From: Albion B. <ba...@bi...> - 2004-06-22 17:20:22
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Greetings, I am a former Chime developer (not affiliated with MDLI) excited about the prospects of Jmol. I am the principle programmer for a NSF sponsored projected named C4 (http://c4.cabrillo.cc.ca.us) which strives to introduce, develop and implement molecular visualization for lower division undergraduate education. I have recently started converting a suite of Java based components I had orginally developed for Chime to work with Jmol. Here is a demonstration page with a few of these components http://rna.ucsc.edu/albion/jmol/index.html (This is a temporary site and will ultimately move to a more permenant server in the near future). These components have been tested with Safari under Mac OS X 10.3, Internet Explorer 6 in Windows 2000 Professional, and Mozilla for Windows 2000 (after downloading the Sun JRE which includes a Java plugin for Mozilla). There are some performance issues on older computers, particularly with refresh that can cause flickering (on Mac OS X). I have also experienced incomplete loading of the Java applet components that occasionally leaves the component present, but with no JSlider drawn. Any suggestions or experiences with how to over come the incomplete loading (a race condition?) would be appreciated. I plan on converting all of my former components to Jmol. These components are only a preview. I have much work to do to document and clean up the underlying code. I suppose these could become an integral part of Jmol if there was enough interest, or simply left as an optional JAR file for download to augment the applet. Comments, suggestions, and questions are welcomed. Cheers, Albion Albion E. Baucom http://rna.ucsc.edu/albion |
From: Miguel <mi...@jm...> - 2004-06-23 11:55:48
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Albion wrote: > I am a former Chime developer (not affiliated with MDLI) excited > about the prospects of Jmol. ... Albion, I am currently travelling and don't have a chance to take a look right now. We are very interested in your contributions ... ... and my personal motivation for working on Jmol is to help with high school and undergrad education. Miguel |
From: Albion B. <ba...@bi...> - 2004-06-23 18:46:37
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Miguel, Im an excited to get onboard with the Jmol development. The C4 project has spent a lot of time working with Chime, and would like to see our work live on with Jmol. When do I become a list member? I replied to the confirmations for joining the developer and user lists (and I got replies claiming I had officially joined, after confirming), but I continue to get messages claiming my posts need to be reviewed by the moderator because I am not a member. Thanks Albion Albion E. Baucom http://rna.ucsc.edu/albion |
From: Jan R. <jr...@im...> - 2004-06-23 12:28:14
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Albion Baucom wrote: >Greetings, > I am a former Chime developer (not affiliated with MDLI) excited >about the prospects of Jmol. I am the principle programmer for a NSF >sponsored projected named C4 (http://c4.cabrillo.cc.ca.us) which strives >to introduce, develop and implement molecular visualization for lower >division undergraduate education. > >I have recently started converting a suite of Java based components I had >orginally developed for Chime to work with Jmol. Here is a demonstration >page with a few of these components > >http://rna.ucsc.edu/albion/jmol/index.html > > > using Mozilla1.7 client JVM1.5.0-beta2 on XP sp2rc2 there seemed to be no crosstalk with jmol. the same is with IE IE script error: line 1 column 33 no object method Regards, Jan >(This is a temporary site and will ultimately move to a more permenant >server in the near future). > >These components have been tested with Safari under Mac OS X 10.3, >Internet Explorer 6 in Windows 2000 Professional, and Mozilla for Windows >2000 (after downloading the Sun JRE which includes a Java plugin for >Mozilla). > >There are some performance issues on older computers, particularly with >refresh that can cause flickering (on Mac OS X). I have also experienced >incomplete loading of the Java applet components that occasionally leaves >the component present, but with no JSlider drawn. Any suggestions or >experiences with how to over come the incomplete loading (a race >condition?) would be appreciated. > >I plan on converting all of my former components to Jmol. > >These components are only a preview. I have much work to do to document >and clean up the underlying code. > >I suppose these could become an integral part of Jmol if there was enough >interest, or simply left as an optional JAR file for download to augment >the applet. > >Comments, suggestions, and questions are welcomed. > >Cheers, > >Albion > >Albion E. Baucom >http://rna.ucsc.edu/albion > > |
From: Miguel <mi...@jm...> - 2004-06-29 16:36:18
