Hi Elaine,

Thank you very much. This is really helpful.

May I ask another question? Do you know how to open a stack of volumes and show them as a movie in the ChimeraX? I know that can be displayed in the "Volume Series" under the volume tab in Chimera, but I can't find it in the ChimeraX. Please let me know if you have any ideas by any chance.

Thanks,
Jianming

From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Thursday, December 19, 2024 12:13 PM
To: junjie han <hanjunjie2014@gmail.com>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] cartoon style setting
 
Hi Junjie,
Cartoon style parameters are per-model (whole model gets the same value) except that you can have different width/thickness within the same model for helix, strand, and coil.  This is described in more detail here:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>

You can also change the assignment of some part between helix, strand, and coil, e.g. as explained in this previous post
<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/7TIULQAIA5P3YJP42JN2QI26OW3P2D63/>

However, if that type of control by secondary structure type only is not sufficient, one possible workaround is to open the structure twice and use different thicknesses on the two models as well as showing/hiding parts of their cartoons (or making those parts 100% transparent) to get the appearance that you want.

Another possibility is to use the "shape" command instead, either "shape ribbon" (rectanglar cross-section, although orientation may not be what you want) or "shape tube" (circular cross-section) for parts of the backbone, probably using only the alpha-carbons.  Examples:

shape ribbon #1/A:10-20@ca width .8 height .2 color cyan
shape tube #1/A:10-20@ca radius 0.75 color tan

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

These make additional models that you can close if you don't want them.  If you combine shape segments with regular ribbon, you may need some residue overlap to prevent having empty spaces between them.

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 18, 2024, at 7:15 PM, junjie han via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hi,
>
> May I ask how I can set the cartoon thick for a specific region of a structure in ChimeraX?
>
> For instance, the command "cartoon style #1/A:10-20 thick" plays an effect on the whole #1 molecule, not only affecting the specific region #1/A:10-20.
>
> Please let me know what the appropriate command is by any chance.
>
> Thanks,
> Junjie