview but not after saving, and with
the third the other way round.
?
as long as your Jmol jar files are located in the jmol dir, then it
should work. I just tested it here, using apache and the unsigned
applet.
as far as calling Jmol.js from an absolute url, well, I don't see why
that wouldn't work. I have done this before with javascript files,
and css files, too:
[[script type=text/javascript src=http://www.molvisions.com/jmol/
Jmol.js]][[/script]]
I guess we will try that, but we are told in the instructions very
clearly to not do so. Perhaps Miguel will comment.
that said, I had better backtrack a little. ;-)
let me say that both are technically possible. however, you may be
running into a peculiarity associated with Jmol.js; if so, I will
have to defer to other folks on that point. it may be true that
Jmol.js does not accept absolute url for the codebase; I don't know.
2. When using a cgi script in the cgi space to write a html page on
the
fly containing a jmol call. I did find a way to do this but it is
messy
and I still do not understand why what I have works, but it does.
Again,
an absolute address would fix things.
this should be fairly straightforward as well. can you show us some
demo code that fails?
The problem here is that the cgi tree is often quite different from the
htdocs tree. Writing a page on the fly, you are in the cgi tree, not the
htdocs tree. I used a set of soft links to fix it up, but I do not
recall exactly how.
Regards, Brian.
regards,
tim
--
Timothy Driscollem: [EMAIL PROTECTED]
molvisions - see. grasp. learn. ph: 919-368-2667
http://www.molvisions.com/im: molvisions
usa:virginia:blacksburg tx: [EMAIL PROTECTED]
Anyone who considers arithmetical methods of producing random digits
is, of course, in a state of sin. - J von Neumann
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Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ.
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Re: [Jmol-users] Relative against absolute addresses
On Mon, Mar 27, 2006 at 08:20:39AM +0200, [EMAIL PROTECTED] wrote: 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 Thanks, Nico. That confirms that there is a block on absolute addresses. I will continue to potter, so at least I will know more about it when you do fix everything in April after I haqve failed. I look forward to you coming back to this project. regards, Brian. --- 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 -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. --- 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 and MediaWiki
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. Regards, Brian. -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. --- 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=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Error when running jmol app
On Mon, Mar 14, 2005 at 09:38:19AM +0100, Egon Willighagen wrote: On Monday 14 March 2005 01:47 am, Brian Salter-Duke wrote: I have got the jmol application working OK on a SGI, but I would like to run it on my own linux box. When I type ./jmol in the jmol directory, it reports:- Warning: Major version number mismatch. Warning: Minor version number mismatch. java.lang.NoClassDefFoundError: javax/swing/JPanel at java.lang.Class.forName(Class.java:native) at java.lang.Class.forName(Class.java:52) at kaffe.jar.ExecJarName.main(ExecJarName.java:58) at kaffe.jar.ExecJar.main(ExecJar.java:59) Does this mean there is something wrong with my java support on this machine? If so, what? The problem is that the Kaffe JVM does not provide Swing at this moment. Jmol requires Swing and thus the Sun JVM. I get very confused about Java nomenclature. What is JVM? I was just about getting my brain around the difference between the runtime environment and the development kit. Am I right that I need to update the development kit in order to run the Jmol application? I had assumed I needed the runtime environment as I was running an application and not developing anything, but I now suspect that this is not so and that I need the JDK. However, going to www.java.com and searching around to download stuff, I always get a page not found. This is with 1.5 and 1.4.2. Which should I get if I can get anything? And where should I get it from. My machine is linux running Redhat 7.2. Brian. Egon -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ --- 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=6595alloc_id=14396op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Picking and measuring
On Tue, Mar 15, 2005 at 08:56:02AM +0800, Chris Pudney wrote: G'day, When the picking mode is one of distance, angle or torsion http://www.stolaf.edu/people/hansonr/jmol/docs/#.set%20(picking) would it be possible to have measurement rendered on the structure (rather than just echoed to the console) both during and at the completion of the pick? A few users have expressed a preference for using a picking-style of interaction (left-click x N) for making measurements rather than the standard style (double-click, left-click x N-2, double-click). So, for example, the user would set the picking mode to angle, left-click three atoms and an angle measurement would be rendered on the structure. A dynamic rendering of the angle would also be displayed as the three clicks are made just as in the standard angle measurement. Being able to