Hi Jose,
We have seen that the recent versions of phenix (1.3) the structure refinement ends with a bulk solvent correction step, something I found quite unusual (absent in other refinement programs and in older versions of phenix, 1.24.1).
- the software is evolving and gets better over time -:) That is, version 1.3 is supposed to be better than 1.24.1, and the latest 1.4 should be better than 1.3.
- it is good to update bulk solvent correction at the end of refinement. For example, the refinement of coordinates may invalidate the mask which in turn invalidates the solvent contribution Fbulk.
We have also seen that the B factor jumps up in this last step (see bellow). Is anybody aware of this?
This is because the trace of overall anisotropic scale matrix is added to atomic B-factors and subtracted from that matrix. This is exactly what CNS does (at least version 1.1).
Do you know how to get rid of this final bss step?
It is not a good idea, so phenix.refine does not have an option to turn it off.
This step is redundant, as bss is also done at the beginning of each ref cycle.
It is not redundant: see above. FYI: there is PHENIX bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb Pavel.
