Upgrade to Jchem 3.2.5 problems

We have just upgraded to Jchem 3.2.5 and Marvin Sketch 3.1.7 and are having problems with some of our reactions that worked in Jchem 3.2.4 and Marvin Sketch 3.1.5. We sent an email about the details of these problems to ChemAxon earlier.


I have attached two of the reactions that are causing problems for us. Something in the upgrade must have caused our reactions to no longer work properly as they were working before the upgrade.


We have also noticed that after we upload a reaction onto our website, we are no longer able to use the "save as" or "copy" functions directly from the java applets. Before the upgrade, we could right click on a reaction and either save it or copy it onto our hard drive. Now when we try to save or copy, we get an error message stating "Cannot convert molecule to mrv, Java bug 4274061 workaround skipped". This is a serious problem for us as the "copy" function is used during editing and not having it available makes it very difficult for us to edit our reactions.


Please let us know if there is anything that can be done to fix these problems.

Thank you for submitting the problem. We will check the problem and get back to you soon.

Quote:

Before the upgrade, we could right click on a reaction and either save it or copy it onto our hard drive. Now when we try to save or copy, we get an error message stating "Cannot convert molecule to mrv, Java bug 4274061 workaround skipped".

It may be a configuration problem. Probably, the upgrade was done wrongly.


How did you upgrade it? Did you delete the whole Marvin directory before upgrade? Are you sure that all files from the Marvin Applets packaged is copied to the proper place?


Copying the new Marvin package into the directory of the old Marvin is not recommended. Mixing of files from different versions can cause unexpected errors. Please delete the directory of old Marvin before you extract the new one.





Have you modified the content of any jar file in the Marvin package?


All jars in Marvin are trusted signed (include digital certifications). If the content of a jar file is modified, the jar file becomes corrupted (no more trusted). Trusted signed jar files are required for applet to be able to access local clipboard and the local file system.





If the above error is not invoked anywhere (in any browser by any machine), the problem may be at client side.


In that case, deleting the browser's and JRE's caches on client machine can solve the problem.


Probably, few deprecated resources left in the cache.


See the related topic how to do it: How I can clear JRE cache?

Thank you for your help. We re-installed both Jchem 3.2.5 and Marvin Sketch 4.1.7 and things are working better. However, we still are having difficulties with one reaction, bt0005, which I have reattached. With the substrate c1cc2ccc3cccc4ccc(c1)c2c34, the reaction should predict O[C@H]1[C@@H](O)c2cccc3ccc4cccc1c4c23. However, it is not producing any products.

Code:

react -a changing -v -r ../molecules/bt0005.mrv "c1cc2ccc3cccc4ccc(c1)c2c34" Total running time (ms) : 2702 Reaction setting (ms)   : 2153 Reactant setting (ms)   : 10 Reaction processing (ms): 539

With bt0005 again, using the substrate c1ccc2c(c1)cc3ccc4cccc5ccc2c3c45, the desired products are O[C@H]1[C@@H](O)c2c3ccccc3cc4ccc5cccc1c5c24 and O[C@H]1[C@@H](O)c2cc3ccccc3c4ccc5cccc1c5c24. While the reaction does predict products, we do not get the desired ones.

Code:

react -a changing -v -r ../molecules/bt0005.mrv "c1ccc2c(c1)cc3ccc4cccc5ccc2c3c45" O[C@H]1C=Cc2c(cc3ccc4cccc5ccc2c3c45)[C@H]1O O[C@H]1C=Cc2cc3ccc4cccc5ccc(c2[C@H]1O)c3c45 Total running time (ms) : 2054 Reaction setting (ms)   : 1568 Reactant setting (ms)   : 7 Reaction processing (ms): 479

This reaction worked to predict the correct products before we upgraded to the new version of jchem and marvin sketch. We are curious if there is any way we can change the reaction so it will work again.





Thank you.

Hi,





The exclude rule you use in the reaction have to be corrected, if you expect the described products.





You can use

Code:

-n, --no-rules <type>               ignore reaction rules,                                       depending on type:                                       r  - ignore reactivity rule                                       s  - ignore selectivity rule                                       t  - ignore selectivity tolerance                                       rs - ignore both reactivity and                                            selectivity rules                                       rt - ignore reactivity rule and                                            selectivity tolerance

command line option to check the products generated without applying reaction rules.

Quote:

However, we still are having difficulties with one reaction, bt0005, which I have reattached. With the substrate c1cc2ccc3cccc4ccc(c1)c2c34, the reaction should predict O[C@H]1[C@@H](O)c2cccc3ccc4cccc1c4c23. However, it is not producing any products.

This call will ignore reactivity and exclude rules:

Code:

react -a changing -v -n r -r bt0005.mrv "c1cc2ccc3cccc4ccc(c1)c2c34" O[C@H]1C=c2ccc3cccc4ccc([C@H]1O)c2c34 O[C@@H]1C=c2ccc3cccc4ccc([C@@H]1O)c2c34 O[C@H]1[C@@H](O)c2cccc3ccc4cccc1c4c23 Total running time (ms) : 1153 Reaction setting (ms)   : 938 Reactant setting (ms)   : 5 Reaction processing (ms): 210

Your expected product (O[C@H]1[C@@H](O)c2cccc3ccc4cccc1c4c23) is there on the list, but the exclude rule filters it out. See also explanation1.jpg.

Quote:

With bt0005 again, using the substrate c1ccc2c(c1)cc3ccc4cccc5ccc2c3c45, the desired products are O[C@H]1[C@@H](O)c2c3ccccc3cc4ccc5cccc1c5c24 and O[C@H]1[C@@H](O)c2cc3ccccc3c4ccc5cccc1c5c24. While the reaction does predict products, we do not get the desired ones.

Same happens in your second example.

Code:

react -a changing -v -n r -r bt0005.mrv "c1ccc2c(c1)cc3ccc4cccc5ccc2c3c45" O[C@H]1C=c2cc3ccc4cccc5ccc(c3c45)c2=C[C@H]1O O[C@H]1C=Cc2c(cc3ccc4cccc5ccc2c3c45)[C@H]1O O[C@@H]1C=c2cc3ccc4cccc5ccc(c3c45)c2=C[C@@H]1O O[C@H]1C=Cc2cc3ccc4cccc5ccc(c2[C@H]1O)c3c45 O[C@@H]1C=Cc2cc3ccc4cccc5ccc(c2[C@@H]1O)c3c45 O[C@@H]1C=Cc2c(cc3ccc4cccc5ccc2c3c45)[C@@H]1O O[C@H]1[C@@H](O)c2cc3ccccc3c4ccc5cccc1c5c24 O[C@@H]1[C@H](O)c2cc3ccccc3c4ccc5cccc1c5c24 O[C@@H]1C=c2ccc3c4ccccc4cc5ccc([C@@H]1O)c2c35 O[C@H]1C=c2ccc3c4ccccc4cc5ccc([C@H]1O)c2c35 O[C@H]1C=c2ccc3cc4ccccc4c5ccc([C@H]1O)c2c35 O[C@@H]1C=c2ccc3cc4ccccc4c5ccc([C@@H]1O)c2c35 O[C@@H]1[C@H](O)c2c3ccccc3cc4ccc5cccc1c5c24 O[C@H]1[C@@H](O)c2c3ccccc3cc4ccc5cccc1c5c24 Total running time (ms) : 1218 Reaction setting (ms)   : 956 Reactant setting (ms)   : 5 Reaction processing (ms): 257

The expected products are on the list, but the exclude rule filters them out, while some of the products are not excluded because they do not fulfil your exclude rule. See explanation2.jpg.





Best regards,


Zsolt