[chimerax-users] drawing helix cartoon without breaks

[Elaine Meng]

Dear Lingyi,
The issue is that even when all the residues are "helix" they might be in different helices from each other, and ChimeraX will still draw a short loop between different helices.   You can fix this by making sure all of those helix residues are in the same helix as each other, using the "ss_id" residue attribute ("SS ID" meaning secondary structure identifier).

Residue attributes:
<http://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>

You can control the attribute values of residues using the "setattr" command.  
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html>

For example, to make sure that residues 130-144 of chain B are all  helix (ss_type = 1) and in the same helix as each other (ss_id 999):

settatr /B:130-144 res ss_type 1
setattr /B:130-144  res ss_id 999

See these previous posts for more explanation and examples:

<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-August/000632.html>
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-March/002008.html>

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 25, 2022, at 7:04 AM, 令怡 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear developers,
> 
> Hello! I recently encountered some problems when using ChimeraX.
> 
> When displaying the structure with cartoon, some helix is displayed as loop (Fig A). How to force it to be displayed as helix? I checked the User Guide and used the command "setattr  sel   residues  is_helix   true" for the selected amino acids, but only some amino acids can be displayed as helix (Fig B). Is that need to change ss_ id? I have tried, but it didn't work.
> I will appreciate it if you could answer my question.
> Looking forward to your reply!
> 
> Best Regards
> 
> Lingyi
>  
> 
> <1DBF6A0C-D523-4CDB-ACB1-D7B975A7836D.png>
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