Unable to fix valence for oxygen in 2-ring structure

User 8961c1b53b

11-05-2012 06:04:49

I've attached an example, of about 20 similiar compounds in my database for which MSketch reports a valence error on the oxygen, but I'm unable to resolve the valence error manually no matter what I do.  I tried to make the bonds "aromatic", but this didn't help.


 I want to use this file in a plugin, but the plugin itself keeps reporting an inconsistent molecular structure.


I'm attaching the simplest file for which I have this error.


 


Thanks


Sam

ChemAxon 23cc8b5e66

14-05-2012 13:49:02

Sam, the valence error on a 3 valence oxygen is correct.
Pelargonidin is known by Marvin Sketch, so you can import its name with the 'Edit > Import Name' menu command, and you will get the correct structure, with a + charge on the oxygen atom. Please have a look at the following wiki page:
http://en.wikipedia.org/wiki/Pelargonidin />(You can add a + charge with the 'Charge' contextual menu item, or select the atom and click on the 'Atom > Charge' menu item.)


However if you still want to draw an erroneous structure to appear as valid, you can switch off the highlighting of the valence errors through modifying the Preferences from the menu. Uncheck the 'Highlight Valence Errors' checkbox on the 'Edit > Preferences > Structure tab'.