[Chimera-users] Create an atom object

Eric Pettersen pett at cgl.ucsf.edu
Tue Dec 15 09:17:29 PST 2020

The Python to place a helium atom named He1 at position x,y,z is:

from BuildStructure import placeHelium
from chimera import Point
atom = placeHelium(residue_name, position=Point(x,y,z))


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Dec 15, 2020, at 8:16 AM, Elaine Meng <meng at cgl.ucsf.EDU> wrote:
> Hi Yasser,
> Chimera does not have a command to do this.  In Chimera you could do it with menu Tools... Structure Editing... Build Structure, the "Start Structure" atom option.  I don't know python, so I can't give details on that.
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start">
> Other possibilities in Chimera are to manually create (with a text editor) a PDB file or marker file and then open it.
> If you use ChimeraX instead, there is a "build start atom" command to do it.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#start>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Dec 15, 2020, at 2:02 AM, Yasser Almeida <yasser.almeida at gmail.com> wrote:
>> Hello,
>> How can I create an atom object, with a given xyz coordinates, via command or python? 
>> Thanks in advance,
>> Yasser
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