Markush in Derby vs mySQL

Hi,

I have a large file with smiles, some of which contain Markush-type structures. If I import the smiles in a mySQL-based database, I get too many consecutive errors due to the Markush structures. If I do the same thing in a local Derby-type database (same import settings), the structures get imported without any errors. What is the reason for this difference?

Cheers

Hi,

I was looking at it, but cannot reproduce it now. We are going to investigate it more. It seems to me more like a bug.

Do you see any exceptions in log during import to Derby and Mysql (View-> IJC log file)? It would be helpful.

thank you for reporting it.

Petr

Is there a way to start with a clean log file? It's hard to see where different activities start and end.

Log is always empty for each IJC start, but you are right, it contains lots of other debugging information (mainly about database operations).

It is also possible to clean log anytime and start from empty again: just click into log panel and press CTRL+L (it's also available in popup menu if you click there with right mouse button).

Can you check the JChem table type that is used. Only certain table types will accept Markush or query structures. If you have Markush or query strucutres in your file then you must use one of those table types, or the 'Any strucutres' table type. You may need to manually change this setting if the automatic detection does not work correclty, though I don't see any reason why this should depend on the database type.

Tim

Sorry. Not an actual relevant reply. Don't see any way to start new topic in order to post.

2 things:

How do i activate/deactivate R-Group setting? Seems to only work selectively & inconveniently.

Next, how can I create bonds to C without C being erased when attempting to attach? Very frustrating!

Thanks!

A. Keil

Structure table type for the mySQL database is JChem standard

Its the table contents setting that I was referring to.  See this page in the user docs for details:
http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/editing_database/editing_entities.html

There are 5 types of contents that are possible for a JChem table:
Molecules
Reactions
Query structures
Makush libraries
Any structures

See the section about half way down that page for more details.

If the setting was Molecules then errors would happen when you tried to insert a Markush structure.

Tim

 

Sorry. Not an actual relevant reply. Don't see any way to start new topic in order to post.

Could you please re-post this to the Marvin forum, as this is a question about drawign strucutres. The Marvin forum is here: https://www.chemaxon.com/forum/forum5.html />and you open a new topic by clicking on the "New topic" button towards the top left corner.

Could you also describe the problems you are having in more detail as its not really clear what problems you are encountering.

Tim

 

Hi Tim,

Table contents were indeed specified as Molecules, so that would explain the error when importing Markush structures then.

Thanks