select the picking mode from the pop-up menu would also be useful in this context. There would be no change to the current means of making measurements - this would just be an additional way of doing it. Thanks, Chris. I'm a Jmol newbie. Could someone please explain this to me? Is it about the stand-alone apllication or using the jmol.js applet? In the use of jmol/js in web application, the right click menu has an item for defing the units of measurements. However, I can not figure out how to display bond legths and bond angles on the molecule image. Is that possible? Is Chris' message above anything to do with this? Brian. --- 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=6595alloc_id=14396op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ --- 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=6595alloc_id=14396op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Reading a G98 optimisation output file with jmol.js
On Tue, Mar 15, 2005 at 07:29:24PM -0500, Miguel wrote: I would like to animate the steps of a G98 optimisation so the user can click though the structures at each step of the optimisation. However jmol.js reads both the input geometry and the standard orientation geometry at each step. These of course can be very different, so stepping through the structures has it flicking from one to the other. Is there a way of only reading one of them, short of suppresing the standard orientation by running G98 with symmetry suppressed? Don't know. Not familiar Gaussian or any of the other programs that people use to generate molecular models. If you are building a web page then I would just create buttons and put explicit 'frame' script commands behind the buttons. Or, if they are very regular you can put 'frame next; frame next;' behind a button and it will skip two frames instantly. Following this advice I came up with the following which seems to work. Frame 1 is the input orientation, so we start at frame 2, the standard orientation. The button then moves on two frames. The rewind button goes back to frame 2. Hope this helps other Gaussian users. tabletrtd script jmolSetAppletColor(palegreen); var script=load images/water_o_g98.log; wireframe 0.1; cpk off; + frame 2; rotate Y -90; anim off; jmolApplet(250, script); /script /tdtd nbsp; nbsp; nbsp; nbsp; nbsp; nbsp; nbsp; /tdtd center script jmolBr(); jmolButton(frame next; frame next;, Move on one frame); jmolBr(); jmolButton(frame 2;, Rewind); jmolBr(); /script /center /td/tr/table Cheers, Brian. Miguel --- 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 -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ --- 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] Error when running jmol app
Hi again, Miquel, On Tue, Mar 15, 2005 at 08:54:37PM -0500, Miguel wrote: However, the java runtime on your system is very old ... it needs to be updated. I realised this. I found I had the rpm.bin for j2re1.4.0_02. I think I downloaded it long ago with an old version of jmol which I never followed through with. I installed this and it put everything in /usr/java/j2re1.4.0_02, but java -version still finds the old version. Good. Do the following: #create a symbolic link to /usr/java/home ... good practice su cd /usr/java ln -s j2re1.4.0_02 home #edit the default path on the system emacs /etc/profile insert this at the bottom of the file- #add java to the front of the path for all users export JAVA_HOME=/usr/java/home PATH=$JAVA_HOME/bin:$PATH done-- Now, log out and log back in java -version This should allow you to run the app. Lovely. That worked well. However, a general question - does it tell you this on any of the assessable java sites? I have not seen anything like this, but of course I could be wrong. I also created JMOL_HOME and a link in my bin directory to jmol. The app is now running fine, but it keeps repeating two warnings to my main window:- 16/03/2005 14:36:31 java.util.prefs.FileSystemPreferences checkLockFile0ErrorCode WARNING: Could not lock System prefs.Unix error code 1212652808. 16/03/2005 14:36:31 java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush system prefs: java.util.prefs.BackingStoreException: Couldn't get file lock Is this a serious problem. Now, assuming that you need to take care of mozilla ... I do not think I do. I have another older version JRE in the mozilla tree itself, which I think got downloaded when my internet banking told me to. It just inserted it direct. su cd /usr/lib/mozilla-* cd plugins ln -s /usr/java/home/jre/plugin/i386/ns610/libjavaplugin_oji.so . I am not running Java 1.4.2, so I don't exactly remember whether that ns610 directory is there or not, but that is the general idea ... put a symbolic link to the correct libjavaplugin_oji.so in your /usr/lib/mozilla-*/plugins directory. Do I need to put /usr/java/j2re1.4.0_02 in my path, or create links, or delete the old java - /usr/bin/java or what? Do what I said above to put /usr/java/home/bin on the path before anything else. Or is this just too old also and I need to download version 5.0? No. 1.4.2 is just fine. Since it installed on your machine then I would leave it alone. Is there any advantage in version 5.0. I managed to download it on to my laptop as I can connect that by broadband and for various reasons I can not connect htis linux box by broadband. I could move it over and install it and