I concur with Kay, particularly with point d) and its consequences.
Sometimes it is obvious which result is better, often it is not. For
example, one of the hkl users was testing new options and found that all
the statistics (including refinement r-free) were worse, but the
experimental and refine
I should also add to Kay's list the following:
The tests we performed assumed that the default values of the programs (d*Trek,
Mosflm 6.13?, XDS) in ~2006 were reasonable, so with tweaking you might get a
better milage, but that was not the point when we had to deal with lots of data
and no tim
Am 20:59, schrieb Van Den Berg, Bert:
I have heard this before. I’m wondering though, does anybody know of a
systematic study where different data processing programs are compared
with real-life, non-lysozyme data?
Bert
Bert,
some time ago I tried to start something to this effect - take a lo
Hi Dirk,
This example compares integration software in combination with the
scaling program, which is what usually happens. Obviously, the scaling
program does more than just scaling, it also handles rejections. It is
possibly this procedure that makes most of the difference. For
example, the defa
CP4BB@JISCMAIL.AC.UK] On Behalf Of
herman.schreu...@sanofi-aventis.com
Sent: 28 January 2011 15:05
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Merging data to increase multiplicity
For me, it means a reflecting-range (as defined by XDS) of 5-10 or more degrees
and spots being visible o
Not sure if you ever got an answer to the original question (but I have had
some mail mishabs today, so perhaps some messages are missing in my thread)
Anyway: for sure NO - you cannot process the data with different parameter
settings and then merge the different integrations as a way to gain in
I see two questions here:
-Can we assume an unrealistically low mosaicity in order to reduce
overlaps.
-Is there any benefit in merging data from the same frames integrated with
different strategy?
As for cheating on the mosaicity, which I euphemistically call "peak sampling",
I think it can gi
A few things that might be worth looking at:
1. How is your beam divergence varying as you fix mosaicity at different
levels? Does it look relatively stable at a realistic value for the
beamline? If I'm remembering correctly, mosaicity and beam divergence
are highly correlated within mosflm.
ng the internet.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Anastassis Perrakis
Sent: Friday, January 28, 2011 8:11 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Merging data to increase multiplicity
: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Merging data to increase multiplicity
... but, back to the main point, my advice would be to only limit the
mosaicity, to get better completeness by avoiding overlaps.
Its not ideal, in the sense that you would be over-estimating the partial
fraction of
On Fri, Jan 28, 2011 at 9:35 AM, wrote:
> [...] due to the 3-dimensional profile fitting.
what is the specific difference between 3-d profile fitting and using
a sliding window of more than one image?
-Bryan
Colin Nave
Sent: Friday, January 28, 2011 3:50 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Merging data to increase multiplicity
Can people say how "high mosaicity" is defined. High relative to what?
Is it high relative to th
4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
herman.schreu...@sanofi-aventis.com
Sent: 28 January 2011 14:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Merging data to increase multiplicity
My experience (unpublished) is that XDS works very well for high-mosaicity
crystals du
: [ccp4bb] Merging data to increase multiplicity
I have heard this before. I'm wondering though, does anybody know of a
systematic study where different data processing programs are compared with
real-life, non-lysozyme data?
Bert
On Jan 28, 2011, at 8:45, "Bosch, Juergen" wrote:
> Mark Robien and I did a "systematic" study on about 30 data sets while we
> were at SGPP.
can you name the detector(s)?
-Bryan
21) 50997-5311 / +31 (15) 2152-501
Mobile: +49 (173) 7000-615
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Van Den
Berg, Bert
Gesendet: Freitag, 28. Januar 2011 14:38
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Merging da
... but, back to the main point, my advice would be to only limit the
mosaicity, to get better completeness by avoiding overlaps.
Its not ideal, in the sense that you would be over-estimating the
partial fraction of most partial reflections, and thus systematically
underestimating intensities
Interesting! But when will it be published? :-)
On 1/28/11 8:45 AM, "Bosch, Juergen" wrote:
Yes.
But we have not published this.
Mark Robien and I did a "systematic" study on about 30 data sets while we were
at SGPP. The easy cases can be processed with anything the difficult cases
worked
Hi Bert,
here is one anecdotal evidence: a couple of years ago, I had one real
in-house 3 A data set from a crystal after a quick iodide soak and
processed the images with denzo/scalepack, mosflm/scala and xds/xscale.
I got lower Rsym, higher I/sig(I) and better anomalous signal with xds.
Mor
Yes.
But we have not published this.
Mark Robien and I did a "systematic" study on about 30 data sets while we were
at SGPP. The easy cases can be processed with anything the difficult cases
worked only with XDS.
This was mostly SeMet data or HA data, so de novo phasing no MR stuff.
If you compar
I have heard this before. I'm wondering though, does anybody know of a
systematic study where different data processing programs are compared with
real-life, non-lysozyme data?
Bert
On 1/28/11 7:58 AM, "Bosch, Juergen" wrote:
I was a bit reductive with my statement (iPhone)
The equation
I was a bit reductive with my statement (iPhone)
The equation below is suppose to read:
If you have bad data, then you need to process with XDS in order to get the
maximum out of your data.
Thanks Tim,
Jürgen
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Bioch
Dear Jürgen,
is this an assignment operator or an equal sign? For if it's the latter it could
read that the result of processing data with XDS are bad data, which is rather
rude and probably not what you meant.
Tim
On Fri, Jan 28, 2011 at 06:55:43AM -0500, Jürgen Bosch wrote:
> Bad data = proces
Ah, yes, I was missing that. The statistics will be wrong. But in principle I
will get an mtz with better data, because I am integrating more observations
which would have been rejected by being missed at low resolution if the
mosaicity was set too low or being rejected by overlaps at high resol
Jose - you're missing the fact that the same dataset processed in
different ways are not statistically independent datasets! Increasing
the multiplicity for independent data reduces the uncertainty because
the calculation of the SU assumes statistical independence.
Cheers
-- Ian
On Fri, Jan 28,
Bad data = processing with XDS
Jürgen
..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1-
Hello all,
I have been trying to squeeze the most out of a bad data set (P1, anisotropic,
crystals not reproducible). I had very incomplete data due to high mosaicity
and lots of overlaps. The completeness was about 80% overall to ~3A. Yesterday
I noticed that I could process the data much bette
27 matches
Mail list logo
