Re: [Jmol-users] Web browser plug-in?
Back to the issue of loading Jmol in a browser when Jmol is not delivered by the server that also delivers the content. I found this page on plug-in development for Safari. http://developer.apple.com/technotes/tn/tn2020.html According to this document, plug-ins for Netscape for MacOS 7-9 can easily be modified for Safari on MacOS X. Might this be done for Chime? (I know this is a Jmol forum, not a Chime forum, but y'all are always talking about Chime, too, so I figured it was a good place to ask.) Also, by following the link in this document to the Netscape Developers' Plug-in page, http://developer.netscape.com/docs/manuals/communicator/plugin/index.htm , I have learned that plug-ins are written in C or C++. So apparently it would not be easy to convert Jmol into a plug-in. But maybe a very simple plug-in that would call Jmol could be written, as described in Chapter 2 of the Netscape documentation. There's still the option of training Safari to call Jmol when a MOL or PDB file or somesuch is loaded, but I haven't found anything that says that's possible, although Miguel suggests it is. Any thoughts? -- Bob Grossman --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Web browser plug-in?
Robert wrote: Back to the issue of loading Jmol in a browser when Jmol is not delivered by the server that also delivers the content. I found this page on plug-in development for Safari. http://developer.apple.com/technotes/tn/tn2020.html This is a useful document for me. Thanks for sending it. According to this document, plug-ins for Netscape for MacOS 7-9 can easily be modified for Safari on MacOS X. Might this be done for Chime? Well, there is the *not insignificant* problem that only MDL has the source code for Chime. If it was easily done then MDL would have done it. Instead, they have officially announced that they will not be supporting OSX and have officially put Chime on and end-of-life plan. (I know this is a Jmol forum, not a Chime forum, but y'all are always talking about Chime, too, so I figured it was a good place to ask.) No problem. Also, by following the link in this document to the Netscape Developers' Plug-in page, http://developer.netscape.com/docs/manuals/communicator/plugin/index.htm , I have learned that plug-ins are written in C or C++. This is true. So apparently it would not be easy to convert Jmol into a plug-in. You are correct that it would not be easy. But it is theoretically possible that this could be done. But maybe a very simple plug-in that would call Jmol could be written, as described in Chapter 2 of the Netscape documentation. There's still the option of training Safari to call Jmol when a MOL or PDB file or somesuch is loaded, but I haven't found anything that says that's possible, although Miguel suggests it is. Any thoughts? Having Safari call the Jmol *application* directly (as a 'helper application') can be done today. This would automatically launch the Jmol application when a .mol or .pdb file was accessed ... whether the user was online or not. The Jmol *application* would be launched, so the user would no longer be working in the context of the web browser. If you think that this would be useful, then we can write up some documents and package things up a little better so that this can be more easily configured. Q: Would it be valuable to have a simpler mechanism to associate the Jmol application with web browsers as a helper application? Miguel --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Web browser plug-in?
Q: Would it be valuable to have a simpler mechanism to associate the Jmol application with web browsers as a helper application? This of course was the MIME handling mechanism, and the reason for chemical/x-pdb etc MIME types. As far as I can tell, OS X does not have a clear mechanism for setting this behaviour in the Safari browser (It might have to be done indirectly via IE which has an obscure GUI for doing this, or via 3rd party programs such as Misfox). If anyone can clarify MIME handling in OS X/Safari I would be grateful. -- Henry Rzepa. Imperial College, Chemistry Dept. +44 0778 626 8220 +44 020 7594 5804 (Fax) --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Web browser plug-in?
Q: Would it be valuable to have a simpler mechanism to associate the Jmol application with web browsers as a helper application? If the Jmol application can be launched automatically whenever a file with MOL or PDB extension was loaded by Safari, that would be a big help. Henry's message seemed to say that making these associations on Safari may be difficult. On every other browser that I know of it can be done. I still think a Safari plug-in that calls the Jmol applet and activates it within Safari would be better, because it's a pain to go back and forth between apps, but as a stop-gap measure, what you suggest is good. OK. Regarding 'stop-gap' ... I want to be clear that any type of Jmol 'plug-in' could not happen before 2005. Maybe I can interest a computer science student here in writing a plug-in that would call the applet instead of the stand-alone app, if you have other priorities right now. I appreciate the offer. But do not underestimate the magnitude of this task ... writing a plug-in is a *major* piece of development ... The user will need a way to tell Safari which file extensions should make it call Jmol. And yes, there needs to be some simple mechanism that installs the plug-in or whatever that trains Safari to call Jmol. (A *very* simple mechanism, please. I know almost no UNIX, and if I wanted to learn it, I wouldn't have bought a Mac!) Given Henry's comment ... we need to see what the Mac folks have to say. Miguel --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Web browser plug-in?