then also clean up the mozialla plugins. (RedHat 7.2 was announced in Jan 2002 ... you may want to consider installing something newer) I am very doubtfull about whether some ab initio codes run well on more recent RHs. There were changes to gcc along the way. You would probably be OK running up to RH9 Perhaps even Fedora Core 1 would work OK. I have updated gcc at various times. I plan to install FC2 as I bought the RedHat Bible for FC2. I plan to upgrade linux on my laptop first and see whether stuff still works without disrupting production on my main machine. Good idea. Indeed. I have seen that people have had some problems with Gaussian 98 and Gamess beyond RH 7.3. I ran j2re-1_4_0_02-linux-i586-rpm.bin and it gave me j2re-1_4_0_02-fcs-linux-i586.rpm. I then ran that as explained above. Good. Now, given the age of 7.2, this may not work ... but I suspect that it will. It seemed to. Thanks for all your help. I am begining to get my head around this now. Brian. Miguel --- 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 -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ --- 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] Error when running jmol app
I have got the jmol application working OK on a SGI, but I would like to run it on my own linux box. When I type ./jmol in the jmol directory, it reports:- Warning: Major version number mismatch. Warning: Minor version number mismatch. java.lang.NoClassDefFoundError: javax/swing/JPanel at java.lang.Class.forName(Class.java:native) at java.lang.Class.forName(Class.java:52) at kaffe.jar.ExecJarName.main(ExecJarName.java:58) at kaffe.jar.ExecJar.main(ExecJar.java:59) Does this mean there is something wrong with my java support on this machine? If so, what? Regards, Brian. -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ --- 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=6595alloc_id=14396op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] codebaseDirectory from CGI scripts.
On Thu, Mar 10, 2005 at 06:31:45PM -0500, Miguel wrote: Brian, When using jmol.js in web pages it tells you to make the codebaseDirectory relative to the calling page not the web server root. Fine. If you do make it relative to the web server root it gives a pop up window to discourage you from doing this. Again, fine. However, I am constructing the web page including the script .. /script code in a CGI perl script, so I am in the cgi tree not the htdocs tree. These trees should be kept separate. How can I avoid using a path relative to the htdocs server root and avoid this popup window coming up? You should still be able to use a relative path ... Look at the path from the perspective of a user of your http server. Let's say that your is in your /cgi-bin directory. Then the root of your server is at .., and the contents of your htdocs directory is accessible from there. www.example.com/cgi-bin/foo.pl www.example.com/brian/jmol/Jmol.js In foo.pl you should say that the codebaseDirectory is ../brian/jmol That is the relative path from the perspective of a user of your web server, even though it is not the relative path within your local file system. After a struggle I did get this to work, but I do not know why it works. I just followed what the error messages in the log were saying it could not find and finished with ../../../jmol which does not make sense to me at present but I guess I'll figure it out some time. The installation I am working on (not my own machine) has so many links to the different web directories that it is difficult to follow some times. The cgi script is also writing scripts to later run in different directories and changing the current directory in the script. Separately ... Let me know if you encounter problems when configuring this using a cgi directory. A few months ago someone contacted me and they had many problems. I don't rememeber exactly what was going on, but I have the impression that the java plugin was doing something strange. In that case, he ended up fixing the problem by using .htaccess to allow cgis to execute from within his htdocs tree. I don't remember exactly what happened, but I have this feeling that I tried out a simple applet and saw that the codebase was messed up when the applet was served out of a cgi-bin directory. I did not have to do anything special. It works fine. Essentially htdocs, cgi-bin abd cgi-data directories are all in /var/www. The third is where data is written in sub-directories. One application for example does the following in the cgi script:- Read a Z-matrix and other data to construct a Gaussian input com file. Set up data to run Gaussian for this file. Uses babel to translate the com file to a pdb file. Queues the gaussian job. Uses jmol to display the molecule on the page that reports what has been done. E-mails the Gaussian run to the user when it finishes. One small concern is that each run gives many error messages in the web error log where it is searching for stuff in org/openscience. I found a message in the archives explaining this and suggesting they can be ignored, but I'll have to ask the administrator to rotate the log file to stop it getting very large. Cheers, Brian. Miguel --- 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 -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ --- 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
