ping sun wrote:
Thanks for your answer.
I guess I did not make it clear. I used the data file for refinement
which is also used for phasing (peak_anomalous.hkl).
Traditionally, people will reprocess the same set of data for
refinement (rescale it in hkl2000 without using the option
"anomalous", to yield the non_anomalous data set:
peak_nonanomalous.hkl ).
So, my question is in refinement which data file should I use? And
what's the difference.
What a horrible procedure! I had hoped that the option in hkl200 to "not
have anomalous set" was defunct - even if you dont EXPECT a significant
anomalous signal it will be there and at the end of structure solution
the weak signal can help distinguish H2O from Cl or some such..
The CCP4 solution is to have a file containing <F> and F+ and F- but to
refine against <F> as a rule.
It is probably better to use F+ and F- as independent measurements, each
with their own sigmaaF but the value of Fcalc will be almost the same
for both values.
If you have significant anomalous scatterering and are using <F> you
need to modify the scattering factor for that atom appropriately.
Here is an extract from $CLIBD/atomsf.lib
Se
34 34 2.840900
17.000599 5.819600 3.973100 4.354300
2.409800 0.272600 15.237200 43.816299
-0.879000 1.139000 -0.178000 2.223000
The values -0.879000 1.139000 are the f' and f" for Cu
wavelength ( 1.54A)
I you think you have complete substitution and are using data at some
other wavelength for refinement you should change the f' and f"
appropriately
( Copy $CLIBD/atomsf.lib to your area and edit it then assign refmac5
ATOMSF my_atomsf.lib etc )
But in practice this is often less useful than you might expect and you
still see holes in your maps at the Se. I blame it on incomplete
substitution
Eleanor
