Actually, when I tried to run the Geometry tool on hexacene with the "very strict" setting I got a message saying

" Bug, optmization did not converge"

The error message in detail is here:

*ERROR: *

*Cannot run plugin: Geometry*

*[BUG] Optimization was not converged.*

*STACK TRACE:*

*java.lang.UnsupportedOperationException: [BUG] Optimization was not converged.*

* at chemaxon.calculations.ProjectedSurfaceArea.optimize(ProjectedSurfaceArea.java:153)*

* at chemaxon.calculations.ProjectedSurfaceArea.run(ProjectedSurfaceArea.java:237)*

* at chemaxon.calculations.Geometry.calculateMoleculeProjection(Geometry.java:336)*

* at chemaxon.marvin.calculations.GeometryPlugin.run(GeometryPlugin.java:703)*

* at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:200)*

* at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:184)*

* at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:107)*

* at chemaxon.marvin.plugin.CalculatorPluginManager.callback(CalculatorPluginManager.java:77)*

* at chemaxon.marvin.plugin.PluginManager.callback(PluginManager.java:92)*

* at chemaxon.marvin.common.swing.MolPanel$6.run(MolPanel.java:3755)*

After you have the thermodynamically favorable tructure, finding a cylinder impostor (or the minimum and maximum bounding cylinders) is not a difficult task. I am actually developing a code in Matlab to see if I can fix this using the xyz geometry I get from Marvin (another bug that you might be able to help me with: when Marvin exports xyz files it ommits the H atoms; can we fix that?). I don't have access to the Marvin code, but if it does indeed try to find the minimum bounding cylinder, then that works well but it has an error in the estimation of the data centerline (which determines the direction of the cylinder). In the cases presented here, estimation of the xyz coordinates centerline is quite trivial (it is the mean of the xyz coordinates). So I don't see how you can get this wrong (I guess you don't try to find a cylinder impostor?).

Interestingly, I cannot replicate my own result for hexacene (I run with strict setting for the optmization, with which it now crashes). With the normal setting in optimization it gives a minimal projection radii of 3.652 (which is still not correct but not as bad as before).

All the molecules I worked with here are in reality 2-dimensional (there is nothing asymmetrical going on in the z direction). This makes it trivial to test the Geometry tool. Other people working with molecules in 3D geometries, have no way of assesing whether the estimates from the Geometry tool are true or not. But knowing that one might get projection radii that are about double the correct values, tells me that one should be extremely cautius when using this tool. I would put it as a first priority in your future revisions.

Will send an email to see if we can figure this out for my current study.