On 10/11/2011 12:33 PM, Garib N Murshudov wrote:
We need better way of estimating unobserved reflections.
Indeed we do! Because this appears to be the sum total of how the
correctness of the structure is judged. It is easy to forget I think
that from the point of view of the refinement
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I am glad the structures that have been solved using the
free-lunch-algorithm as implemented in shelxe did not know they were not
allowed to be solved. Of course there is DM involved, as has been
pointed out ;-)
On 10/12/2011 10:12 PM, Edward A.
Here we are I presume only worried about strong reflections lost behind
an ice ring. At least that is where the discussion began.
Isnt the best approach t this problem to use integration software which
attempts to give a measurement, albeit with a high error estimate?
The discussion has
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On 10/11/2011 09:58 PM, Ethan Merritt wrote:
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
In the limit yes. however limit is when we do not have solution, i.e. when
model errors are very large. In the limit map coefficients
Tim Gruene wrote:
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On 10/11/2011 09:58 PM, Ethan Merritt wrote:
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
In the limit yes. however limit is when we do not have solution, i.e. when model errors are very large. In
the
On Wednesday, October 12, 2011 01:12:11 pm Edward A. Berry wrote:
Tim Gruene wrote:
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On 10/11/2011 09:58 PM, Ethan Merritt wrote:
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
In the limit yes. however limit is when we
Dear Ethan,
Thankyou for the reference, but actually it's the wrong paper and anyway
my only contribution to the 'free lunch algorithm' was to name it (in the
title of the paper by Uson et al., Acta Cryst. (2007) D63, 1069-1074). By
that time the method was already being used in ACORN and by the
On Tue, 2011-10-11 at 15:24 +, Bruno KLAHOLZ wrote:
However, once you have determined and refined your structure it may be
worth predicting the intensity of these spots and put them back for
map calculation,
REFMAC does this by default, because
expected value of unknown structure factors
On Tue, Oct 11, 2011 at 10:34 AM, Ed Pozharski epozh...@umaryland.eduwrote:
CNS defaults to excluding them. As for phenix, I am not entirely sure -
it seems that phenix.refine does too (fill_missing_f_obs= False), but if
you use the GUI then the fill in option is turned on.
In practice, it
On Tue, Oct 11, 2011 at 10:34 AM, Ed Pozharski epozh...@umaryland.eduwrote:
expected value of unknown structure factors for missing reflections are
better approximated using DFc than with 0 values.
better, but not always. What about say 80% or so complete dataset? Filling
in 20% of Fcalc (or
On Tue, 2011-10-11 at 10:47 -0700, Pavel Afonine wrote:
better, but not always. What about say 80% or so complete dataset?
Filling in 20% of Fcalc (or DFcalc or bin-averaged Fobs or else - it
doesn't matter, since the phase will dominate anyway) will highly bias
the map towards the model.
Hi Ed,
On Tue, Oct 11, 2011 at 11:47 AM, Ed Pozharski epozh...@umaryland.eduwrote:
On Tue, 2011-10-11 at 10:47 -0700, Pavel Afonine wrote:
better, but not always. What about say 80% or so complete dataset?
Filling in 20% of Fcalc (or DFcalc or bin-averaged Fobs or else - it
doesn't
On Tue, 2011-10-11 at 11:54 -0700, Pavel Afonine wrote:
Yep, that was the point - sometimes it is good to do, and sometimes it
is not, and
Do you have a real life example of Fobs=0 being better? You make it
sound as if it's 50/50 situation.
--
Hurry up before we all come back to our senses!
Do you have a real life example of Fobs=0 being better?
Hopefully, there will be a paper some time soon discussing all this - we
work on this right now.
You make it
sound as if it's 50/50 situation.
No (sorry if what I wrote sounded that misleading).
Pavel
If the model is really bad and sigmaA is estimated properly, then sigmaA will
be close to zero so that D (sigmaA times a scale factor) will be close to zero.
So in the limit of a completely useless model, the two methods of map
calculation converge.
Regards,
Randy Read
On 11 Oct 2011, at
In the limit yes. however limit is when we do not have solution, i.e. when
model errors are very large. In the limit map coefficients will be 0 even for
2mFo-DFc maps. In refinement we have some model. At the moment we have choice
between 0 and DFc. 0 is not the best estimate as Ed rightly
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
In the limit yes. however limit is when we do not have solution, i.e. when
model errors are very large. In the limit map coefficients will be 0 even
for 2mFo-DFc maps. In refinement we have some model. At the moment we have
On 10/11/11 12:58, Ethan Merritt wrote:
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
In the limit yes. however limit is when we do not have solution, i.e. when
model errors are very large. In the limit map coefficients will be 0 even
for 2mFo-DFc maps. In refinement we
Best way would be to generate from probability distributions derived after
refinement, but it has a problem that you need to integrate over all errors.
Another, simpler way would be generate using Wilson distribution multiple times
and do refinement multiple times and average results. I have
On 10/11/11 12:58, Ethan Merritt wrote:
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
In the limit yes. however limit is when we do not have solution, i.e. when
model errors are very large. In the limit map coefficients will be 0 even
for 2mFo-DFc maps. In
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