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Albion and Jan wrote: >>I have recently started converting a suite of Java based components I had >>orginally developed for Chime to work with Jmol. Here is a demonstration >>page with a few of these components >> >>http://rna.ucsc.edu/albion/jmol/index.html >> >> >> > using Mozilla1.7 client JVM1.5.0-beta2 on XP sp2rc2 there seemed to be > no crosstalk with jmol. > > the same is with IE > IE script error: > line 1 column 33 no object method If you are sure of this then it should be filed as a bug with Sun. Miguel |
From: Bob H. <ha...@st...> - 2004-06-23 16:16:31
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Albion, please tell me more about your NSF grant. It sounds exciting. My observation: The page loads extremely slowly, in agreement with my experience with Java controls. See some work we have done recently in: http://www.stolaf.edu/people/hansonr/jmol http://www.stolaf.edu/people/hansonr/jmol/doc http://www.stolaf.edu/people/hansonr/jmol/doc/examples It is much faster to load simple anchor tags with JavaScript scripting. Bob Hanson Albion Baucom wrote: >Greetings, > I am a former Chime developer (not affiliated with MDLI) excited >about the prospects of Jmol. I am the principle programmer for a NSF >sponsored projected named C4 (http://c4.cabrillo.cc.ca.us) which strives >to introduce, develop and implement molecular visualization for lower >division undergraduate education. > >I have recently started converting a suite of Java based components I had >orginally developed for Chime to work with Jmol. Here is a demonstration >page with a few of these components > >http://rna.ucsc.edu/albion/jmol/index.html > >(This is a temporary site and will ultimately move to a more permenant >server in the near future). > >These components have been tested with Safari under Mac OS X 10.3, >Internet Explorer 6 in Windows 2000 Professional, and Mozilla for Windows >2000 (after downloading the Sun JRE which includes a Java plugin for >Mozilla). > >There are some performance issues on older computers, particularly with >refresh that can cause flickering (on Mac OS X). I have also experienced >incomplete loading of the Java applet components that occasionally leaves >the component present, but with no JSlider drawn. Any suggestions or >experiences with how to over come the incomplete loading (a race >condition?) would be appreciated. > >I plan on converting all of my former components to Jmol. > >These components are only a preview. I have much work to do to document >and clean up the underlying code. > >I suppose these could become an integral part of Jmol if there was enough >interest, or simply left as an optional JAR file for download to augment >the applet. > >Comments, suggestions, and questions are welcomed. > >Cheers, > >Albion > >Albion E. Baucom >http://rna.ucsc.edu/albion > > >------------------------------------------------------- >This SF.Net email sponsored by Black Hat Briefings & Training. >Attend Black Hat Briefings & Training, Las Vegas July 24-29 - >digital self defense, top technical experts, no vendor pitches, >unmatched networking opportunities. Visit www.blackhat.com >_______________________________________________ >Jmol-developers mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr |
From: Albion B. <ba...@bi...> - 2004-06-23 17:22:03
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Greetings, Thanks for your replies. Evidently there is version matrix that needs to be established for Java<->Jmol communication. I am getting wildly different compatability on different platforms and browsers. I need to figure out what browser and Java requirements are for the following browsers and platforms Windows 2K/XP ----------------- - Internet Explorer - Mozilla - Netscape Navigator Mac OS X ----------------- - Safari - Mozilla - Netscape Navigator * Internet Explorer (I don't belive this is going to be supported in future releases, and appears not to have full LiveConnect support in its current version anyway) My tools require a full implementation of LiveConnect. Up to some point in the near past, IE in Windows did not support inter-applet communication, or at least not in a capacity that allowed my tools to communicate with Chime. Much to my suprise I found that my latest installation of Windows and IE DID support inter-applet communication using my tools with Jmol. But Im not sure how universal this communication is. Someone has already experienced problems with IE in XP SP2/rc2; the applets load, but there is no communication. My questions regarding IE are: - Did IE change its LiveConnect support recently? - Are there security levels within IE that prohibit inter-applet communication? That is, if I set the security features of the browser to high (or strict), does that abolish features of LiveConnect? - Should I expect to see a difference between IE on Windows 2K and XP? Also, looking at my server logs, I find that I have a lot of 404 (file not found) messages for components of Jmol. It appears that during the page loading that the client is