Try typing dss in the console and then show as cartoon again, sometimes it doesn't work immediately. That is most likely the problem.

Otherwise of course it could be that your dihedral angles have changed and therefore the secondary structure really is different. But I would doubt this to be the case for the entire Protein xD.

Sir, I did try this and this is what I am getting in pyMol. I think that only the helix and coil details specific to amino acids have lost during the simulation.

For your reference I am attaching the screenshot.

Ignoring incomplete residue /mode2_a1.0//A/217  ...

Are you sure that this doesn't only have backbone structure ?

Otherwise there is something wrong with the structure ^^'

If you want you can PM me the PDB file and I can have a look myself.

Thank you for your quick response. Please your your inbox, I have sent you the files.

So the quick and dirty fix to this was to use the webserver

https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::SABBAC

Another fix (that didn't work either with my Rosetta isntallation or specifically for the protein of the questioner) is to use

the Rosetta apps ca_to_allatom (https://www.rosettacommons.org/docs/latest/application_documentation/utilities/ca-to-allatom) and then fixbb (https://www.rosettacommons.org/docs/latest/application_documentation/design/fixbb) which will

model the side chains.