Problem with Metabolizer

Dear Chemaxon community, I have problems with Metabolizer. I have drawn structure for metabolism analysis, then I click ok to add it to the analyzer but nothing happens. Structure is not added. Also when I am downloading reactions database I get the error message that the number of reactions in one file is more than one. Are these problems common and what are the solutions?

I have moved this topic to the appropriate forum. The Metabolizer experts will respond soon.

Regards, Edvard

Dear bestdrug,

Please note that the proper use of Metabolizer application is the following:

First of all, you have to set up a Reaction Library. When you launch Metabolizer at the first time, you will be prompted to do so. If you do not have a proper library set, you should choose Configuration/Reaction Library from the menu, and open a library file.

Please note, that a proper library file is a single file - usually with multiple reactions in it. In most cases this is an MRV, or RXN file. (Of course other formats with multiple reaction and property support can be used as well)

Please, also note that multiple molecule files zipped can not be used as a reaction library. The reaction library should be a single file (it can be zipped however, but zip should contain only that single file)

After a proper library setup, you will be able to perform calculations with Metabolizer. File/New Metabolism will raise a dialog where you can specify your initial substrates. You can add molecules by pressing the + button at the dialog toolbar, or you can open an existing file by the button with the folder icon. When you have at least a substrate in the list, you can click the ok button.

When you created your new metabolism, the substrates you selected should appear in the Metabolic Tree section of the window. Then you can start to calculate the metabolic pathway with the Run options, or manually by expanding the nodes.

Please, let me know if any of these operations fail, or behaves differently. According to your report, there was a problem with setting the initial substrates. If the problem still exists, please give informations about your operating system and java version, and - if possible - the input substrate file (or molecule). Any error messages reported could be useful as well.

Regards,

Istvan Cseh

I am using chemaxon_reaction_library.mrv and I get the error about that the file contais more than one reaction. Then when I have drawn or loaded chemical structure I just can\t add it, I just click ok and nothing happens. So both of these looks like a bugs, or like I need to reinstall everything again, or maybe some Java problem (but I have the same trouble on two different non related PCs).

I му attached screenshots of both errors.

Thank you for the screenshot, it explains the situation well. The reactions you try to load into Metabolizer are chemical reactions that can be used with Reactor. They are often multimolecular (two or more reactants).

Metabolizer works with biotransformation libraries that are unimolecular (the reactant is a single substrate). Please see the corresponding files here:
http://www.chemaxon.com/jchem/doc/user/configfile_download.html

Please note, that only a small demo set of biotransformations is available at the moment for download, though you can add your own biotransformations using the reaction editor. We are working on an extensive biotransformation library, however.

Thank you! This helps moving forward. Hm now I have some license issues. I remember that I've got some free academic license a month ago. I hope it's not so short, because I haven't chance to test anything because of issue mentioned above. But if there is time limitation how can I prolong it because I had no chance to test.

I've seen also that there are really very few reactions in the library. Is it difficult to create new ones. I never participated in such process, but it would be interesting to try to participate in such library creation as developer (voluntter developer for example).

If you have an academic license, it should work with Metabolizer. Otherwise please turn to our sales department for a new license. The corrently available biotransformation library is very short indeed, actually it is a small demo set. We are working on a larger one that contains more than 200 human phase one biotransformations. Your help would be appretiated I will contact you gladly to discuss the details.

HI,

I can confirm that all academic package licenses downloaded since Aug 26th included Metabolizer functionality (it was launched around then and this was added). So I don't expect your academic package license is causing problems.

Cheers/Alex