Eleanor Dodson wrote:
> Jim's point is that SigI is manipluated in the program, and its value
> reflects the
> programmers ideas. If you want to make your hair stand on end process the
> same data with
> SCALEPACK and MOSFLM and get the "Riso" between the 2 SIG estimates! 50% on a
> good day is
> the typical value.
>
> The reason for this is:
> SIGI from the imaghes is based on rather uncertain physics and <I/SigI>
> for the
> unmerged data is pretty useless..
> But SIGI from the data merging can be estimated much more precisely by
> comparing the
> scatter of observations which in an ideal world would be equal. This is done
> by what
> scalepack calls the CHI**2 testand SCALA "modifying SD to make the SigI
> reflect a normal
> distribution" . This is quite a good method if you have high enough
> multiplicity and the
> symmetry equivalents are not subject to the same systematic errors - not so
> likely if you
> have offset your crystal etc.. But of course that is not always the case and
> then <I/SIGI>
> isnt very useful..
>
> Howeve it should be a reasonable measure if there is fair multiplicity.. and
> you should
> always quote that!
>
>
>
> Anthony Duff wrote:
>>
>>
>> When I asked about "I on sig I" as to whether one should report: (1)
>> <I/SIGI>; (2)
>> <I>/<SIGI>; or (3) I/SIGI, the responses were that it is <I/SIGI> that
>> should be
>> reported, although it seems that "I/SIGI" cannot be reasonably interpreted
>> as anything
>> other than <I/SIGI>.
>>
>> Bart Hazes put it most clearly (noting that Jim Pflugrath is uncertain that
>> reporting
>> I/SIGI has much merit all):
>>> - Well because of the first commandment. "Thou shalt report <I/SigI>"
>>>
>>> - Without it a Table 1 wouldn't be a Table 1 would it?
>>
>> As Fred. Vellieux said
>>> You can compute a column containing I/SIGI using SFTOOLS,
>>> then compute its average value.
>> in detail...
>>
>> sftools
>> read mymtzfile.mtz
>> complete# calculate completeness in 20 bins
>> calc col IoSI = col IMEAN col SIGIMEAN / # polish mathematics.
>> # creates IoSI = IMEAN/SIGIMEAN
>> plot col IoSI versus resol# gives average (IoSI) in 20 bins
>> checkhkl# read average (IoSI)
>>
>>
>>
>> Having said all that, I note that colleagues using scalepack are liable to
>> report:
>> <I>/<SIGI>, calculating it themselves using "average I" and and "average
>> error" from the
>> last table of the scalepack log file,
>> or
>> <I/SIGI>, but not for unique reflections, but for all reflections, taken
>> from the last
>> line of the table "Summary of reflection intensities and R-factors by batch
>> number". A
>> quick investigation has revealed that I/SIGI for all reflections can be very
>> much
>> greater than I/SIGI for unique reflections.
>>
>> It seems to me that it is impossible to obtain the correct <I/SIGI> from a
>> scalepack log
>> file.
>> Is this correct?
>>
>> I'm wondering if there is any consistency in the value to be found in the
>> headers of pdb
>> files following "REMARK 200 <I/SIGMA(I)> FOR THE DATA SET"
>>
>> Anthony
>>
>> ----------------------------------------------------------------------
>> Anthony Duff
>> Postdoctoral Fellow
>> School of Molecular and Microbial Biosciences
>> Biochemistry Building, G08
>> University of Sydney, NSW 2006 Australia
>> Phone. 61-2-9351-7817 Fax. 61-2-9351-4726
>> ----------------------------------------------------------------------
>>
>
