[chimerax-users] Getting rid of a gap in a helix ribbon

[Luca Pellegrini]

Hi Elain,

Setting the same ss_id value for the whole helix did it.

setattr <helix boundaries> res ss_id <#id>

Apologies, you had already explained this: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-August/000632.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-August/000632.html>
I did google it, but didn’t hit on the right word (discontinuous).

Best wishes,
Luca

Luca Pellegrini, PhD
Department of Biochemistry
University of Cambridge
Cambridge CB2 1GA
UK



> On 8 Mar 2021, at 15:36, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Luca,
> I can't say exactly since I don't have this structure to look at.  My guess is that you not only need to set the residues as helical, but also make sure they are all in one helix instead of two different helices.  I.e. there are structures with contiguous runs of helical residues but they need to be drawn as helices A and B instead of one long helix, whereas in this case it sounds like you want the latter.  So you may need to change not only the residue attribute ss_type (or maybe you don't need to change that one at all) but also ss_id for all of the residues in either the first part or the second part.
> <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 Mar 8, 2021, at 5:17 AM, Luca Pellegrini <lp212 at cam.ac.uk> wrote:
>> 
>> Hi,
>> The cartoon drawing of one helix in my structure has a gap in the middle, where it is drawn as a coil. I would like to draw the whole helix as a continuous ribbon. If I select the two consecutive residues at the gap and type: 'setattr sel res ss_type 1' the gap remains. So it looks like the residues at the gap are already helical, as the C-end and N-end residues of two consecutive helices.
>> This looks trivial to fix but I can’t figure it out at the moment…
>> Thanks for your help.
>> Best wishes,
>> Luca   
> 

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