Will someone knowledgeable shed light on these issues at the ccp4
meeting next month?
Thanks
Andreas
Frank von Delft wrote:
Hi Manfred
thanks a lot for your comments, since they raise some interesting
points.
R_pim should give the precision of the averaged measurement,
hence the name. I
Yup, there is that. It doesn't help make the decision, though, of how
much to include. And the other problem is it requires higher redundancy
than I usually have when living on the edge of completeness vs death.
(It's not multiplicity-weighted, is it?)
(It's other problem is that it is hid
Hi Frank,
maybe this is an opportunity to state that there is indeed a way to
assess radiation damage by looking at an R-factor plot, but that
R-factor is R_d [1], not R_pim.
The formula and some explanation is in the CCP4 wiki at
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/R
There are useful plots from scala showing various measures v frame
number. I usually look at those and do some hand waving to decide where
the increasing R_xs indicate you are measuring nothing, or measuring
something different from the first frames because of radiation damage
Eleanor
Frank
Hi Frank,
of course R_pim is just one number and it may not be discriminatory
enough to decide when to stop including images. But I can say from
my own experience that R_pim will not drop forever. I have seen
data sets with R_pim values of 0.5% to 2.0 A or better resolution,
but never R_pim values
Yes of course; but the photons don't care what axis is being rotated
about, they kill just as rapidly.
phx.
George M. Sheldrick wrote:
When discussing this issue, perhaps we should not lose sight of
the fact that the statistics behind Rp.i.m. assume 'independent
observations'. Surely doing m
When discussing this issue, perhaps we should not lose sight of
the fact that the statistics behind Rp.i.m. assume 'independent
observations'. Surely doing more than one rotation about the
same axis is likely to repeat the same systematic errors?
George
Prof. George M. Sheldrick FRS
Dept. Stru
Hi Manfred
thanks a lot for your comments, since they raise some interesting
points.
R_pim should give the precision of the averaged measurement,
hence the name. It will decrease with increasing data redundancy,
obviously. The decrease will be proportional to the square root
of the redundancy
Hi Frank,
thanks a lot for your comments, since they raise some interesting
points.
R_pim should give the precision of the averaged measurement,
hence the name. It will decrease with increasing data redundancy,
obviously. The decrease will be proportional to the square root
of the redundancy if o
iginal Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Frank von Delft
Sent: 07 December 2008 22:16
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] R pim and Rmeans
Hi Manfred
I've been using and thinking Rmeas ever since I first saw it; but
(embarrassingly) I&#
Hi Manfred
I've been using and thinking Rmeas ever since I first saw it; but
(embarrassingly) I've only just woken up to Rpim -- so thanks for the
prompt. So I trawled the original references (Weiss and Hilgenfeld,
1997) to find out why it has the form it does, but I must have skimmed
too qui
Debajyoti Dutta schrieb:
Dear members,
I have a little query hare about Rpim and Rmeans. How these are used to
mark data quality, and how can one calculate it.
Thak you for your reply in advance.
Sincerely
Deb
check out the "R-factors" article in CCP4 wiki at
http://strucbio.biologie
Dear Sir,
Thank you for such nice replies. All of them helped me a lot.
Sincerely
Deb
On Sat, 06 Dec 2008 Manfred S.Weiss wrote :
>
>Dear Deb,
>
>R_meas or R_rim is a merging R-factor which is independent of the
>redundancy or multiplicity of the data (hence its name), R_pim
>stands for prec
Dear Deb,
R_meas or R_rim is a merging R-factor which is independent of the
redundancy or multiplicity of the data (hence its name), R_pim
stands for precision indicating merging R-factor. R_pim
gives you the precision of the averaged measurement, which is
the one you are actually using for struct
In addition to the Weiss paper ...
Diederichs, K and Karplus, PA (1997). Improved R-factors for
diffraction data analysis in macromolecular crystallography. Nature
Structural Biology 4(4): 269-275.
On Dec 5, 2008, at 8:06 PM, Debajyoti Dutta wrote:
Dear members,
I have a little query h
ject: [ccp4bb] R pim and Rmeans
Dear members,
I have a little query hare about Rpim and Rmeans. How these are used to mark
data quality, and how can one calculate it.
Thak you for your reply in advance.
Sincerely
Deb
Dear members,
I have a little query hare about Rpim and Rmeans. How these are used to mark
data quality, and how can one calculate it.
Thak you for your reply in advance.
Sincerely
Deb
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