Hi Miguel,
there are limits and they are applied to total B-factor:
- minimal Biso should be positive;
- anisotropic ADP matrix is always enforced to be positive definite.
Pavel.
Thanks, it is clear now.
I have a last concern, though. Does phenix impose minimal values to
the refined ADPs? I
Hi Pavel,
Thanks, it is clear now.
I have a last concern, though. Does phenix impose minimal values to
the refined ADPs? I guess it does not, for I have found nothing like
that in the documentation. But, if it does so, are they imposed to the
individual B-factors or the B-overall is also ta
Hi Miguel,
Right, but why this happens only in the final bss step ? Why not in
the first one?
It's arbitrary: one can do it every macro-cycle as well. The main idea
is to have a total B-factor in ATOM records written out to a PDB file.
I have noticed the behaviour described by José when I r
Hi Pavel,
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
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 t
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). We have also seen that the B factor jumps up in
this last step (
