Thank you, Frank, for pointing this out
Here is the link to that presentation again:
www.ysbl.york.ac.uk/refmac/Presentations/Refmac_February.ppt
Garib
On 24 Apr 2010, at 12:05, Frank von Delft wrote:
Hi Garib, the link you sent doesn't work from here,
phx.
On 24/04/2010 00:17, Garib Murshudov wrote:
I think your procedure is good with current technology. At early
stages twin refinement may give misleading results.
An intuitive resoning for low R factor would be: Twin is summation
of intensities. As you sum intensities two things happen: 1)
distribution of intensities become more symmetric (departs from
wilson distribution or chisquared distribution with degrees of
freedom 2 in case of acentric reflections) 2) distributions become
narrower. As distribution becomes narrower probability that
differences between randomly selected values from the population
with this distribution is small will be higher. Hence R factors
will be smaller. When errors in model becomes comparable with the
errors in experiment then differences between observed structure
and calculated structure factors become more "independent" and R
factors become comparable. In practice it never happens (errors in
model are always higher than errors in experimental data which is
understandable). So "twin" R factor always going to be lower than
corresponding non-twin R factor.
As a general rule: One should be careful in comparing R factors
from two different crystals. R factors are not only dependent on
errors in coordinate model. But they are dependent on many
statistical properties of crystal, twinning is just an example of
such properties.
There are some warnings about twin refinement for extreme cases on
the presentation from www.ysbl.york.ac.uk:/y/people/garib/
Presentations/Refmac_February.ppt, slides number 17 and 18
(apologies if it sound like as self promotion)
regards
Garib
On 23 Apr 2010, at 22:56, Jon Schuermann wrote:
Hari,
What twin tests have you run? Results? If your data really is
P43212 and you drop to P212121 you will still have the additional
two-fold operator in your data. An operator is a mathematical
operator, which could be crystallographic or twin.
I never refine a structure with twin refinement from the
beginning (even if I suspect it is twinned). I do iterative rounds
of model building and conventional refinement until I cannot get
the R-factor any lower. Depending on many factors (resolution,
twin fraction, etc.), I usually get stuck in the mid-30's. At this
point I will investigate twin refinement or other possible SG's.
If you start using twin refinement too early in the model building
process, I have seen programs report much too low R-factors and
exaggerated twin fractions. Probably, a programmer like Garib or
Peter could comment on why.
Jon
On 04/23/2010 04:28 PM, hari jayaram wrote:
I am refining a twinned dataset in possible spacegroup P212121 .
Pointless thinks it is P43212 , but based on reading this posting
(http://www.phenix-online.org/pipermail/phenixbb/2007-September/000501.html
) I think it is P212121.
The starting R/Rfree after molecular replacement ( single site
mutant) was 34/38 to 2.2 A
After an initial round of restrained refinement ( without twin
refinement) and minimal rebuilding I got the R/Rfree to 30/34
Then I did an amplitude based twin refinement - The twin fraction
was 0.48 k,h,-l and 0.52 h,k,l and The r/rfree became 24/29
After a little more rebuilding ( a few residues out of 800
residues in ASU) and another twin refinement I got an r/rfree of
22/27 . Now the twin fraction was 0.87 (h,k,l) and 0.13 (k,h,-1)
The maps looked a little better allowing me to fix a few more
residues
Finally the same twin refinement gives me no twin operators and
the R/Rfree is 22/26
All the twinning tests indicate a serious twinning in my
crystal. Any ideas why I am seeing this
Hari
--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439
email: [email protected]
Tel: (630) 252-0682
Fax: (630) 252-0687
