[chimerax-users] discontinuous helices in tube mode

[Elaine Meng]

Hi Yazan,
ChimeraX uses the HELIX records in PDB (and the equivalent information in mmCIF).  If those lines say it is one long helix, you should get one long tube. ChimeraX uses an “ss_id” attribute to identify which residues are in the same helix. For example, if the HELIX records say that 10-19 is the first helix and 20-25 is the second helix, residues 10-19 would have ss_id = 1 and 20-25 would have ss_id = 2.  You could try setting all the residues that you want in one tube as the same “ss_id” value using “setattr” before showing cartoon, e.g.:

setattr ss_id 2 /A:10-25

… to set residues 10-25 in chain A as helix 1 of the structure.  This is probably easier than trying to edit the secondary structure information in the input file.  Of course the residues would also have to be defined as helix (not strand or coil) but it sounds like your structure already has them defined as helix.

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

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

> On Aug 19, 2019, at 9:39 AM, Yazan Abbas <yazan.abbas at gmail.com> wrote:
> 
> Hi, 
> 
> Is there a parameter that can be changed to control how "cartoon style modeH tube" draws a continuous helix? In my model, most of my helices are broken up into 2-4 discontinuous helices (especially the long, curved ones). 
> 
> In pymol (cylinders mode) and chimera (pipes and planks depiction), the same helices are drawn as a single, continuous helix, suggesting that my model is ok. I tried adding a HELIX definition in the pdb file, and also tried forcing chimeraX to draw a helix using the setattr command, but neither strategy has helped. I also tried playing with the dssp energyCutoff with no success.
> 
> Thanks, 
> 
> Yazan