Re: [Jmol-users] Jmol 11.7.1 - 11.7.3 new features
so is it still causing that problem? I can't see how IOException can
be an unknown value
On Mon, Dec 15, 2008 at 10:43 AM, Rolf Huehne wrote:
> Robert Hanson wrote:
>> Rolf, please check now. I have no idea about the IOException problem.
>> What an odd error. I'm certainly not having that issue -- you might
>> need to do a clean build.
>>
> I always do a cleanup before compiling Jmol ("ant clean; ant").
>
> Regards,
> Rolf
>
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If nature does not answer first what we want,
it is better to take what answer we get.
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Re: [Jmol-users] Jmol 11.7.1 - 11.7.3 new features
Robert Hanson wrote:
> Rolf, please check now. I have no idea about the IOException problem.
> What an odd error. I'm certainly not having that issue -- you might
> need to do a clean build.
>
I always do a cleanup before compiling Jmol ("ant clean; ant").
Regards,
Rolf
--
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Re: [Jmol-users] Jmol 11.7.1 - 11.7.3 new features
Rolf, please check now. I have no idea about the IOException problem. What an odd error. I'm certainly not having that issue -- you might need to do a clean build. The problem with -w should be fixed. The problem was that I changed the way the -x option works, so that it just appends ";exitJmol" to the script. I've now changed the -w option so that it simply appends to --jmolScript2 the proper write command. Also, on a Windows machine, at least, you have to be careful to only have 9 parameters. So it may be important to tie parameter values with their flag: jmol -iong400x500 -s "t2.spt" -J "color carbon pink" -j "background green" -w "JPG 100:t.jpg" Here I've added the quality after JPG so that I could save two parameters. (This is also new -- that you can add the quality this way.) This could be why some flags were not processed. Remove the -i flag to see what the scripts and script files that will be processed are. Bob On Mon, Dec 15, 2008 at 6:09 AM, Rolf Huehne wrote: > Robert Hanson wrote: >> I think this is all fixed now. The sequence of execution is: >> >> file load >> -J (Jmol script as argument) >> -s (script file name as argument) >> -j (Jmol script as argument) >> -x (exit) >> >> The -n switch (no display) adds an implicit -x, and it is executed >> only after the final script is run. Basically what the -x switch does >> is add ";exitJmol" to any second script present. >> >> So, for example, the following worked for me: >> >> jmol -ion -J "myparam = 3" -s "t.spt" -j "set echo top left;echo >> @myparam;cartoons on;write image 400 400 JPG \"t.jpg\";" "1crn.pdb" >> > There are still some problems in version 11.7.18 with the command-line > switches. > > Now the script supplied with '-s' is not applied any more before the > image requested with "-w" is written. (no '-j' present) > This will break existing batch pipelines with Jmol. > > If '-j' is also present the image doesn't even display the structure > (loaded within the '-j' script) but only "Jmol". And the image also > hasn't the size requested with '-g' but only the size of the "Jmol" text. > > By the way, when I tried to compile the latest SVN version (revision > 10492) I got the following error message: >[javac] java/Jmol/src/org/jmol/export/image/ImageCreator.java:203: > cannot resolve symbol >[javac] symbol : constructor IOException (java.io.IOException) >[javac] location: class java.io.IOException >[javac] throw new IOException(e); >[javac] ^ >[javac] Note: Some input files use or override a deprecated API. >[javac] Note: Recompile with -deprecation for details. >[javac] 1 error > > Regards, > Rolf > > -- > 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 > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- 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 and Google Web Toolkit
El 15 Dec 2008 a las 11:46, Raphael André Bauer escribió: > it seems that your observation is right and using the jmol.js breaks > the GWT. However it is easily possible to use jmol without jmol.js and > thus avoiding this problem. An idea is to use the Firebug plugin for > Firefox that gives you the "real" html generated by jmol.js. A simple > copy and paste into the GWT application solves that issue and GWT and > Jmol work nicely together... It will likely work without any trouble, but note that Jmol.js renders different code depending on the browser (at least for insertion of the applet). So it's not that simple. That's one of the reasons why using Jmol.js is the recommended method. The best would be to find the exact confilct between GWT code and Jmol.js code. -- 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 and Google Web Toolkit
