Dear Chen,
you should only exclude resolution ranges when you actually have
ice-ring contamination in your data: did you decide on that by hand or
is it based in your case on some automatic analysis? If you have this
situation then the completeness will indeed go down - after all, there
are possib
Hi, All CCP4 users,
This might be a little off-topic, but I cannot find a mail list for XDS.
During XDS processing, we can exclude the resolution range to "remove" ice
ring.
In my case, when I excluded these range, the completeness at this range
will be much lower, ~45%.
N 1/d^2DmidNmeas
Hi, All CCP4 users
--
***
Charles Chen
Research Instructor
University of Pittsburgh School of Medicine
Department of Anesthesiology
**
###
Automated outlier rejection in scaling will handle a lot of things,
including ice. Works better with high multiplicity. Unless, of course,
your ice rings are "even", then any integration error due to ice will be
the same for all the symmetry mates and the scaling program will be none
the wi
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. Berry
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 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
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 limit
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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 coefficie
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 stra
> 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. I
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 not
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 refineme
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
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 poin
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 19:
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
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
Hi Ed,
On Tue, Oct 11, 2011 at 11:47 AM, Ed Pozharski wrote:
> 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 or else - it
> > doesn't matter, since the phase wi
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 or else - it
> doesn't matter, since the phase will dominate anyway) will highly bias
> the map towards the model.
DFc,
On Tue, Oct 11, 2011 at 10:34 AM, Ed Pozharski wrote:
>
> "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 DFcalc or bin-av
On Tue, Oct 11, 2011 at 10:34 AM, Ed Pozharski wrote:
> 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 will be turned on fo
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 facto
I've used a technique called "annealing", which amounts to holding an index
card between the cryo stream and the crystal for a few seconds then removing
the card quickly.
In my experience, about 70% of the time the diffraction is worse and about 30%
of the time the ice rings will be gone with s
Francis,
I would like to bring your attention to our paper in Acta Cryst D Volume
66 (6), 741-744 (2010) where we deal with spots under the ice-rings. We
have been very successful in eliminating the ice-rings and recover the
data underneath. If you are interested you can request the Python scr
If the ice rings are really sharp, they trigger the bad
background rejection in denzo/HKL2000. To reject more spots,
increase the "reject fraction 0.7" parameter to something
greater than .7. This rejection is on a spot by spot basis,
so spots with good background between the rings should not
be a
ssage d'origine-
De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Francis E
Reyes
Envoyé : Tuesday, October 11, 2011 5:17 PM
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Ice rings...
All,
So I have two intense ice rings where there appear to be lattice spots in
between
All,
So I have two intense ice rings where there appear to be lattice spots in
between them.
I understand that any reflections that lie directly on the ice ring are
useless, however, how do software programs (HKL2000, d*Trek, mosflm, XDS) deal
with these intermediate spots?
It would seem t
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