Dear ChimeraX team,
Maybe it is a silly question but I have been trying to add atoms on ChimeraX but I have not found the way, is there any possibility? I need to plot a channel on my protein but I do not manage to do it without that.
Thank you in advance.
Best wishes, Aritz
Hi Aritz, For adding hydrogens: see command "addh" http://rbvi.ucsf.edu/chimerax/docs/user/commands/addh.html
For adding an individual atom (start structure) or adding/changing atoms connected to an existing molecule (modify structure): Build Structure tool (in menu under Tools... Structure Editing) http://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html
For adding "markers" (balls or spheres, but implemented as atoms): Marker Placement tool (in menu under Tools... Volume Data): http://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 26, 2020, at 8:53 AM, Aritz Roa Eguiara aritz.eguiara@cpr.ku.dk wrote:
Dear ChimeraX team, Maybe it is a silly question but I have been trying to add atoms on ChimeraX but I have not found the way, is there any possibility? I need to plot a channel on my protein but I do not manage to do it without that. Thank you in advance. Best wishes, Aritz
Yes! Thank you very much.
All the best,
Aritz
On 26 Mar 2020, at 21:22, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Aritz, For adding hydrogens: see command "addh" https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Faddh.html&data=02%7C01%7Caritz.eguiara%40cpr.ku.dk%7C196403770043476e073308d7d1c3676b%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637208509507969785&sdata=4vnOlAJ9ISQLdhi9%2F6k1EGagZGqhDhKjFLTriEOHZ94%3D&reserved=0
For adding an individual atom (start structure) or adding/changing atoms connected to an existing molecule (modify structure): Build Structure tool (in menu under Tools... Structure Editing) https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fbuildstructure.html&data=02%7C01%7Caritz.eguiara%40cpr.ku.dk%7C196403770043476e073308d7d1c3676b%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637208509507969785&sdata=roJBMy37qKY%2F25IE5Y3M7CGRcePsO%2FXt7m27K2EFjlA%3D&reserved=0
For adding "markers" (balls or spheres, but implemented as atoms): Marker Placement tool (in menu under Tools... Volume Data): https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fmarkerplacement.html&data=02%7C01%7Caritz.eguiara%40cpr.ku.dk%7C196403770043476e073308d7d1c3676b%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637208509507969785&sdata=SoTFjTfj6v755WT7rTQa%2B86EAN7VgYQ3wEg5zRyJ58Y%3D&reserved=0
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 26, 2020, at 8:53 AM, Aritz Roa Eguiara aritz.eguiara@cpr.ku.dk wrote:
Dear ChimeraX team, Maybe it is a silly question but I have been trying to add atoms on ChimeraX but I have not found the way, is there any possibility? I need to plot a channel on my protein but I do not manage to do it without that. Thank you in advance. Best wishes, Aritz
participants (2)
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Aritz Roa Eguiara -
Elaine Meng