Hi,
If you have the correct solution, clashes may be due to loops. It may be
an idea to clip these off for the molecular replacement calculations
(loops might be shorter in the structure-to-be-solved than in the search
model, they may have different conformations in the
structure-to-be-solved than in the search model, a common property of
loops is that they sometimes have different conformations).
You didn't provide much information about what was precisely done wrt
molecular replacement calculations, I notice... So what I write is just
guesswork.
If you have little experience with molecular replacement, it may be a
good idea to get advice from a colleague who has plenty and can sit next
to you and guide you through the process (again, this is guesswork).
HTH,
Fred.
LISA wrote:
Hi all,
I am trying to solve one structure by molecular replacement with
phaser in CCP4. This a complex of a multi-domain domains with small
ligand. I have structues of this protein in apo state and with other
similar ligand. The space group of this crystal is P21. This crystal
should have 4 molecules in ASU. I used the full protein as model but
did get any sol and LLG is below zero. Then each domain were used as
the search models in phaser with rotation and tranlsation. I can the
get high z score (>20), and LLG is raising. It looks like I get the
right sol, but it have more 50 clashes. Why phaser give wrong sol
with so high z socre? Can anyone give me some suggestion to solve my
strucutes? Thank you.
Best
Lisa
