Changing Stereochemistry

Hi Folks,





Some of our users have entered in a compound with Marvin (A in attachment) and save it to Oracle (jchem cartridge) but when they query it back it displays a different stereochemisty ( B in attachment) . Any ideas why?





Also, noticed that when our users draw a compound containing a large ring with a benzene attached, when they query the structure back into marvin the benzene is distorted (so it nearly looks like a 5-sided ring.





Cheers.





Peter





PS Marvin 4.1.13

Hi,





It seems to me that the two molecule is equal.





Why do you think they are different in stereochemisty?





Moreover the B molecule has superfluous wedge bond at the five membered ring. (This is a bug which does not changes stereochemistry, but we have already fixed it.)





Clould you attach the molecules which has clean problems so I can examine it.





Please note that we have improved our cleaning algorithm since 2007 September 18 (Marvin 4.1.13).





Andras