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On Aug 3 2006, [big5] ¼B®aªY(OZ) wrote:
Dear ALL:
My data had a high Z-score(>10) with A template, but not output pdb. I
check it out twice, it still not output pdb file.
With the same conditions, another Z-score(<10) was obtained with B
template. And this time, we had a output pdb file. However, the score
from B template was small than the one from A template. It confused me a
lot. Any one had some appropriate explanation about that? Thank you very
much.
Hi
With the bigger (A) template, there were 2 clashes so Phaser rejected the
possible solutions. However, with 763 residues, 2 CA-CA clashes isn't bad,
so you should just rerun the job setting the number of allowed clashes
(given by the PACK command) to 2. You will probably find that one less well
conserved loop packs badly. However, I hope that the four possible
solutions all refine to a common solution! The B template was only about
half as big, so it's not surprising that it doesn't have the small clashes.
Randy Read
