Dear Dale, > 1) There is a need for additional validation of structure factor > depositions. > > My recollection is that the output of SF Check is available to > the depositor via ADIT on the RCSB site. I have found that report > to be quite helpful in checking for gross errors in my structure > factor files. > > The Electron Density Server performs similar checks. It shows > that the R value for 3ftt is 6.4% with a correlation coefficient > between Fo and Fc of 0.996. > > The EDS flags entries as "interesting" if the calculated R value > is more than 5% higher than the reported R value. Maybe it should > also note when the R value is more than 5% lower. > > The tools for validating structure factors exist but perhaps could > be put more "in the face" of the depositor to more strongly encourage > that they be looked at. Thank you for stressing this again. I had a look at the PDB_REDO results for 3ftt. It uses a procedure similar to that of the EDS, so I wanted to make sure 3ftt was rejected because R(-free) could not be reproduced. However, 3ftt was not in PDB_REDO for a different reason: the R-free set had no information content. That is, all reflection have the same status flag. There are frequent discussions in the CCP4BB about the (un)importance of keeping the R-free set. It would certainly be nice if the PDB would also warn about R-free set problems to the depositor. Funny thing for the status flags of 3ftt: all reflections are marked 'x' (i.e. unmeasured). We should have known that there was something wrong with them.
Cheers, Robbie Joosten
