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If I understand correctly, the values from the log-file
are the post-refined cell parameters, these are what you
should use.
In early versions of scalepack, the cell parameters at
the top of the scalepack output (".sca") file seemed to be
taken from the very first denzo (".x") file read, and
were sometimes quite inaccurate.
I had the impression that the last several versions,
1.79.9 at least, have corrected this and now the postrefined
values are put at the top of the output file. Someone correct
me if I am wrong, because in that case I need to go back
to inserting cell param in the scalepack2mtz com file.
Ed
Alessio Accardi wrote:
Hi all,
I am very sorry if I have a somewhat trivial question, but I am quite
new to the crystallography world.
I process my data with Denzo followed by Scalepack and I noticed that
the unit cell parameters in the scalepack .log file and in the final
output *.sca file are different; not by much, at most around 1-1.5%.
This is the readout from the middle of the scalepack.log file:
Hkl's refined: 379123 N.Chi**2: 1.227 Decrease: 0.000 * 379123
= 0.5
Film # a b c alpha beta gamma crysz
crysy crysx mosaicity
1 232.332 97.983 170.963 90.000 131.210 90.000 75.087
18.917 135.045 1.082
2 232.332 97.983 170.963 90.000 131.210 90.000 75.126
18.942 135.056 1.082
3 232.332 97.983 170.963 90.000 131.210 90.000 75.124
18.933 135.057 1.082
4 232.332 97.983 170.963 90.000 131.210 90.000 75.126
18.930 135.056 1.082
5 232.332 97.983 170.963 90.000 131.210 90.000 75.117
18.908 135.052 1.082
And this is the readout from the top of the output.sca file:
230.822 97.684 170.202 90.000 131.114 90.000 c2
First of all which of the two sets of values is the correct one to use
in refinement? I would guess that the right one is the one in the .sca
file as the hkl's and intensities refer to that unit cell, but I am not
sure. Also, why are the values different? do they reflect different
stages of refinement of the processed data? if so, is the one in the
.sca file the more refined one?
Thank you
Alessio
Brandeis University