Q: Would it be valuable to have a simpler mechanism to associate the Jmol application with web browsers as a helper application? If the Jmol application can be launched automatically whenever a file with MOL or PDB extension was loaded by Safari, that would be a big help. Henry's message seemed to say that making these associations on Safari may be difficult. There is no GUI in Safari for setting these things (unlike eg Mozilla); a program called Misfox (by the author of iCab, another Mac browser) seems to set the MIME type at the Unix level, but Safari ignores this. Thus if the server sets a MIME of chemical/x-mdl-molfile, Safari will simply download the file but make no attempt to open it (actually, any page which embeds eg 10 files will result in 10 downloads) It gets worse! OS X seems to think that .jar files are documents rather than applications (as evidenced by trying to place a .jar into the dock, it will only go into the document part of the dock). Thus setting the MIME type in Mozilla and specifying jmol.jar as the application fails, since the system thinks you are trying to open one document with another! IE will allow you to define new MIME types, but trying to associate this with a .jar file again fails (since a .jar is a document, and its greyed out). Yes, it is incredible that Apple could produce such a broken system. Of course, it may just be my system that is broken; can any other OS X user reproduce any of the above? -- Henry Rzepa. Imperial College, Chemistry Dept. +44 0778 626 8220 +44 020 7594 5804 (Fax) --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Web browser plug-in?
Henry's message seemed to say that making these associations on Safari may be difficult. There is no GUI in Safari for setting these things (unlike eg Mozilla) :-O and every other web browser on the planet! It gets worse! [snip] Yes, it is incredible that Apple could produce such a broken system. Nick Greeves ... file a bug report! :-) Miguel --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Web browser plug-in?
Rzepa, Henry sent [8.55p gmt 2004 March 17 Wednesday] : Q: Would it be valuable to have a simpler mechanism to associate the Jmol application with web browsers as a helper application? If the Jmol application can be launched automatically whenever a file with MOL or PDB extension was loaded by Safari, that would be a big help. Henry's message seemed to say that making these associations on Safari may be difficult. There is no GUI in Safari for setting these things (unlike eg Mozilla); a program called Misfox (by the author of iCab, another Mac browser) seems to set the MIME type at the Unix level, but Safari ignores this. Thus if the server sets a MIME of chemical/x-mdl-molfile, Safari will simply download the file but make no attempt to open it (actually, any page which embeds eg 10 files will result in 10 downloads) I am researching how this behaves, but I admit - it has me stumped right now. It gets worse! OS X seems to think that .jar files are documents rather than applications (as evidenced by trying to place a .jar into the dock, it will only go into the document part of the dock). true...and not true. ;-) if you launch the .jar file it appears in the applications part of the Dock; you can then choose to keep it there. but you can not drag it there de novo. I believe this is because jar files are not recognized as packages. Thus setting the MIME type in Mozilla and specifying jmol.jar as the application fails, since the system thinks you are trying to open one document with another! IE will allow you to define new MIME types, but trying to associate this with a .jar file again fails (since a .jar is a document, and its greyed out). Yes, it is incredible that Apple could produce such a broken system. Of course, it may just be my system that is broken; can any other OS X user reproduce any of the above? I can confirm this behavior, though I can't tell why Mozilla fails trying to open a pdb file with jmol.jar. regards, :tim -- timothy driscoll molvisions - molecular graphics visualization http://www.molvisions.com/ usa:north carolina:wake forest --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id70alloc_id638op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Web browser plug-in?
Robert B. Grossman sent [2.05p gmt 2004 March 17 Wednesday] : If the Jmol application can be launched automatically whenever a file with MOL or PDB extension was loaded by Safari, that would be a big help. I still think a Safari plug-in that calls the Jmol applet and activates it within Safari would be better, because it's a pain to go back and forth between apps, but as a stop-gap measure, what you suggest is good. Maybe I can interest a computer science student here in writing a plug-in that would call the applet instead of the stand-alone app, if you have other priorities right now. The user will need a way to tell Safari which file extensions should make it call Jmol. And yes, there needs to be some simple mechanism that installs the plug-in or whatever that trains Safari to call Jmol. (A *very* simple mechanism, please. I know almost no UNIX, and if I wanted to learn it, I wouldn't have bought a Mac!) I think it was Miguel who mentioned using a signed applet in lieu of a plug-in. this seems a simpler and more robust solution, but maybe I don't understand the problem correctly. why wouldn't a signed applet work here? regards, :tim -- timothy driscoll molvisions - molecular graphics visualization http://www.molvisions.com/ usa:north carolina:wake forest --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id70alloc_id638op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Web browser plug-in?
Robert, I've recently upgraded to MacOS 10.3, and I use Safari nearly exclusively. I was wondering whether there are plans or has been progress in creating a Jmol plug-in for the Safari Web browser? Panther 10.3/Safari works well with the existing JmolApplet. You should be able to see some simple examples at: http://jmol.sf.net/preview The basic JmolApplet has always worked on OSX and on Safari ... although there were some trouble areas. Apple's previous implementations of Java Safari were deficient in certain areas (most notable LiveConnect). But the base Jmol did work. The good news is that Apple fixed a large number of issued with 10.3 Panther. So, as far as I know, almost everything works today. After all, Jmol is touted as a substitute for Chime, and Chime is a plug-in. But Chime works only with the ancient Netscape 4.7 on the Mac platform. Agreed. Also, why is there no Paste function in Jmol (stand-alone app)? I tried to paste a URL into the Open URL window, but I was unable. This is not something that Jmol has control over. Each platform needs to implement basic user interface features in accordance with the user-interface guidelines of that platform. Works fine on Linux and on Win32 ... Looks like a bug that Apple hasn't fixed yet :-( Miguel P.S. Jmol's graphics are beautiful! Thanks! --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Web browser plug-in?
