MarvinSketch makes a distinction between atom mapping and atom numbers—the latter are (I believe) the numbers from the molfile. Those should match the atom numbers in Jmol.

Just confirmed, in fact—atom numbers in MS (View > Misc > Atom Numbers) and atom numbers in Jmol (viewable by hovering or selectable through atomno=) are the same.

Cheers, Mike

On Sun, Jul 31, 2011 at 3:54 PM, Richard Ball <rgb@ellerbach.com> wrote:
Thanks Mike. The problem I want to provide a solution for (assuming there is one) is: if someone has/gets a .mol file with a complex multi-stereocenter molecule how can they get the R/S assignment for the particular atoms in the .mol file while retaining the identity of those atoms.

Marvinsketch + marvinview does provide a version of the molecule and assign the stereocenters, and, at the moment, this looks like the best option. But all connection to the atom identifiers in the .mol file is lost is it not? Ideally, the chemist looking at the molecule in Jmol and the chemist looking at it in marvin_* could refer to the same atom label when discussing a particular stereocenter.

I'll probably contact the Chemaxon folks and ask if retaining the atom labels from the mol file is possible.

Rich

On Jul 31, 2011, at 2:11 PM, Michael Evans wrote:

Rich--although its 3d capabilities are not as good as jmol, marvin sketch can do r/s assignment in 2d or 3d mol files. If that's all you're after, check out marvin sketch.

http://chemaxon.com/marvin

Cheers, Mike

On Jul 31, 2011 1:04 PM, "Richard Ball" <rgb@ellerbach.com> wrote:
>
> On Jul 31, 2011, at 7:11 AM, Egon Willighagen wrote:
>
>> Hi all,
>>
>> On Sun, Jul 31, 2011 at 2:12 AM, Robert Hanson <hansonr@stolaf.edu> wrote:
>>> On Sat, Jul 30, 2011 at 3:42 PM, Richard Ball <rgb@ellerbach.com> wrote:
>>> Egon, what do you recommend?
>>
> [snip]
>
>> That said, other Open Source software that implements (part of) the
>> rules include OpenBabel and OPSIN. With the CDK and the online
>> resolver, we have a few tools to compare against each other.
>
> I had a look at OpenBabel and as far as I can tell the only tool there is obchiral which just identifies if an atom is chiral, it doesn't determine what the configuration label is.
>>
>> I would advice against trying to implement these rules, particularly
>> because they are mostly needed for coming up with IUPAC names, which
>> Jmol does not do anyway.
>
> I have no interest in the IUPAC name but, whether a center is R or S makes a big difference in synthetic chemistry route definition let alone the 3D structure consequences for conformation.
>
> I agree that developing this ability for Jmol is too big of a task for Bob (or any of the others interested in Jmol development). I was just hoping that someone in this community knew of a tool that did a good job on any arbitrarily complex molecule.
>
> Rich
>
>
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--
Mike Evans
Organic Chemistry Graduate Student
Moore Group
University of Illinois, Urbana-Champaign