Dear All,
I experienced an odd observation with some philosophical consequences (here we go again) When I run a model obtained from a perhaps popular but until further examination unnamed server, and validate through coot/validate, the model kills probe/reduce which normally works great. Following observations: Normally, 3 windows appear: Generic objects, Flips, Molprobity Probe clash gaps; and the H-added model and the little dots and spikes are displayed. For that model I get only the Flips window with 'no adjustment', and an empty Molprobity Probe Clash Gaps Window. The model has only a CRYST1 record, does NOT contain a B factor or occupancy column it HAS a TER record. OK, I probably can paste/awk those missing columns in there with fake values. But now the consequences: Also the PDB adit server rejects that model, although I cannot see why one should not be able to do at least a geometry validation with coordinates alone. Particularly the sucker models returned from structural bioinformatics servers (which understandably and in rare humbleness do not contain occs or Bs), need exactly this validation the most. The model in question has overlapping backbone sections and rmszs >70. What means are left for a user to validate such stuff? If the PDB wants to be a true structure resource for users, it should allow such minimum validation of any coordinate model, and not reject everything that does not fit stringent deposition criteria. I do not need CRYST or TER records and not even B's or Occs if I want to know if a model is really bad. I think that these weird models that are spit out by certain bioinformatics servers are a lot more hazardous to an innocent user than a poor experimental model. Cheers, BR ----------------------------------------- Trigger warning --------------------------------------------------- This message may or may not contain references to issues of privilege and oppression including but not limited to enantiophobia, point classism, heteroatomism, transbondism, cisbonding, sizeism, curvature, references to color, alcohol, blood, small insects, disgusting cells, and any combination thereof that may cause symptoms ranging from discomfort and anxiety to violent physical response in sensitive individuals and must therefore be labeled as potentially hazardous to your comfort and well-being.
