Hi, everyone,
Wladek has informed me that the profile fitting radius should be set by
default to 1/8 the size of the detector, which would correspond to 40 mm
on our MAR 325 CCD. They will change that in their next release. And
thanks for the incredibly quick response from everyone, it has not even
been a day, and not even a working day, on a holiday weekend!
Engin
meindert lamers wrote:
Hi Engin,
I have seen the same with HKL2000, especially with weak diffracting
crystals.
Don't know if this is correct, but another way to overcome this is to
lower the value of "error density" during integration.
I've seen the value for error density vary between different sites
(beamlines). In one particular case the value was 3.3, which resulted
in a completeness of 1.1% (!) in the outer shell. Mosflm/Scala
reported a completeness of ~70%
Trying different values for error density gave me:
value compl overall / outer shell
3.3 61.4 / 1.1
2.0 67 / 3.7
1.0 76 / 12
0.3 88 / 47
0.1 94 / 83
I wouldn't know how to choose the correct value for error density
(probably different for each detector), so I looked at the quality of
the electron density maps to decide which value to use.
Meindert
************************************
Meindert H. Lamers, PhD
Kuriyan lab - Molecular and Cellular Biology
University of California, Berkeley
527 Stanley Hall, QB3
Berkeley, CA 94720-3220
Tel: (510) 643 0164 (Fax: 2352)
************************************
On Apr 11, 2009, at 6:11 PM, Engin Ozkan wrote:
Hi,
The problem was the profile test failing as suggested by Wladek and
Lothar (thanks to both, for continuous teaching since grad school). I
was using a profile fitting radius of 25 (not the default 10), so
that's why I assumed profile fitting was not the problem. But now, I
have played with the profile fitting radius (PFR), and below are the
numbers.
PFR Compl% Compl% (high res bin)
25 81 63
50 96 80
60 98 86
And with hindsight, it was very embarrassing to find in my log file
"count of observations deleted due to zero sigma or profile test",
which tells me the problem. And again, because mosflm was giving me
100% complete datasets, it had to be a scalepack-specific
implementation.
Interestingly, at a PFR of 50, a single profile covers almost a
fourth of the image. Any input on that one?
Engin
----- Original Message -----
From: "Wladek Minor" <[email protected]>
To: [email protected]
Sent: Saturday, April 11, 2009 5:11:40 PM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] HKL2000 and incompleteness
Try to increase profile fitting radius.
WM
------Original Message------
From: Ted Erickson
Sender: CCP4 bulletin board
To: [email protected]
ReplyTo: Ted Erickson
Subject: Re: [ccp4bb] HKL2000 and incompleteness
Sent: Apr 11, 2009 7:56 PM
So before I lose it because of HKL2000, I have two questions, and I'd
appreciate any answers to either:
1. Can there be another reason for incompleteness that I am missing
(other
than blind region at higher res., overlaps, overloads, and "not
enough many
frames")?
Another explanation for incompleteness could be due to crystal
packing that
results in an asymmetric diffraction pattern. The discrepancy between
HKL2000 and mosflm maybe a result of the resolution cutoff, however,
this is
only a speculation.
Ted
www.P212121.com
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