Simple Templates toolbar icons not working (MvSketch 5.3.5)

We just upgraded from 5.2.6 to 5.3.5 and the simple templates toolbar icons (that we added to our customized configuration) are not working anymore. You can click on the icon but the ring does not show under the mouse icon when over the canvas.

I am able to reproduce on your website. Go to http://www.chemaxon.com/marvin/examples/applets/sketch/embed.html, unselect the tools toolbar using View -> Toolbars -> Tools and select the simple templates toolbar in the same menu. Adding a benzene ring (or any other template) from that toolbar does not work anymore.

Please, advise.

Thanks,

David

Collaborative Drug Discovery

Do you use an absolute pathway to tell MarvinSketch where your templates file is located?  If so, see this discussion.

Thanks for the hint but I don't think that is the problem here.

Our configuration loads correctly. All the expected icons are where they should.

The issue is that the "simple templates" toolbar icons do not work with 5.3.5. You can reproduce the issue on the Chemaxon site by following the directions in my original post.

Hi,

unfortunatelly some files are missing form the applet jars, and we have not noticed this fact before. The next release, that going to be released in a couple of days, will contain the fix.

Sorry for the inconveniences.

Regards,
Istvan

Thanks Itsvan,

We will update once the new release is out.

David

I am seeing (sort of) this problem in Marvin (5.3.6 build 2010-07-15).

I downloaded this version of Marvin and attempted to place it in a application that previously used 5.1 (not sure the exact version).  Everything seemed to work well (sketch opens correctly, I can draw simple structures, etc).  I dug a little deeper and although everything seems to work some of the generic templates won't render in the editing area.  When I click naphthalene, the template hightlights and when I click in the editing area, a depiction of the molecule appears (great).  The problem is when I click Benzene (right next to naphthalene), the icon highlights but when I click in the editing area, no structure appears.  It appears most of the generic templates are like that.

I can only assume this is a configuration issue.  What should I do?

Thanks in advance,

Jim

Hi,

this symptome is caused by the miss or unavailability of the isotopes.data file. It should be located in the marvin_codbase/chemaxon/isotopes.data path, and it is a gzipped file. If you are using IIS, then you can have permission problems, in this case please check the Applet FAQ.

I think you sould prefer a clean install, and you should not overwrite an old marvin codebase. Old files can ruin things, and your users may have to clean the java cache, to work well with the new applets.

Best regards,
Istvan

Istvan,

Thanks so much for the quick response.  I've followed your advice.  I've totally removed the previous Marvin codebase, re-downloaded the Marvin web developers zip, extracted it, verified that isotopes.data file exists (and it properly gzipped), cleared by java cache through the console, but I'm still seeing the same behavior.

I've attached a screen shot of the folder contents.

I am using IIS 7 and have followed all the advice given in the link you supplied.  The previous marvin installation (5.1) worked correctly so I'm relatively sure that my IIS and java installations are not the problem. 

It seems like the template file for naphthalene and benzene is being read but while the definition for naphthalene is valid, the benzene on is not...  Is there something different between how those two templates are read in the applet?

Thanks,

Jim

Hi,

can you please confirm that the applet behaves the same way on our site? You can reach our examples here.

Please also confirm that the isotopes.data file is reachable on your server directly from a web browser.

If the isotopes.data file is reachable and our examples are working, then i will need some information about the used browser, and java version. If you have any exceptions on the java console, that can also be useful.

Regards,
Istvan

Istvan,

Thanks for the reply.

The applet on your site works perfectly.  I'll double check the availability of the isotopes.data file when I get in tomorrow.

Is there a way to double check the contents of the isotopes.data file?  It's obviously binary.  Can I gunzip it and read it's contents?

(sorry) I know I keep harping on this but how is naphthalene different from benzene in the template section?  Why does one work and other doesn't?

-Jim

Hi Jim,

it is because of the inner representation of the atoms, and the molecule structure. Naphthalene do not need the isotopes.data file, but when you try to load the benzene, marvin needs it for some checks.

I can reproduce this behaviour if i delete the isotopes.data and start Marvin without it, that's why i am think that the file is missing or inaccesible.

You can reach the file from our applet here: https://www.chemaxon.com/marvin/chemaxon/isotopes.data but it has to be the same as the one you find in the applet package. You can use gzip to uncompress it, if you want, but if i were you then this would be the last one i check.

A'm a bit afraid i was not clear enough, so just for sure: you should check that, if you write the web url of the isotopes.data on your site into a browser - such as in the link i give you - then you can download it.

Regards,
Istvan

Istvan,

I'm impressed.  (and I shouldn't have asked so many questions).

I am using IIS on Windows 7 with Java 1.6.0_21 and Marvin 5.2.6.  I received no errors in my java console or any other messages or alerts that Marvin wasn't loading correctly.

As soon as I added a MIME type ".data" and "application/x-gzip-compressed" through the IIS manager console, everything works perfectly.

I tested the mime type was working correctly by navigating to the URL you specified (on my server) and the file was downloaded.  Before the MIME type was added, IIS responded to that same URL with a "HTTP Error 404.3 - Not Found" error.

Thanks so much for the help.

Jim