[Chimera-users] File conversion: strange behaviour

[Eric Pettersen]

...and if you are getting the Mol2 file from Amber, try to get a PDB  
file instead.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Dec 22, 2010, at 10:16 AM, Elaine Meng wrote:

> 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
> -----
> 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
>
>
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