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Help with clean2dOpts
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Bin

Joined: 27 Jun 2006
Posts: 28

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Link to postPosted: Thu May 16, 2013 11:37 pmPost subject: Help with clean2dOpts Reply with quote

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

 

bzaicsek
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Joined: 10 Oct 2012
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Link to postPosted: Tue May 21, 2013 10:39 amPost subject: Reply with quote

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 

Bin

Joined: 27 Jun 2006
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Link to postPosted: Tue May 21, 2013 10:12 pmPost subject: Reply with quote

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

Yingyao

Joined: 30 Sep 2004
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Link to postPosted: Tue May 21, 2013 10:20 pmPost subject: Reply with quote

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

Peter
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Joined: 02 Nov 2011
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Link to postPosted: Mon May 27, 2013 3:53 pmPost subject: Reply with quote

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

Peter
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Joined: 28 Feb 2008
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Link to postPosted: Wed Jun 11, 2014 1:04 pmPost subject: Reply with quote

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

Regards,

Peter

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