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@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@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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users