Secondary structure assignment

[fedaa.attana.17@…]

Hello,

I'm seeing slight differences when using the dssp command in ChimeraX on a set of PDB structures I defined 18 months ago. These small changes (1 or 2 amino acid shift in some proteins) significantly impact the definition of loops that I've been studying.

Could there have been updates to the dssp function that might explain this? If so, how could I refer back to the version I originally used?

I appreciate your guidance.

Best regards,
Fedaa

[pett]

Hi Fedaa,

There have been some changes to how dssp operates in order to try to increase efficiency for large structures, but AFAIK there really shouldn't be any differences between the results of the new and old implementations, though I suppose it might be possible in cases where the decision between coil and non-coil was very close. I just checked several structure with the new vs. the old implementations and saw no differences.
Nonetheless if you need to access the old implementation and you were doing these calculations 18 months ago, then you were either using the new (at the time) 1.3 release or possibly the older 1.2.5 release. You can download an older release by going to the ChimeraX download page (​https://www.cgl.ucsf.edu/chimerax/download.html) and clicking on the "Older Releases" link near the top of the page. There is no problem installing several releases of ChimeraX on the same machine -- they won't interfere with each other.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab