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 Eric Pettersen UCSF Computer Graphics Lab
On Dec 15, 2020, at 8:16 AM, Elaine Meng <meng@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@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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