In the following structure, if the iPr group is contracted, Marvin 5.2.6 says that the double bond configuration is Z. If the iPr group is expanded or ungrouped, it says that the double bond configuration is indeterminate. It should give the same answer regardless of whether the group is expanded or contracted. (In this case, indeterminate is a better answer.)
My final exam has come and gone, so I no longer have quite the same sense of urgency. My next exam is in February. I hope you will have both the E/Z bug fixed and the user-controlled sketcher window restored by then?
Tamas ChemAxon personnel
Joined: 21 May 2004
A student drew this structure in response to a question. The problem was that Marvin told the student that the stereochemistry was Z, but when the shortcut groups were ungrouped by JChem, JChem interpreted it as indeterminate. Marvin should have told the student that the stereochemistry was indeterminate. I don't think the wedge bonds are relevant to the bug.
yes, the wedge bonds are not relevant to the bug. It's a problem of the sgroups.
To show this I have produced the image below. It shows the bug once more on the left side for the sgroup iPr. Replacing this iPr by Cl gives the indeterminate icon (?). Moving the Cl-atom down produces the Z-configuration and now (Z) is correctly shown.
I have tested other sgroups. With Et sometimes it works correctly, sometimes not. With larger sgroups it gets worse. But it's difficult to reproduce the results.
Currently we are focusing on Marvin 5.3.0. It will be released in a couple of days. Immediatelly after the release, we hold an internal meeting about tasks priorities for 5.3.1 and about the milestones for 5.4. After this meeting, I can tell you how your tasks are scheduled.
I would like to inform you that we had to make an urgent patch release that was named 5.3.1, therefore the fix promised in this topic will be included only in the patch release coming at the end of March (probably named 5.3.2).
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