Configuration and geometry calculation

Using the internet-applet of MarvinSketch and doing the following:


1) Insert-Template-Amino Acids-L-Isolecin


2) Edit-Add-Absolute Stereo


Nothing happens, why ? (Using the on my machine installed


Marvin-programs I get the configuration assigned as 2S-3S, OK).





Then using in the applet


3) Tools-Geometry-Geometry


in the geometry window appears the 2R-3S configuration, why ?


In the steric hindrance window it is still 2S-3S.


(Same result in the applet and the installed program)


See screenshot149.png





Then using in the applet


4) Tools-Conformation-Conformers


all Conformers have the 2S-3S-configuration, OK.


See screenshot150.png





What is wrong in step 3) ?

Thank you for the report. We will check what's wrong with the geometry plugin, and come back with the answer soon.

Found a bug in the Geometry plugin. It will be corrected in the next release - thanks again for reporting it.

Thank you. The topic is very important for me.


I will give a course in February !





Above, I had a first question in my first post.


What's the answer for it ?

In the View -> Misc -> R/S labels, select "ALL". (Having "up" - solid - or "down" - hatched - triangles specifies the stereo configuration for 3D generation. Displaying R/S labels can be turned off independently - which seems to be the default on the web demo.) For further info on "Add absolute stereo" see http://www.chemaxon.com/marvin/doc/user/stereo-doc.html.





You can work around the above mentioned bug (having wrong configuration in the Geometry plugin) in the current version the following way: before calling Tools -> Geometry -> Geometry, call Edit -> Clean -> 3D -> Clean in 3D. (If required, you can clean back to 2D in the steric hindrance window)

Thank you. I will try the workaround.





It would be fine, to have the default setting in the web demo


as "Displaying R/S labels in the main window",


as in the installed version.


It is a very good feature, you should show it to visitors of the web page.

The web demo uses the default settings, while the installed applications uses the last used ones. This might explain the difference you experienced.