Clash detection for overlapping chains

[ChristineSchulz]

Hi there, great work!
I found the package looking for a way to detect overlapping chains from AlphaFold3 predictions. It found the overlapping chains, but also reports loads of close side chain contacts, like this one:

Is there a way to either change the cutoff for clash detection, or get a more detailed reporting to see the severity of the clash?

[janikkokot]

Hi, I am glad that this tool is useful for your work!

The clash detection is in the get_clashes function under src/topmodel/check/clashes.py and uses the VDW-radii of the atoms involved to judge wether it is a clash or not (clash if distance is shorter than the combined vdw radii - 0.5 angstrom).

I agree that for the python package a more flexible parameter setting would be valuable, either via a cutoff, or by allowing to specify a selection string on what to calculate clashes (i.e. only between side chains and backbone, ...).

Are you using this tool in the command-line or as a python package?

[ChristineSchulz]

I used both, but I am more interested in the command line tool. A flexible parameter for the 0.5 angstrom would to the trick for me!

My failed structure predictions include interatomic distances of ca. 0.8 - 1.5 angstrom. Alphafold3 itself does not filter them out, unfortunately.