Thank you so much!! I used the very first solution. Select... Chemistry... element... H. It was exactly what I was looking for. Mazin -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, July 17, 2023 6:28 PM To: Mazin Nasralla <pymna@leeds.ac.uk> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] How do I colour all my hydrogen atoms grey? Hi Mazin, You can select all the hydrogens at once using the menu: Select... Chemistry... element... H and then use Actions...Color... from editor to interactively choose the exact color. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menuselect> You can also easily use a command with the element symbol, but I don't know exactly what shade of gray you want. If you have the shade already in the color editor, then: color fromeditor H ...or if you have the name or hex code of the color you want: color #d89dd89dd89d H color light gray H See "color" command and command-line specification (includes element symbols, etc.): <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.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 Jul 17, 2023, at 9:20 AM, Mazin Nasralla via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hello,

I imported an x,y,z model of water molecules into Chimera.

I want to create an image of my water structure so I am setting the background to grey. That works.

But I would prefer to set the hydrogen atom colour to light grey. I can't work out how to do that. I can select each individual atom, and then colour edit it but that will take ages.

Is there a simple command line solution?

Thanks Mazin