[chimerax-users] Reasign secondary structure for back-bone trace

[Eric Pettersen]

I'm talking about the oxygen connected to the non-α–carbon backbone carbon of every amino acid.  If it is missing, dssp will not compute secondary structure.

--Eric

> On Jan 18, 2023, at 1:10 AM, Enrico Martinez <jmsstarlight at gmail.com> wrote:
> 
> Hey Eric,
> actually I am using a backbone subset defined by Gromacs during the computing. Are you talking about backbone or main-chain sub-space?
> I am using the latest version of ChimeraX but also I do have a ChimeraX daily installed on the same machine..
> Cheers,
> Enrico
> 
> Il giorno mar 17 gen 2023 alle ore 19:19 Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> ha scritto:
> Hi Enrico,
>         Do you have all the backbone atoms, including the backbone oxygen?  What version of ChimeraX are you using?
> 
> --Eric
> 
>         Eric Pettersen
>         UCSF Computer Graphics Lab
> 
> 
> > On Jan 17, 2023, at 7:26 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
> > 
> > Dear Chimera-X users!
> > I am working on the visualization of a trajectory containing only back-bone atoms of the protein obtained from the PCA. When I load this multi-pdb ensemble to Chimera-X I can see only back-bone traces without any secondary structure information. I've tried to use dssp command to re-assign the secondary structure but it did not change the visualization state. Would it be possible to do it in some automatic fashion via some built-in command?
> > Many thanks in advance
> > Cheers
> > Enrico
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