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Yes I think this would be legitimate provided any comparison between the Rfree and Rwork was done with the value of Rwork based only on the subset of strong refls. It clearly would be wrong to compare Rfree based only on strong refls with Rwork based on all refls, i.e. incl the weak ones. The advantage would be that Rfree would not be sensitive to the exact ratio of the number of strong to weak refls that happened to be in the test set. So the SU(Rfree) would be reduced thus making any statistical tests based on the value of Rfree-Rwork (or better Rfree/Rwork) much more reliable. -- Ian > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > Behalf Of [EMAIL PROTECTED] > Sent: 08 November 2006 17:49 > To: [email protected] > Subject: Re: [ccp4bb]: Pseudosymmetry and free R sets > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > I'm guessing this is translational pseudosymmetry, where > spots that should be fully absent in I222 are faintly present > in the P212121 data? In that case, I think the indices of > the individual spots should be the same either way, and you > should just keep the old Rfree indices and expand the set from there. > > Thought for the community as a whole - in cases where some > fraction of the spots is systematically weak, should the > Rfree set be chosen only from the strong ones, since the > translational symmetry and not the structural details is > dictating the overall magnitude of the weak ones? > > Phoebe Rice > > At 01:57 AM 11/8/2006, you wrote: > >*** For details on how to be removed from this list visit the *** > >*** CCP4 home page http://www.ccp4.ac.uk *** > > > > > >Hello, > > > >We have solved the structure of a protein that crystallised in space > >group > >I222 with 1 molecule per asymmetric unit. After refining the > structure > >to > >3.5 A, we obtained a different crystal form that diffracts to higher > >resolution; in this case, the space group appears to be P21212, with > >the same unit cell as the first type of crystals and 2 molecules per > >asymmetric unit. The packing between the two molecules in the P21212 > >asymmetric unit is identical to that of symmetry-related > molecules in > >the > >I222 crystals, suggesting that the space group of crystal > form 1 could > >also be P21212, with non-crystallographic symmetry giving rise to > >strong > >pseudo-I222 symmetry at low resolution. > > > >Since we have already refined our model against the low > resolution data > >processed in I222, what would be the best way to define a new free R > >set in order to continue refinement against the higher > resolution P21212 data? > >If our interpretation is correct, I would think that using a > completely > >new set would introduce some bias; on the other hand, is > there any way > >to somehow take into account the pseudo-symmetry we observe? > > > >Thank you for any advice, > > > >Zorg > > > >_________________________________________________________________ > >Stay in touch with old friends and meet new ones with Windows Live > >Spaces > >http://clk.atdmt.com/MSN/go/msnnkwsp0070000001msn/direct/01/? > href=http: > >//spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/fri > ends.aspx& > >mkt=en-us > > > > -------------------------------------------------------------- > ------------------------------------------------------------- > Phoebe A. Rice > Assoc. Prof., Dept. of Biochemistry & Molecular Biology The > University of Chicago phone 773 834 1723 fax 773 702 0439 > http://bmb.bsd.uchicago.edu/index.html > http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html > > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. 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