Entry 215 presented a challenge for the validation pipeline. Because it's a full-atom structure, we used standard Molprobity analysis. However, because there were no proteins or nucleic acids the report came out essentially blank (no Ramachandran or side-chains outliers).
Bad Clashes >= 0.4 Angstrom:
Sorry: PROBE output is empty. Model is not compatible with PROBE.
One way to approach such entries in the future might be to treat them as CG and do an excluded volume calculation. To do that we have to figure out two issues:
1) choose an appropriate atomic radii database, because atom_site table doesn't provide radii
2) tune the performance of the excluded volume calculation algorithm, because it wasn't designed to handle 250k+ particles systems.
Entry 215 presented a challenge for the validation pipeline. Because it's a full-atom structure, we used standard Molprobity analysis. However, because there were no proteins or nucleic acids the report came out essentially blank (no Ramachandran or side-chains outliers).
Moreover, the clashscore calculation also failed:
One way to approach such entries in the future might be to treat them as CG and do an excluded volume calculation. To do that we have to figure out two issues:
1) choose an appropriate atomic radii database, because
atom_sitetable doesn't provide radii2) tune the performance of the excluded volume calculation algorithm, because it wasn't designed to handle 250k+ particles systems.