Hi Alasdair
On 11 Sep 2009, at 09:46, Alasdair K. Mackenzie wrote:
Greetings CCP4-ers,
I have been running some TLS refinement which does wonders for my R/
Rfree
values, but seems to give some spurious Bfactors/ADPs for the
waters, e.g.
B= 2.
These low Bfactors appear relatively consistent with the residual
protein
B-factors (i.e. the pdb output from REFMAC), but when i use TLS
analyse to
apply the TLS contribution to the total B-factors for the model, the
low
water B values seem crazy.......i apparently have a water with a B-
factor
of 2 interacting with a side chain with a B-factor of 60............
Has anyone encountered this type of thing before?
Yes.
I have reported this to Garib some time ago and I believe the active
Refmac people are working on this.
and does anyone have a
good solution for getting around the problem?
Mhh...
Latest Refmac versions seem to consider waters directly bound to the
protein as members of the various TLS groups.
You can override this by using
TLSD WATERS EXCLUDE
You can give it a go and see if it helps.
Best
Roberto
cheers,
Al
