At the moment refmac does extremely simple selection. First structure
factor label and the first sigma that has similar name to the first
structure factor, if not then the first sigma.
It works for a class of cases but it cannot be universal. While we are
on this matter I think it would be good to not mix input mtz and
output mtz from refinement. They may have completely different
meaning. I.e. for refinement always original mtz after scala/truncate
with correct space group assigned should be used.
Structure factors in the output mtz may have been modified by the
programs and these modifications are based on some assumptions that
may or may not be correct at the time of that program processing that
dataset. As information changes (e.g. better model) modification may
also change.
i hope I did not add more confusion.
Garib
On 30 Nov 2009, at 10:43, Bernhard Lohkamp wrote:
Hi,
the automatic selection of structure factors for refinement happens
in Refmac and not in Coot. This is one for Garib. I dont know
exactly how Refmac chooses which structure factors to use, but it
certainly should write the selected ones in the log file (maybe
newer versions of refmac already do so?!). If you want to make sure
Refmac uses the structure factors you want, then select the
corresponding option and do not trust Refmac to do the job for you.
Furthermore you probably should work with the original mtz file when
doing refinement. In that case there wont be too many different
options to pick the 'wrong' structure factors for refinement as well.
Hope this helps,
B
P.S. Kevin, I guess you misunderstood the problem. It's about SF
used in refmac (via Coot) rather than (auto)open mtz files.
Dear Paul,
There seems to be a problem with the automatic asignment for F and
SIGF when using a file from phaser (processed by autoproc). The
FCTR column seems to be used instead of F but there is no reference
what has been used in the logfile (sample attached). Unfortunately
the only indication something went wrong is the high R-Factor,
which in this case could also be due to the fact that the MR
solution is incorrect.
Best rega <<refmac-from-coot-0.log>> rds,
Alexander
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