[Chimera-users] Converting sdf file into mol2 format

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 29 11:58:27 PDT 2015

Hi Mahendra,
I agree that Chimera is not the way to convert 2D diagrams to 3D structures.  Besides what Eric mentioned, you can probably find lots of programs that are meant to do this by searching the web.  For example, here is another with a web server (but I haven’t tried it, so can’t say how well it works):


Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 29, 2015, at 11:42 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Mahendra,
> 	Your coordinates are two-dimensional, not three-dimensional.  Chimera is not going to be able to correctly determine the atom types for a two-dimensional compound, nor appropriately protonate it, nor properly minimize it.    You could directly write a two-dimensional mol2 file from the sdf simply by dropping the runCommand("minimize") step of the processing script, but many of the mol2 atom types would be wrong.
> 	I think you need to use some other tool for your conversion.  Maybe Open Babel?
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> On Apr 29, 2015, at 11:01 AM, Mahendra B Thapa <thapamb at mail.uc.edu> wrote:
>> Dear Chimera users,
>> I am trying to convert sdf file ( downloaded from diversity set data from 'http://scs.illinois.edu/htsf/compound_collection/nci.php') into mol2 format. When I ran the command chimera --nogui processSDF.py
>> as given the previous posting ( http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004974.html), I got the following error messages:
>> Cannot find consistent set of bond orders for ring system containing atom #0.73:1 at N1
>> ---
>> Unknown redo atom type: N3
>> Traceback (most recent call last):
>> Any suggestions for correcting these errors will be a good help for me.
>> Thank you,
>> Mahendra Thapa
>> University of Cincinnati,OH

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