[Chimera-users] File conversion: strange behaviour
pett at cgl.ucsf.edu
Wed Dec 22 10:20:32 PST 2010
...and if you are getting the Mol2 file from Amber, try to get a PDB
UCSF Computer Graphics Lab
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.
> I hope this clarifies what is going on,
> 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
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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