[chimerax-users] Adjusting coil width

[Edgar A Hodge]

Thanks for all the help! I appreciate it.

Best,
Eddie

On Fri, Jun 11, 2021 at 11:50 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Actually not too bad (see attached image, from using the example commands
> I sent before), although I think the usual cartoon appearance in ChimeraX
> is much better for showing secondary structure.  Some other programs
> actually draw ribbons like this, or at least I've seen similar in paper
> figures.
>
>
> On Jun 11, 2021, at 11:31 AM, Tom Goddard via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Hi Edgar,
>
> The reason the width and height of a coil part of a ribbon can't be
> adjusted is because the coil has no defined twist orientation.  For beta
> strands there are certain backbone atom positions used to decide what
> direction the flat face of the strand faces, and for alpha helices there
> are different rules to determine which direction the ribbon flat face is
> in, but for coils there are no rules in the code for how a flat face of the
> coil would be oriented.  That is why Elaine's suggestions were about
> hacking it so the coil could use the rules normally applied to beta
> strands.  I suspect it would look horrible.
>
> Tom
>
> On Jun 11, 2021, at 8:10 AM, Elaine Meng via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> 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
>
>
>
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