[chimerax-users] change residues to helix

[Meinan Lyu]

Dear Elaine,

Thank you very much. You have totally understood me and I tried what you
suggested, it works very well. Thanks again!

Best wishes,
Meinan


On Mon, Feb 24, 2020 at 4:42 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Meinan,
> It would be useful if you would say what structure you are displaying, so
> I could check your commands exactly and make sure the residue numbers etc.
> are right.  However, I can see that there are two issues:
>
> (1) your “setattr” command actually changes all of chain A into helix.
> Instead of :467-469/A it should be /A:467-469.  The first one means all
> residues 467-469 (in all chains) plus all of chain A, whereas I’m guessing
> you mean 467-469 in chain A only.  This is explained here:
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#implicit>
>
> (2) even though you set the entire chain to type helix, there are still
> thin pieces because it is trying to show that the residues don’t belong to
> the same helix as each other.  In other words, there will be a thin piece
> between 10 and 11 if residues 1-10 are one helix and residues 11-20 are a
> different helix.
>
> If you want the residues to be in the *same* helix as each other, you’d
> need to give them all the same ss_id attribute, e.g.:
>
> setattr /A:1-20 res ss_id 999
>
> <http://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.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 Feb 24, 2020, at 12:12 PM, Meinan Lyu <mxl1032 at case.edu> wrote:
> >
> > Dear cgl.ucsf.edu,
> > In chimerax, Helix is disrupted for some reason, could I change the
> intermediate residues into helix? There are two ways I tried, 1: use 'dssp'
> command, 2: use 'setattr :467-469/A res ss_type 1'. But both didn't not
> work. Could you tell me how to change this?
> > Best regards,
> > Meinan
>
>
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