Loss of focus from "More" window in Marvin

I started using IJC yesterday (for querying/filtering a local database), and I must say that I am very impressed! Really nice application!!


I have two questions/quirks:





* If I build a 'Structure' query, run it and then double-click the query structure to edit the query in the Marvin popup, when I press "More" in Marvin to e.g. add/edit SMARTS patterns in the query structure, I can't get focus on the "More" window (this is in Winows XP). I have to close Marvin, press "Show all" to sort of reset the query, bring up the query from the projects tab, double-click again, and then the "More" window works again. This only happens after having run a query once, the first time I edit it the "More" popup always works, but the second time it never works.


On that note, is there any way from inside IJC to edit (and save) the actual query text? I see it in the "Query As Text" panel, but I haven't found anywhere to actually change it other than through the "graphical" Query panel.





* I started the filtering with an SD-file of 150 K compounds, which was used to build a local database. This was queried with a number of substructures/SMARTS patterns, resulting in n lists of unwanted compounds. I joined these to a total "bad list" of ~20K compounds. Then I want to export the 130K "good" compounds as an SD-file to continue working with. The way I found was to first make a list of all 150 K compounds, subtract the 20 K bad ones from that list through list logics, set the "domain" to the 130 K list and then do "Export to file". This was rather slow, applying the 130 K list to the database took like some tens of minutes (compared to the searches and list creations which were all seconds), and the "Export to file" I let run over night (but this was saved over the network, that could be one reason for the very slow export). How should one perform an operation such as this one in an efficient way?





Thanks!





/Best regards, Micael

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I must say that I am very impressed! Really nice application!!

Thank you. We appreciate these types of comments!

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I can't get focus on the "More" window (this is in Winows XP).

Yes, this is a bug. We are aware of it and will hopefully have it fixed soon

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is there any way from inside IJC to edit (and save) the actual query text?

No, this cannot be edited. It is just for informational purposes. The query has to be defined using the query builder or the form based query.


The actual query can of course be saved (use the Lists and Queries window)

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How should one perform an operation such as this one in an efficient way?

This is an interesting scenario. The list management features are optimised for small lists as this is typically what we expected to be most commonly used. For very large lists performance will be slow. I think your approach is pretty good for now, but is clearly not ideal.





One alternative way might be to add an extra boolean field that defined the "bad" compounds, and then you could use this field as a filter before exporting. You can set the values by:


1. running your query (or applying the list) to get just the set of strucutres you want to mark as "bad"


2. set one of the values to true. select that cell and copy it to the clipboard


3. Select all the cells for the boolean field (e.g the entire column)


4. Paste the "true" value into those cells.


5. Repeat 1-4 for each query/list


6. Run a new query where the boolean field is null (or false depending on whether you set the field up with a default value).


7. Export the results.





We will also think about other improvement that can be made to IJC to improve this.

The problem with the More window should now be fixed in the IJC 2.3 release.


The UI of Marvin has changed in some ways as it uses Marvin 5.0. The More window is now named the Periodic System window.