[Chimera-users] File conversion: strange behaviour

[Elaine Meng]

Hi George,
If you want Chimera to understand the atom types when you read the Mol2 file back in, when saving the Mol2 do *not* use the option to "Write Amber/GAFF atom types instead of Sybyl atom types".  If you use the default settings in the "save Mol2" dialog, it will write a standard Mol2 file with Sybyl atom types, and you can read the file back in without problems.  The Amber/GAFF type option is for people who wanted to know the force field type assignments, but is not suitable for reading back into Chimera.

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#mol2>

I hope this clarifies what is going on,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 22, 2010, at 9:41 AM, George Tzotzos wrote:

> Hi everybody,
> 
> I'm attaching a  pdb file <3og.pdb>. This file on conversion from amber11 (ANTECHAMBER) yields 3og.mol2 which Chimera renders as per snapshot below. The two big blue spheres should be oxygen atoms. Selecting the molecule and trying to colour by atom has no effect other than colouring the atoms that are adjacent to the blue spheres.
> 
> Any explanation for this behaviour?
> 
> Many thanks and best regards
> 
> George