[Chimera-users] atom type labels ?

Eric Pettersen pett at cgl.ucsf.edu
Tue Jun 26 10:58:39 PDT 2012

On Jun 26, 2012, at 9:17 AM, Marek Maly wrote:

> Hello,
> is there any way how to obtain atom-type labels when loading
> molecular structure using *.prmtop and *.inpcrd/*.rst/*.mdcrd Amber files ?
> These atom types are indeed available in *.prmtop file, but I didn't know
> how to visualize them in Chimera.
> I was hoping to find this possibility under "Actions->Label->other..." but
> I didn't find this item on the actual list.

Hi Marek,
	Chimera treats trajectories from various formats quite generically, and by default only handles the data available in all formats (including series of PDB files) such as atom name, connectivity, atom positions, etc.  I have added handling for format-specific data (so far only charge) on a per request basis.  I will open a request ticket in the Chimera Trac database for handling atom type data (you'll be on the recipient list).  Unfortunately, it will probably take some time before I'm able to get to it.  Sorry!
	If you trajectory consists of standard amino acid or nucleic acid residues, you could run the AddCharge tool which will assign the standard Amber types to the atoms using an attribute named 'gaffType' which would then show up in the interfaces you were using.


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