S implicit H bug in Marvin 5.10

User 870ab5b546

31-08-2012 17:49:54

Draw CS(C)([O-])[O-].  Now press the + button and increase the charge on S to 2+.  Notice that Marvin also adds implicit H atoms to S.  This is a very severe bug.  I should be able to draw C(C)([O-])[O-] without the H atoms appearing on the S.  The same thing happens if you start with CS(C)(=O)[O-] and add a single + to S.


Similar things happen on the back end.  If I go into Edit -> Source and edit C[SH2++](C)([O-])[O-] to remove the H atoms, I can get a good picture of C(C)([O-])[O-].  But if I submit it to the back end, JChem still thinks there are H atoms on S.  For example, it will calculate the MW as 96 instead of 94.


I cannot emphasize enough how severe this error is.  It's one thing to write something ridiculous like NH74+ and have Marvin not recognize it as ridiculous.  It's completely different for Marvin to take a correct structure and convert it into an incorrect one.  Please fix immediately!

ChemAxon 25dcd765a3

03-09-2012 12:58:38

Dear Bob,


I have checked the problems you mentioned in the new forthcoming release Marvin 5.11


1)  CS(C)([O-])[O-] if you add one + you get SH+, if you add an other you get S2+
2)  CS(C)(=O)[O-] after import the S has one implicit H, adding one + the implicit H is removed and you get S+


3)  after importing C(C)([O-])[O-] you wil not get any implicit Hydrogen atom and the calculated mass is:  94.0088


4) Starting from a plain N and adding + charge you will get: NH3, (NH4)+, (NH3)2+, (NH2)3+, (NH)4+, N5+, valence error N6+


 


As far as I see all theses bugs are fixed in the new version. It is under testing phase.


Sorry for the inconvenience and thank you for the report.