[chimerax-users] circular balls instead of residue

[Revan Katte]

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 at 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 at 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 at 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 at 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 at 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 at uthct.edu
> > Professional Website: Google Scholar LinkedIn
> >
> >
> >
> > _______________________________________________
> > ChimeraX-users mailing list
> > ChimeraX-users at 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 at uthct.edu <Revansiddha.Katte at uthct.edu>*
Professional Website: Google Scholar
<https://scholar.google.com.tw/citations?user=phuOXjgAAAAJ&hl=en> LinkedIn
<https://www.linkedin.com/in/dr-revan-katte-3b53a788/>
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