first let's find out what's breaking the GWT. It's probably something simple. On Mon, Dec 15, 2008 at 6:03 AM, Angel Herraez wrote: > El 15 Dec 2008 a las 11:46, Raphael André Bauer escribió: >> it seems that your observation is right and using the jmol.js breaks >> the GWT. However it is easily possible to use jmol without jmol.js and >> thus avoiding this problem. An idea is to use the Firebug plugin for >> Firefox that gives you the "real" html generated by jmol.js. A simple >> copy and paste into the GWT application solves that issue and GWT and >> Jmol work nicely together... > > It will likely work without any trouble, but note that Jmol.js > renders different code depending on the browser (at least for > insertion of the applet). So it's not that simple. > That's one of the reasons why using Jmol.js is the recommended > method. > The best would be to find the exact confilct between GWT code and > Jmol.js code. > > > > -- > 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 > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- 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 and Google Web Toolkit
El 15 Dec 2008 a las 11:46, Raphael André Bauer escribió: > it seems that your observation is right and using the jmol.js breaks > the GWT. However it is easily possible to use jmol without jmol.js and > thus avoiding this problem. An idea is to use the Firebug plugin for > Firefox that gives you the "real" html generated by jmol.js. A simple > copy and paste into the GWT application solves that issue and GWT and > Jmol work nicely together... It will likely work without any trouble, but note that Jmol.js renders different code depending on the browser (at least for insertion of the applet). So it's not that simple. That's one of the reasons why using Jmol.js is the recommended method. The best would be to find the exact confilct between GWT code and Jmol.js code. -- 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 11.7.1 - 11.7.3 new features
Robert Hanson wrote: > I think this is all fixed now. The sequence of execution is: > > file load > -J (Jmol script as argument) > -s (script file name as argument) > -j (Jmol script as argument) > -x (exit) > > The -n switch (no display) adds an implicit -x, and it is executed > only after the final script is run. Basically what the -x switch does > is add ";exitJmol" to any second script present. > > So, for example, the following worked for me: > > jmol -ion -J "myparam = 3" -s "t.spt" -j "set echo top left;echo > @myparam;cartoons on;write image 400 400 JPG \"t.jpg\";" "1crn.pdb" > There are still some problems in version 11.7.18 with the command-line switches. Now the script supplied with '-s' is not applied any more before the image requested with "-w" is written. (no '-j' present) This will break existing batch pipelines with Jmol. If '-j' is also present the image doesn't even display the structure (loaded within the '-j' script) but only "Jmol". And the image also hasn't the size requested with '-g' but only the size of the "Jmol" text. By the way, when I tried to compile the latest SVN version (revision 10492) I got the following error message: [javac] java/Jmol/src/org/jmol/export/image/ImageCreator.java:203: cannot resolve symbol [javac] symbol : constructor IOException (java.io.IOException) [javac] location: class java.io.IOException [javac] throw new IOException(e); [javac] ^ [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -deprecation for details. [javac] 1 error Regards, Rolf -- 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 and Google Web Toolkit
On Fri, Dec 12, 2008 at 5:13 PM, Raphael André Bauer wrote: > Hey folks, > > > did anybody already try to use Jmol inside a GWT application? afai can > see there are "natural" problems using the jmol.js together with the GWT > (as it breaks the GWT javascript appearently). > > Does anybody have this up and running in a productive environemnt and has > any good advice how to set it up (use applet tag, omit blablabla)? Hey Raphael, it seems that your observation is right and using the jmol.js breaks the GWT. However it is easily possible to use jmol without jmol.js and thus avoiding this problem. An idea is to use the Firebug plugin for Firefox that gives you the "real" html generated by jmol.js. A simple copy and paste into the GWT application solves that issue and GWT and Jmol work nicely together... Raphael -- 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
