Hurrah!!! I have quite often found that the packing requirements are too
tight and ifell that they need at least to be given as a % of the CAs .
MOLREP actually has a more sensitive packing check which looks at the %
of the molecule which overlaps, and that is less likely to reject good
solutions.
Eleanor
Airlie McCoy wrote:
Manfred was kind enough to give us the data to check his F432 case
with Phaser, and I am happy to say that in our hands the solution was
clear, with TFZ=23, however the model had 16 clashes and so the
default job did not report a solution. This has inspired us to look
again at being able to detect cases where there is a clear solution
but that loop variations between the model and target cause Phaser to
throw out solutions because they fail the packing test.
Airlie McCoy
On Nov 13 2007, Manfred S. Weiss wrote:
Dear Kristof,
I recently had lots of trouble with molrep in space group
F432. Both Phaser and Molrep failed, only Amore produced
a solution.
Hope that helps.
Manfred.
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On Tue, 13 Nov 2007, Kristof Van Hecke wrote:
Dear all,
When running Pointless 1.2.0 (see summary below), I get the cubic
space group P 4 3 2
(mosflm gave P 2 3 or P 4 3 2)
<!--SUMMARY_BEGIN-->
Best Solution space group P 4 3 2
Reindex operator: [h,k,l]
Laue group probability: 1.000
Systematic absence probability: 0.975
Total probability: 0.975
Space group confidence: 0.964
Laue group confidence 1.000
<!--SUMMARY_END-->
However, although I have multiple models (ensemble) with
approximately 30% sequence identity (44% homology), I'm not able to
get any reasonable solution with Phaser.
As we know the protein can form dimers and even trimers, is it
possible that Poinless is giving a higher space group because of
pseudo-symmetry in this case..?
Does anyone has got experience with Pointless and this kind of space
group please..?
Many thanks
Kristof
--------------------------------------
Kristof Van Hecke, PhD
Biomoleculaire Architectuur
Celestijnenlaan 200 F
B-3001 Heverlee (Leuven)
Tel: +32(0)16327477
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