Specifically, the American Chemical Society now provides MOL files and other online content in the Web versions of their publications, but it does not deliver applets to render the content. (Maybe it should, but it doesn't.) (Perhaps we should suggest that they consider using Jmol :-) Actually, I've already done this. (I think I suggested Marvin, too, which is free to scientific publishers, but Jmol would be just as good or better.) The publishers at ACS, though, are novices when it comes to Web content. The first time I published a paper with MOL files as EWOs (Extended Web Objects, their name for Web-only content) in late 2002, I had to back-and-forth with them a dozen times before I could convince them that they needed to include the MIME type of the MOL file when they delivered it to the browser. I have just published another paper with MOL files as EWOs, and now they have stripped all of the return characters from the MOL files (probably from transferring them across platforms), so even Chime can't display it properly. I alerted them to the problem several days ago, and it still hasn't been fixed. :-( The problem is made worse by the fact that the publishing folks don't like to communicate directly with the authors. They want the editors to act as a buffer. Then communication ends up like the child's game of Telephone. Argh! In any case, if you can convince ACS to deliver applets along with the EWOs, you will have done a great service to the chemistry community. Meanwhile, though, we need another solution. Here are my personal thoughts/comments ... in random order: * In general, it is extremely expensive to develop and maintain plug-ins. To the best of my knowledge, there is no well-defined standard Plug-in architecture (although Netscape's API is probably somewhat standard). This means that plug-ins have to be developed on a per platform/browser basis. This is very costly and painful, and can only be undertaken by companies that have significant financial resources. That is why Chime went down the toilet. * The Applet architecuture was designed to replace this. Everyone fell in love with Applets because they were supposed to solve this problem ... cross-platform compatibility and a standard interface to the Browser. * It is possible to install an applet locally. This is called a *signed* applet. * It may be possible for us to create a JmolApplet that could be installed locally as a signed applet and would operate offline by detecting the mime-type ... I do not know ... but I will put it on my list of things to investigate. A signed applet would be a great alternative to a plug-in. I didn't know such a thing was possible. This morning I also sent an email to Manfred Schubert, who has created at least two very nice plug-ins for Safari (http://www.schubert-it.com), about converting Jmol to an applet. Maybe you can get in touch with him and discuss the possibilities. -- Bob --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Web browser plug-in?
Miguel Howard schrieb: Robert wrote: ... Robert, OK, now I understand. You want something that is installed on the local machine and does not require a web server. Specifically, the American Chemical Society now provides MOL files and other online content in the Web versions of their publications, but it does not deliver applets to render the content. (Maybe it should, but it doesn't.) (Perhaps we should suggest that they consider using Jmol :-) configure Jmol like RasMol make a script file, starting Jmol with the temporary file from the browser http://www.imb-jena.de/ImgLibPDB/docs/RasMolInfo.html (that is an application for load pdb inline with RasMol and Chime, I'd like to mention at this point, again) I have noticed, that the Jmol application has a Open URL (which does not work for me), so you may cut and past the link from a web page. What about a command line switch -url or jmol.sh -e 'load pdb http://www.rcsb.org/pdb/cgi/export.cgi/1PLC.pdb?format=PDBpdbId=1PLCcompression=None; jmol.sh -script http://www.imb-jena.de/cgi-bin/rascript.exe?CODE=1plc this would be nice. Regards, Jan --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Web browser plug-in?
Jan wrote: configure Jmol like RasMol make a script file, starting Jmol with the temporary file from the browser http://www.imb-jena.de/ImgLibPDB/docs/RasMolInfo.html If I understand you correctly, this will launch the Jmol application as a helper application outside the browser. Unfortunately, it will not display within the context of the browser (like Chime) (that is an application for load pdb inline with RasMol and Chime, I'd like to mention at this point, again) This is not forgotten ... I have been giving a lot of thought to inline loading and how best to handle it. I have noticed, that the Jmol application has a Open URL (which does not work for me), In what way does this not work? so you may cut and past the link from a web page. What about a command line switch -url or jmol.sh -e 'load pdb http://..' That is a good suggestion. Miguel --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Web browser plug-in?
Miguel Howard schrieb: Jan wrote: configure Jmol like RasMol make a script file, starting Jmol with the temporary file from the browser http://www.imb-jena.de/ImgLibPDB/docs/RasMolInfo.html If I understand you correctly, this will launch the Jmol application as a helper application outside the browser. yes Unfortunately, it will not display within the context of the browser (like Chime) that's true (that is an application for load pdb inline with RasMol and Chime, I'd like to mention at this point, again) This is not forgotten ... I have been giving a lot of thought to inline loading and how best to handle it. I have noticed, that the Jmol application has a Open URL (which does not work for me), In what way does this not work? I'm wrong, I may have made a typing error with copy and past, it's fine :-) Regards, Jan --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
