Clean in 3D

Hello,





I'm looking for more information on the 3D Clean option in the Edit menu. Specifically, I'd like to know what the difference is between the "Fast" and "Fine" options. Also, what is the "Choose Conformer" option doing? Names of algorithms/methods being used would be helpful.





I'm an infromatics person, not a chemist. I'm just trying to get a better understanding of these concepts so I can answer questions from some of our chemists.





Thanks,


Al

Hi Al,





The method is still under development, and the details are going to be available in a research paper.


We are trying to build up as many temporary structures, conformers of the fragments, as it is possible (or allowed by the options, like fast or fine, fast allows less, fine allows more structures in the cache). The quality of the structures is measured by a simple energy function (Dreiding type molecular mechanics) and normally we give back the "best" (lowest energy) structure from the final ones. Choose conformer allows the user to choose one of the possible structures. Currently, specially if explicit hydrogens are used, the user often get the same structure in the conformer window multiple times. This is going to be fixed in a later release.


The low-level options for the 3D clean module can be reached via molconvert in batch mode.





I hope this short answer helped. Please, do not hesitate to ask more specific questions.





Ödön