could I ask a very dumb question?
I'm trying to remove salt fragments with standartizer (keep largest fragment) when importing the csv file into table entity in InstantJChem, but it seems that nothing happens. All salt fragments are retained in the imported table, and all of them are retained after export. I haven't found a menu option to perform a standartization of the table.
Standartizer file attached.
What am I doing wrong?
I think this is just a display issue. By default the structures are displayed in their original (unstandardized) form. This is because standardization is mostly related to structure searching, and not necessarily related to structure display.
You can however tell IJC to display the structures in standardized form. To do this change the display settings for the column (grid view) or the structure widget (form view). In the settings you will see an option to 'Display as standardized' See here for more details:
But is there a way to strip counterions with IJC? I know about 'Display as standardized' option, but I need export structures to .sdf in the standartized form.
Thank you very much, this is just what I needed.
Thanks a lot, I've got the same problem and now it is solved. Perhaps it would help if one could choose if standartized or non-standartized structures are exported into the file from Instant Chem.
I guess this procedure works for structures that you want to add to an existing database, but what is the procedure for correcting structures that are already in a database (without having to export everthing first, and then basically recreating the database after standardization)?
Hi, I was aware of this procedure and applied it, but again, it doesn't actually fix the structures: a wrongly drawn nitro will look OK after standardization (provided that one ticks the 'Display as standardized' box in the Customize widget settings), but after exporting to SD the wrongly drawn nitro is preserved.
Yes, it actually should not change the structures in the database itself. Standardizer defines in memory structure representation which is used for searching.
However it's possible to run the standardizer on a structure file. This can be done in stand alone Standardizer or in IJC: see it in IJC User's guide.
Hope it helps.