Unit cell dimensions not found

Question

Unit cell dimensions not found

Closed this issue 7 months ago · 1 comments

JavierSanchez-Utges commented 7 months ago

I have pre-processed my structures, to split into chains, and as a result some metadata are lost, such us the unit cell dimensions'. I get this warning from MDAnalysis:

~/miniconda3/envs/ob/lib/python3.7/site-packages/MDAnalysis/coordinates/PDB.py:747: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values.
  warnings.warn("Unit cell dimensions not found. "

I think it is just to extract the coordinates, so it should not have any effect on the GrASP featurisation of the atoms, should it?

Thanks!

Answer 1 · 2024-04-09T15:22:20.000Z

This should be fine. This warning happens when u.dimension == None which means the distances in MDA will not consider periodic boundaries. I find it safer to remove these anyway because I've seen artifacts from it in the past.