trying to find the Jmol components via a URL to a specific folder, rather than in the JAR file. For instance I get requests like this GET /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en.class I just extracted the contents of the JmolApplet.jar file into the directory that contains my Java demos to see if this alleviates the problem, but I need to figure out why client browsers are trying to access the Jmol components with an absolute URL rather than via the JAR archive. My HTML source tags are defined as follows <applet name="jmol" code="JmolApplet" archive="JmolApplet.jar" width="640" height="480"> I was under the impression that that should direct the client to find the class files in the JAR file pointed to by the archive specifier. Any comments on what is going on here? Regards, Albion Albion E. Baucom http://rna.ucsc.edu/albion |
From: Miguel <mi...@jm...> - 2004-06-29 15:49:50
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> > Greetings, > > Thanks for your replies. > > Evidently there is version matrix that needs to be established for > Java<->Jmol communication. I am getting wildly different compatability on > different platforms and browsers. I have not observed any major incompatibilities. With the exception of MacOS X 10.2, everything in the JavaScript <-> Applet world seems pretty clean to me. > I need to figure out what browser and > Java requirements are for the following browsers and platforms > > Windows 2K/XP > ----------------- > - Internet Explorer IE 5.5 or higher > - Mozilla 1.2 or higher > - Netscape Navigator 4.76 or higher in the old world. I don't know about the newer versions. > Mac OS X > ----------------- I will not offer support for anything other than 10.3 Panther. Previous versions were too broken. > - Safari I think it is 1.2 ... whatever came with Panther. > - Mozilla Don't know > - Netscape Navigator Don't know > * Internet Explorer (I don't belive this is going to be supported in > future releases, and appears not to have full LiveConnect support in its > current version anyway) Will not be supported ... no LiveConnect and MSFT has dropped support. > My tools require a full implementation of LiveConnect. Up to some point in > the near past, IE in Windows did not support inter-applet communication, I have never experienced any problems with IE. You say 'inter-applet communication' ... this can get complicated. If two applets are on the same HTML page then it always works. If tow applets are on different pages (in different frames) then it can get pretty ugly. > or at least not in a capacity that allowed my tools to communicate with > Chime. Chime is not an applet, it is a plug-in. There may well have been problems with communications between plugins. > Much to my suprise I found that my latest installation of Windows > and IE DID support inter-applet communication using my tools with Jmol. I have never experienced any problems. > But Im not sure how universal this communication is. You should start with getting things to work when they are on the same page. Then I will help you after that. > Someone has already > experienced problems with IE in XP SP2/rc2; the applets load, but there is > no communication. I am not aware of this. > My questions regarding IE are: > > - Did IE change its LiveConnect support recently? No. LiveConnect support on IE for *applets* has been very stable for at least 4 years. > - Are there security levels within IE that prohibit inter-applet > communication? Not that I am aware of. However, you *must* use the applet attribute mayscript='true' in order to be able to call JavaScript from a Java Applet (but I don't think that is what you are trying to do) > That is, if I set the security features of the browser to > high (or strict), does that abolish features of LiveConnect? Don't know ... it certainly might. > - Should I expect to see a difference between IE on Windows 2K and XP? None ... behavior should be exactly the same. > Also, looking at my server logs, I find that I have a lot of 404 (file not > found) messages for components of Jmol. It appears that during the page > loading that the client is trying to find the Jmol components via a URL to > a specific folder, rather than in the JAR file. For instance I get > requests like this > > GET /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en.class This is Java trying to do localization for language support. The file does not exist in the .jar file so it tries to go to the server. This is not a problem. > I just extracted the contents of the JmolApplet.jar file into the > directory that contains my Java demos to see if this alleviates the > problem, but I need to figure out why client browsers are trying to access > the Jmol components with an absolute URL rather than via the JAR archive. > My HTML source tags are defined as follows > > <applet name="jmol" code="JmolApplet" archive="JmolApplet.jar" width="640" > height="480"> You should *always* use 'mayscript="true"' to ensure better portability to old browsers. Which JVM