On Mar 12 2007, Andy Purkiss wrote:
Quoting Andrew Wong <[EMAIL PROTECTED]>:
I was using Phaser for some MR with a data set in P1 (may not actually
be P1, but..), and in every run I always got a list of "solutions" that
all have TFZ=100.0, with a very small LLG (around 0 or even in the
negative). The RFZ is like 4 or less. The solution(s) are definitely
wrong, but I'm just curious why Phaser is doing that? Could the
TFZ=100.0 'solutions" possibly mask out the real solutions?
Is this not because the translation search has no fixed origin (for the
first molecule). In other words, all points are the same and placing the
molecule fixes the origin allowing search for a second molecule. I will
check what my P1 search showed, when I get into work!
Yes, that's basically it. Because there's no translation search for the
first molecule in P1, there's no TFZ score, so the value of 100 is put in
arbitrarily as a placeholder. I can see that would be a bit confusing when
there are multiple alternative solutions. Perhaps we should just repeat the
RFZ score.
On the particular case at hand, if the LLG scores are all around zero,
perhaps the model resembles the true structure less than expected for the
level of sequence identity (for instance because of unexpected
flexibility), or the assumed content of the asymmetric unit is too low?
Randy Read
