To add to Garibs answer - it is a good idea if your data set is pretty
complete - but can enhance model bias if it is not .
Eleanor
Garib Murshudov wrote:
On 18 Mar 2009, at 01:47, Bernhard Rupp wrote:
I mean *absent* reflections here with fobs=0
----------------------------
Dear All,
during processing some mtz files I noted that some programs complete
the reflection list by padding missing reflections.
a) for Refmac (which did not pad reflections automatically) I
read that
1) for 2mFo-DFc: Fwt = DFc in case Fo=absent
2) for mfo-fc : Fwt=0 for Fo=absent
It is true. Although there are other options (i.e. ignore them). Many
tests showed that recovering missing reflections this way (i.e.
replacing them with their approximately expected values) give better
maps that not using them at all.
b) how does PHENIX/refine handle the fobs = absent reflections
in either case?
c) Prime and switch maps also have padded reflections, but here
I am at a loss,
because the maps seem to acquire very high positive
density - i.e. the distribution
seems atypical when read into say Xtalview. Might be a
result of the density modification
procedure? Can I get the observed reflections only from P&S?
Could the program authors kindly shed some light or references on the
treatment of absent reflections in their
respective programs? In most cases, the padded reflections have not
much effect, as expected from their weights.
Thx, br
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@qedlife.com
bernhardr...@sbcglobal.net
http://www.ruppweb.org/
-----------------------------------------------------------------
People can be divided in three classes:
The few who make things happen
The many who watch things happen
And the overwhelming majority
who have no idea what is happening.
-----------------------------------------------------------------
