Help with clean2dOpts

I have two structures,  A is O=C3[C@H]2[C@H]1C=C[C@H](O1)[C@H]2S(=O)(=O)N3c4ccc(Br)cc4, and B is CCO[C@@H]1C[C@@H]2CC[C@H](C1)N2c1nccs1.

The structure A in Marvin with toff is much better,  so we decided to use this option in Marvinsketch,  however,  the structure B  looks worse with this option.  Could you tell me how to tune the Marvinsketch's options to get similar result in ChemDraw.

 

Thanks

 

Dear Binzhou!

   Toff means, that you do not want to use allready defined structures during clean. If a result is pretty with Toff it means it was cleaned according to an algorithm of us. We have some common structures that is usually cleaned differently, and they are collected in a template file.

   The problem is you can not use only the algorithm for one exceptional structure and the template library for an other exceptional structure. However you can set a template file for new special structures with the T{filename} option to use it during cleaning.

   I hope, it solves the problem.

Regards:
Balázs 

Thanks for the reply. However Marvinsketch will take some arbitrary smiles from user in our application.  a fixed template file is not a option.  So what is the best bet for the most user structures? Toff ,  Tf or  without clean2dopts?

Thanks

The question may be rephrased as, how to get ChemDraw-like 2D displays in Marvin for structure B? Thanks

Currently, there is no way get ChemDraw-like 2D display for structure B.

We will improve our clean to provide nicer structure. Unfortunately we are really busy for our next release, 6.1, so I can't promiss, it will be ready until that.

Regards,
Peter

I'm happy to inform you that the clean of structure B is fixed in Marvin 6.3.

Regards,

Peter