[chimerax-users] Adjusting coil width

[Elaine Meng]

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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> 
> 
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