#isolde — Public Fediverse posts

This step is important for two reasons. The MD force field will produce a distribution of bond lengths and angles that doesn't quite match the distribution expected by the validation suite run by the #PDB deposition server, so omitting this last refinement will cause many things to be flagged as outliers. The other reason is that #ISOLDE doesn't (yet) refine atomic b-factors, so omitting this last refinement would leave nonsensical b-factors in the model.
15/19

After this exhaustive first pass inspecting each residue, I try to clear the biggest problems flagged by #ISOLDE's validation tools (there are always some). Clashes are rare because atoms that are too close strongly repel each other under the MD force field. Ramachandran and rotamer outliers are rare in #AF2 models, but can arise when the simulation distorts the model. These problems often point to regions where the map is ambiguous, and where the model needs more attention.
12/19

At this point, I use #ISOLDE to do manual fitting. If the map has a low resolution, I apply secondary structure restraints to the model. I start with a global simulation to let the model settle, which I let run until the dots in the interactive Ramachandran plot have reached an equilibrium. With #AF2 models, there shouldn't be Ramachandran outliers in the first place, but this is a good overview of how many residues are moving. I want them to settle in the nearest density before I continue.
8/19

Job shadowing day for my daughter and her friend here at #CERN: with an #ATLAS physicist, an #Agile coach for a CompEng team, and an Isotope scientist at #Isolde they experience what a fascinating and diverse place #CERN is, great fun! #WomenInScience #WomenInStem #TakePart https://careers.cern/job-shadowing