Not displaying compounds when selecting "standardize&qu

Hi,

I'm using InstantJChem 5.3.1 and when I select the "Display as standardized" option all the compounds are not displayed anymore.

 

Is this a bug or am I missing something?

 

Thanks.  Guillermo.

This seems to be working for me with default standardization, so maybe its a problem due to your particular standardizer configuration. Could you send the standardizer config (the XML file) so that we can investigate.

Thanks

Tim

Hi Tim,

 

Sure thing.  However, this is the first time I'd have to look for such file.

 

Let me know where it is that I can find the file (I'm using Ubuntu) and I'll post it for you.

 

I look forward to hearing from you.

 

Thanks.  Best, Guillermo.

Go to the Schema Editor and select the entity. Then select the Standardizer tab and save the standardizer configuration to file (use the button in the top left corner).

Tim

Hi Tim,

Sorry for the delay in my reply.

Forgive me but I am not following you.  When I click on a molecule on the grid I don't see any Standardizer tab.

Any chance you could post a couple of screenshots to show me how I can get to where I need to be?

Thanks for your patience.  Guillermo.

I was thinking that you might have set a custom standardizer that that the standardizer settings was what was causing the problems. To see the standardizer open the schema editor, select the entity that is involved and in its customizer in the main window select the Standardizer tab.

In addition it would be useful to see any output from the log file  (View -> Instant JChem Log file) and information about your setup (Help -> About Instant JChem).

Thanks

Tim

Hi Tim,

Here's a screenshot of what I see and a copy of the log.

You will have to forgive me, but I still can't find a way to see a standardizer tab.

If you could share a couple of screenshots to show how to get there it would be great.

Thanks. Guillermo.

By the way, the standardize box was left unchecked since I soon as I check it the compounds are not longer displayed.

Thanks. Guillermo.

Its the schema editor that you need to use to define the standardizer.

See here for docs:
http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/editing_database/schema_editor.html

Open the schema editor by double clicking on the database schema node in the projects window.

A screenshot is attached.

Tim

Hi Tim,

Thanks for the note and the picture.  It helped me figure out how to get to the tabs you were referring to.

The difference I see bewteen your screenshot and mine is that yours says that a default is going to be used while mine simply says I don't have a license for a standardizer.

The strange thing is the problem with the standardizer happens randomly. In other words, some DBs do show starndarized while others (like in this case) no compunds are shown if stardardizer is selecte.

I hope this sheds more light on this.

Thanks Tim.  I look forward to hearing from you.

Best, Guillermo.

No, I'm afraid it still doesn't make much sense to me.

Could you look in the log file (View -> Instant JChem Log file) and see if there are any errors when viewing the strucutres in standardized form. If so then can you send us details of the errors.

Also, can you send info about your setup (Help -> About Instant JChem, and then copy and paste the contents.

Thanks

Tim

Hi Tim,

Here are 2 text files with the info you requested.

Let me know if there is anything else to help figure out what's going on with InstantJChem.

Thanks. Best, Guillermo.

The text for the log was only a very short part of the log and didn't contain any useful information.

Can you send the complete text of the log, having tried to display one of the tables where display as standardized is not working correctly (so that any errors might have been written to the log).

Thanks

Tim

Hi Tim,

Here's the complete log after selecting the standardizer option.

At this point no stuctures are displayed (see attached picture).

Let me know if there is anything else I can do to help.

Thanks Tim. My best, Guillermo.

I'm afraid this is a bit baffling. There are no errors reported in the logs, so its really not clear what is happening.

Does this happen consistently with certain data? e.g. if you import the same data into another table does it happen there again? If so can you provide us with some sample data so that we can try to reproduce the problem.

If it not related to the data itself, is there anything else that you can think of that might be the cause. What seems particularly strange is that you say it only happens some time, so working out what it is that makes it happen is going to be the key to solving it.

Sorry for the problems.

Tim