Hi Revan, The spheres are showing the VDW radii of the atoms. If you want to change the VDW radii see command "size" -- just be aware that it will also affect any other calculations that use atomic VDW radii (molecular surface, contacts, clashes, etc.). <https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html> The User Guide has help pages for all the commands, tools, etc. <https://rbvi.ucsf.edu/chimerax/docs/user/index.html> I hope this helps, Elaine

On Mar 9, 2023, at 9:46 AM, Revan Katte via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Elaine Meng,

Thank you very much for your help. It is extremely beneficial to me.

I have one more question: how can I make that sphere ball bigger?

Thanks!

Revan

On Thu, Mar 9, 2023 at 10:44 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Revan, You can show any atom you want as a sphere. You have to show the atom (not just ribbons) or else you won't be able to see that it is a sphere. For example, commands to open 1gcn and show residue 10 as spheres:

open 1gcn show :10 style sphere

But maybe you want to put a ball at the alpha-carbons of residues but these atoms are not shown because the ribbon is shown instead. You would use the "suppress false" option of ribbons/cartoons if you want to show backbone atoms at the same time as the ribbon, for example to show 1zik chain A residues 2-12 alpha-carbon balls:

open 1zik show /A:2-12@ca style @ca sphere cartoon suppress false

You only need "cartoon suppress false" if you want to show both cartoon (ribbon) and backbone atoms at the same time. You could also just hide the cartoon, for example command:

hide cartoon

I described commands because it is easier to do in email, but you can also do the same things with selections and the Actions menu and/or toolbar icons. You may want to try some ChimeraX tutorials if you want to learn more: <https://www.rbvi.ucsf.edu/chimerax/docs/quickstart/index.html> <https://www.rbvi.ucsf.edu/chimerax/tutorials.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 9, 2023, at 8:21 AM, Revan Katte via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello sir/Madam,

I'm labeling (or marking) the residues of my protein structure with Chimerax.

So I want to use circular balls instead of residue, but he doesn't have that option.

Could you please assist me with this?

Thank you! Revan

-- Revan Katte, Ph.D. Postdoctoral Research Associate, Prof. Maolin Lu Laboratory, Department of Cellular and Molecular Biology, The University of Texas Health Science Center, Tyler, Texas 75708, USA. E-mail: Revansiddha.Katte@uthct.edu Professional Website: Google Scholar LinkedIn

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

Dear Revan, Works for me: open 1gcn show :10 style sphere size atomRadius +1 Tested using ChimeraX version 1.5 Elaine

On Mar 9, 2023, at 12:49 PM, Revan Katte via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Elaine Meng;

I followed your instructions, but it still does not work.

Thank You! Revan

On Thu, Mar 9, 2023 at 12:27 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Revan, The spheres are showing the VDW radii of the atoms. If you want to change the VDW radii see command "size" -- just be aware that it will also affect any other calculations that use atomic VDW radii (molecular surface, contacts, clashes, etc.).

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html>

The User Guide has help pages for all the commands, tools, etc. <https://rbvi.ucsf.edu/chimerax/docs/user/index.html>

I hope this helps, Elaine

...

On Mar 9, 2023, at 9:46 AM, Revan Katte via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Elaine Meng,

Thank you very much for your help. It is extremely beneficial to me.

I have one more question: how can I make that sphere ball bigger?

Thanks!

Revan

On Thu, Mar 9, 2023 at 10:44 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Revan, You can show any atom you want as a sphere. You have to show the atom (not just ribbons) or else you won't be able to see that it is a sphere. For example, commands to open 1gcn and show residue 10 as spheres:

open 1gcn show :10 style sphere

But maybe you want to put a ball at the alpha-carbons of residues but these atoms are not shown because the ribbon is shown instead. You would use the "suppress false" option of ribbons/cartoons if you want to show backbone atoms at the same time as the ribbon, for example to show 1zik chain A residues 2-12 alpha-carbon balls:

open 1zik show /A:2-12@ca style @ca sphere cartoon suppress false

You only need "cartoon suppress false" if you want to show both cartoon (ribbon) and backbone atoms at the same time. You could also just hide the cartoon, for example command:

hide cartoon

I described commands because it is easier to do in email, but you can also do the same things with selections and the Actions menu and/or toolbar icons. You may want to try some ChimeraX tutorials if you want to learn more: <https://www.rbvi.ucsf.edu/chimerax/docs/quickstart/index.html> <https://www.rbvi.ucsf.edu/chimerax/tutorials.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 9, 2023, at 8:21 AM, Revan Katte via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello sir/Madam,

I'm labeling (or marking) the residues of my protein structure with Chimerax.

So I want to use circular balls instead of residue, but he doesn't have that option.

Could you please assist me with this?

Thank you! Revan

-- Revan Katte, Ph.D. Postdoctoral Research Associate, Prof. Maolin Lu Laboratory, Department of Cellular and Molecular Biology, The University of Texas Health Science Center, Tyler, Texas 75708, USA. E-mail: Revansiddha.Katte@uthct.edu Professional Website: Google Scholar LinkedIn

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

-- Revan Katte, Ph.D. Postdoctoral Research Associate, Prof. Maolin Lu Laboratory, Department of Cellular and Molecular Biology, The University of Texas Health Science Center, Tyler, Texas 75708, USA. E-mail: Revansiddha.Katte@uthct.edu Professional Website: Google Scholar LinkedIn

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users