are you using? MSFT or Sun Java Plug-in? > I was under the impression that that should direct the client to find the > class files in the JAR file pointed to by the archive specifier. Correct. But if the file is not found then it will continue to look on the web server. In the case of language files this should not be an issue. > Any comments on what is going on here? I just took another look ... and there is something that I do not understand. You say that you are seeing a reference to JmolPopupStructure_en.class ... that is not right. It should be referring to a .properties file, not a .class file. I bet that you are using the MSFT JVM and that there is some type of minor compatibility problem. Nevertheless, this should not keep anything from running. Note that I am only around for about 36 hours ... then I will be unavailable for a few days. Miguel |
From: Albion B. <ba...@bi...> - 2004-06-29 21:30:28
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Miguel, Greetings! Thanks for the in-depth reply. Here is a follow-up. > > or at least not in a capacity that allowed my tools to communicate with > > Chime. > > Chime is not an applet, it is a plug-in. There may well have been problems > with communications between plugins. Yes, of course. I forgot about that. Very important point. This is the reason I have suddenly discovered LiveConnect working properly. It was Applet<->Plug-in support that was lacking in IE. Thanks for the reminder. My bad. Another reason why JMol is a great alternative! > > But Im not sure how universal this communication is. > > You should start with getting things to work when they are on the same > page. Then I will help you after that. OK. My tools already have built in abilities to talk to Applets in frames, but I haven't tried it yet. > > Someone has already experienced problems with IE in XP SP2/rc2; the > > applets load, but there is no communication. > > I am not aware of this. This is the first real problem I have encountered, other than out-of-date, missing or improperly installed JRE for Mozilla, or Safari on the Mac. > > - Did IE change its LiveConnect support recently? > > No. LiveConnect support on IE for *applets* has been very stable for at > least 4 years. Got it. The Applet/Plug-in reminder makes this question moot. Thanks. > > That is, if I set the security features of the browser to > > high (or strict), does that abolish features of LiveConnect? > > Don't know ... it certainly might. OK. This is something we might want to test or be aware of for future user issues concerning lack of communication between applets. This could be a "gotcha" somewhere down the road. > > Also, looking at my server logs, I find that I have a lot of 404 (file > > not found) messages for components of Jmol. It appears that during the > > page loading that the client is trying to find the Jmol components via > > a URL to a specific folder, rather than in the JAR file. For instance > > I get requests like this > > > > GET /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en.class I just received another users inquiry to this very problem. This might warrant some more time. Something is a little funny here ... > Which JVM are you using? MSFT or Sun Java Plug-in? Good question. I didn't have the problem, another user did when they tried load the page. We might consider a "checklist" of versions when reporting problems - OS - Browser/Version - JMol version - JVM > I just took another look ... and there is something that I do not understand. > > You say that you are seeing a reference to JmolPopupStructure_en.class ... > that is not right. I've got loads of these 404 messages in my server log: % grep 404 access_log | awk '{print $7}' | sort -u /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure.class /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en.class /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en_GB.class /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en_GB.properties /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en.properties /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en_US.class /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en_US.properties /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_fr.class /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_fr_FR.class /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_fr_FR.properties /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_fr.properties /albion/jmol/org/openscience/jmol/ui/JmolPopupWords.class /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_en.class /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_en_GB.class /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_en_GB.properties /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_en.properties /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_en_US.class /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_en_US.properties /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_fr.class /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_fr_FR.class /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_fr_FR.properties /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_fr.properties > It should be referring to a .properties file, not a .class file. I bet > that you are using the MSFT JVM and that there is some type of minor > compatibility problem. Well, these are in my server log, and not generated by my local clients (at least none my of my local IP addresses are popping up), only by other clients accessing the page, so I don't know what client/JVM they are using other that what is listed in the access_log. The browsers listed in the log with these messages are the following Mozilla/5.0 (compatible; Konqueror/3.2; Linux) Mozilla/4.0 (Windows XP 5.1) Java/1.4.2_04 Mozilla/4.0 (Windows 2000 5.0) Java/1.4.2 and some that just say Java/1.4.2 That is all for now. Albion Albion E. Baucom http://rna.ucsc.edu/albion |
From: Miguel <mi...@jm...> - 2004-06-30 11:10:08
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>> > But Im not sure how universal this communication is. >> >> You should start with getting things to work when they are on the same >> page. Then I will help you after that. > > OK. My tools already have built in abilities to talk to Applets in frames, > but I haven't tried it yet. Different browsers work in different ways. On Netscape 4.* and with the current versions of Konqueror it is impossible for Applets in different frames to establish direct communications. The only mechanism is to use JavaScript as an intermediary. >> > That is, if I set the security features of the browser to >> > high (or strict), does that abolish features of LiveConnect? >> >> Don't know ... it certainly might. > > OK. This is something we might want to test or be aware of for future user > issues concerning lack of communication between applets. This could be a > "gotcha" somewhere down the road. Yes ... would be good to know. >> > Also, looking at my server logs, I find that I have a lot of 404 (file >> > not found) messages for components of Jmol. It appears that during the >> > page loading that the client is trying to find the Jmol components via >> > a URL to a specific folder, rather than in the JAR file. For instance >> > I get requests like this >> > >> > GET /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en.class > > I just received another users inquiry to this very problem. This might > warrant some more time. Something is a little funny here ... > >> Which JVM are you using? MSFT or Sun Java Plug-in? > > Good question. I didn't have the problem, another user did when they tried > load the page. We might consider a "checklist" of versions when reporting > problems > > - OS > - Browser/Version > - JMol version > - JVM > >> I just took another look ... and there is something that I do not >> understand. >> >> You say that you are seeing a reference to JmolPopupStructure_en.class >> ... >> that is not right. > > I've got loads of these 404 messages in my server log: > > % grep 404 access_log | awk '{print $7}' | sort -u > > /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure.class > /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en.class > /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en_GB.class > /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en_GB.properties > /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en.properties > /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en_US.class > /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_en_US.properties > /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_fr.class > /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_fr_FR.class > /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_fr_FR.properties > /albion/jmol/org/openscience/jmol/ui/JmolPopupStructure_fr.properties > /albion/jmol/org/openscience/jmol/ui/JmolPopupWords.class > /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_en.class > /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_en_GB.class > /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_en_GB.properties > /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_en.properties > /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_en_US.class > /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_en_US.properties > /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_fr.class > /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_fr_FR.class > /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_fr_FR.properties > /albion/jmol/org/openscience/jmol/ui/JmolPopupWords_fr.properties > >> It should be referring to a .properties file, not a .class file. I bet >> that you are using the MSFT JVM and that there is some type of minor >> compatibility problem. The code that is looking for these localization files is outside of Jmol. I doubt if there is anything we can do about it. Since it seems to be looking for both .class and .properties files then I assume that is their mechanism. It now seems to me that this is not a problem. Miguel |