Hi Ed,in the new cell (long a axis), the reflections H K L are related by H=2*h K=k L=l to those of the old (short a) cell. I would expect that the R-factor of those H K L reflections with even H from the new crystal form is low (at least at low resolution) against the h k l reflections of the old crystal form. (I'd also expect that they are stronger than the odd-H reflections.) You can obtain the R-free flag for these reflections by creating a file with h k l R-free-flag from your old dataset, multiplying all h by 2 (it should be possible to do this with the CCP4 program "reindex", using "reindex HKL h+h, k, l" as the only input line), and using that for the new data.
This procedure gives you R-free flags for half of the reflections of your new dataset (those with even H).
Those reflections with odd H are of course "new"; they are not (directly) related to any reflections of the old crystal form. You may want to randomly assign R-free flags to them; there is (I think) a task in ccp4i which takes care of partially missing R-free flags.
HTH, Kay Am 20:59, schrieb Thomas Edwards:
Dear BB Sages, I have a problem where I think I could very easily do the wrong thing. And I don't really want to do that... We have solved a new structure using zinc SAD phases (1 zinc in 27kD, 2 Zn/AU - Shelx, RESOLVE, ARPwARP. Cool.). In p21 30 109 65 90 105 90 at 2.5A However, we have now collected 1.9A data. In p21... 60 109 65 90 107 90 4 chains per AU instead of 2 with a doubling of a. Self rotations with the new data suggest 2 two-folds, one quite near crystallographic. It seems that the doubling of the a edge is adding an NCS two-fold that is almost crystallographic. Now, having refined against the 2.5A data to R/Rfree of about 25/30 we would like to use that model to do MR against the new high res data (We didn't collect Zn peak data for the new crystal - didn't think we'd need it.....). I have done that and found 4 mols with Phaser in about 60 seconds. Still cool. So, we would like to transfer Free R flags to the new data to avoid refining against what had been labelled as Free R. My problem is - how do I do that properly? I am worried that some of the working data in the bigger cell will be correlated with Free data via the near crystallographic NCS. I clearly don't want to just copy them from the old mtz file with a0 I recall some discussion about this from years ago on the BB but can't find the right threads. Can anybody point me to the correct way to do this please - I presumably want to label with Free R flags symmetry related Free R labelled reflections from the old data that are related by the new NCS 2-fold (that is close to crystallographic) in the new data. Right?? If I have worded that correctly... I am hoping that will make sense to somebody. I think that the solutions that were recently suggested for lower vs higher symmetry in the same unit cell do not apply here. One suggestion has been to do the MolRep, choose new free Rs, give it all a good hard shake with high temp simulated annealing and hope that any bias is gone. I'm not sure that I am comfortable with the word "hope" here... But, if the consensus of opinion of the wise folk at the BB is that this will pass muster at the point where the charming and delightful referees are commenting on the extremely high impact (obviously :-) manuscript, then I will quote you all! I await your wise words. Free R. Again. Sorry. Cheers Ed ______________ T.Edwards Ph.D. Garstang 8.53d Astbury Centre for Structural Molecular Biology University of Leeds, Leeds, LS2 9JT Telephone: 0113 343 3031 http://www.bmb.leeds.ac.uk/staff/tae/ -- A new scientific truth does not triumph by convincing opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it. ~Max Planck
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