[chimerax-users] Adjusting coil width

[Elaine Meng]

Hi Eddie,
As mentioned in the "cartoon style" help, width does not affect coil.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>

This is because the coil width is always taken to be the same as the coil height.  What are you trying to do?  Make the whole protein have a flat ribbon (i.e. width>height)?  I only ask because if you want to do that, it's possible, but requires messing up all of the secondary structure assignments of the protein.

If you want to make the coil width different than height, you would have to do something really clunky: reassign the coil secondary structure, e.g. assign it as strand.  However, it is worse than that, because there are still coil-like connecting regions between each separate secondary structure segment (each individual helix and strand).  So the only way to get rid of anything that looks like coil is to make the whole protein into one helix or one strand.  I'll give an example of making it into one helix since if you made it into a strand, you'd have to use another command to get rid of the arrowhead on one end.  Commands:

setattr protein residue ss_type 1
setattr protein residue ss_id 0

The first command assigns everything as helix.  The second one says that it is all the same helix, not multiple consecutive helices.

Setattr command:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html>

Attribute names, residue level:
<https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 10, 2021, at 11:18 PM, Edgar A Hodge via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> I'm struggling to adjust the coil width. This seems easy to do using the "cartoon style" command, but I can't seem to figure it out with coils.
> Thanks!
> Eddie