Probably easiest to start again with the correct FreeR
You can perturnb the strucures
pdbset xyzin MR.pdb xyzout- MRshaken.pdb
NOISE 0.3
That moves everything a bit.
Or if you do enough cyles the FreeR should increase steadily to a
sensible value then level off
Easiest to use the GUI and click the button - add FreeR from existing
mtz file!
Eleanor
Harry M. Greenblatt wrote:
BS"D
Dear All,
Someone has come to ask my opinion about some inhibitor-protein
complexes they have refined, isomorphous with a known native structure
(P21212). After a short look at the statistics, I became suspicious
about the R-free selection for the new complexes. Indeed, the person
was not careful about taking the the same R-free set as the native.
Each complex had a new R-free set, and Refmac was used (i.e., they did
not benefit from simulated annealing, which according to some would
have saved the situation). So the difference between R and Rfree is
about 2-3% for each structure, since the structures are biased to a
large fraction of the new Rfree set. Technically, the process was
incorrect, but how can they remedy the situation (short of starting
from scratch with the proper Rfree set)? Run simulated annealing now,
and then a round of Refmac?
Thanks,
Harry
-------------------------------------------------------------------------
Harry M. Greenblatt
Staff Scientist
Dept of Structural Biology [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
Weizmann Institute of Science Phone: 972-8-934-3625
Rehovot, 76100 Facsimile: 972-8-934-4159
Israel
