Hello,
How can I create an atom object, with a given xyz coordinates, via command or python?
Thanks in advance,
Yasser
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
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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participants (3)
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Elaine Meng
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Eric Pettersen
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Yasser Almeida