[chimerax-users] discontinuous helices in tube mode

[Yazan Abbas]

Thanks Elaine, that was helpful!

Best,

Yazan

On Mon, Aug 19, 2019 at 1:09 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>
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