Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

2019-06-12 Thread Jonathan Cooper
The images do seem available via the RCSB page:  https://proteindiffraction.org/project/6nkq/ On Wednesday, 12 June 2019, 22:43:26 BST, Gerard Bricogne wrote: Dear Ian and James,     This PDB entry, apart from having the peculiarity of having 6 molecules in the asymmetric unit but

[ccp4bb] Some Phenix R-free set queries

2019-06-12 Thread Jonathan Cooper
In the Phenix reflection file editor, where you pick the R-free set, there are two boxes where you can enter the fraction of reflections to go into the test set (see below), but they don't seem to talk to each other. Change the one in the "More options" sub-menu and the other stays the same

Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

2019-06-12 Thread Ian Tickle
Dear Jon & Randy I did a test of this using the 2FUQ data which is one of the problematic cases you mention where the NCS is nearly crystallographic (in this case an NCS 2-fold parallel to b in P212121): Transformation matrix: -0.2 0.01204 0.00354 0.01200 0.99989 -0.00918 -0.00365

[ccp4bb] wwPDB ligand validation updates

2019-06-12 Thread John Berrisford
Hi Our recent update to the wwPDB validation reports provides much clearer validation information for ligands. We now include 2-dimensional diagrams of ligands, highlighting geometric validation criteria and, for structures determined by X-ray crystallography, 3-dimensional views of electron