DSSP in ChimeraX

[r.joosten@…]

Dear ChimeraX developers,

As the current developers of DSSP we would like you to consider adding (support for) the latest DSSP version in ChimeraX. The current version detects PPII-helices (also known as kappa-helices) and has elaborate native mmCIF support. It now directly annotates coordinate files in mmCIF with all the DSSP output. That is, a separate DSSP file is no longer needed. That said, the latest DSSP version can still read PDB files and create legacy DSSP formatted files. A description of the new DSSP is available as preprint on https://www.biorxiv.org/content/10.1101/2025.04.11.648460v1

The DSSP functionality is available as a C++ library under a BSD license (https://github.com/PDB-REDO/dssp) and we are happy to help you integrate it if you are interested.
To help reading DSSP-annotated mmCIF files we have a mmCIF dictionary at https://pdb-redo.eu/dssp/dssp-extension.dic. We are happy to help you with that as well of course.

We are very much interested in collaborating on DSSP integration as we think this would benefit both your and our users.

Best wishes,
Robbie Joosten

Department of biochemistry
Netherlands Cancer Institute

[pett]

Hi Robbie,

It would great to integrate the latest DSSP, but as always life is a series of tradeoffs. The person in charge of mmCIF I/O (Greg Couch) is on vacation until the 21st, and when he gets back I'll discuss the possible ways the integration could happen with him. I can think of a couple of practical hurdles off the top of my head. One is that ChimeraX doesn't even use C++17 yet, much less C++20, so there would be some work there. Another is I'm pretty sure we would want DSSP to work on native ChimeraX data structures since we would not want to make a temporary copy of, say, a 500,000+ atom structure just to determine its secondary structure elements.
At any rate, I'll get back to you with a better assessment once Greg returns.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab