Respected Sir,
Yes, the weight mentioned in the paper was
weight matrix, but the one i used was the
option under "Refinement parameters- weighing
term (when auto weighing is turned off)".
But If I really wasnt to change the weight matrix
where should I change (in the code?)?
No, I dint mean a big difference, not in the
coordinates, but the values of R-factors and
other terms. I thought it was quite different.
So you mean that it is not of much concern?
Thanking you
With Regards
M. Kavyashree
-----Ian Tickle <ianj...@gmail.com> wrote: -----
To: ka...@rishi.serc.iisc.ernet.in
From: Ian Tickle <ianj...@gmail.com>
Date: 10/14/2011 04:00PM
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Optimisation of weights
Hi your X-ray weight of .08 seems very small, the optimal value is
normally in the range 1 to 4 (I usually set it initially at the
median, i.e. 2.5). But which weight keyword did you use "WEIGHT
MATRIX .08" or "WEIGHT AUTO .08" (the latter is I think undocumented,
so I'm guessing the first)? Anyway I would strongly advise the
latter: the difference is that the MATRIX weight is on a completely
arbitrary scale, whereas the AUTO weight is at least relative to the
theoretical value of 1 (even though the optimal value may not be 1 in
practice, at least your initial guess will be in the same ball park).
Note that what Refmac calls "automatic weighting" is not the same as
what X-PLOR, CNS & phenix call "automatic weighting" (at least that's
my understanding). "WEIGHT AUTO" in Refmac is the same as "WEIGHT
AUTO 10", whereas auto-weighting in X-PLOR corresponds to "WEIGHT AUTO
1" in Refmac. Not surprisingly these give quite different results!
The optimal B factor weight is also around 1, see the paper for
typical values.
I'm still not clear precisely what you meant by ""there was quite a
difference". I don't see that big a difference between the 2 runs,
just a slight tightening up of the geometry. Are you saying you see
big differences in the refined co-ordinates? That would be a cause
for concern.
Cheers
-- Ian
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