*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***
I don't see how that situation could ever arise in practice - the proportions of reflections in the strong and weak subsets must be nearly equal throughout reciprocal space, since they are separated by only 1 in one of the indices, so the probability of randomly selecting zero refls for the test set from the strong subset within a resolution shell must be vanishingly small. The point I was making (and I think Phoebe was also implicitly making) was that because of the inevitable big difference in R factors between the strong & weak subsets, any variation in the ratio of the number of strong and weak refls due to random sampling error would magnify the error in the estimate of Rfree and thus make it less useful as a statistic. Also as Phoebe pointed out most of the structural information is contained in the strong subset, the weak subset merely contains information about minor deviations (e.g. differences in side-chain conformations) from the pseudo-translational symmetry (that's why they're weak!). Rfree is really only useful as an indicator of major errors in the structure (such as mis-tracing the main chain!), and such information will be contained only in the strong subset. Presumably if you have made such an error, the error itself will just be duplicated by the translational pseudos-symmetry so the weak subset will contain no information about the error. -- Ian > -----Original Message----- > From: Oganesyan, Vaheh [mailto:[EMAIL PROTECTED] > Sent: 08 November 2006 19:46 > To: Ian Tickle > Subject: RE: [ccp4bb]: Pseudosymmetry and free R sets > > But that may mean that there will be no reflections marked > for r-free in highest resolution shell. Isn't random > selection random enough? > > Vaheh Oganesyan, PhD > Scientist II > MedImmune, Inc. > One MedImmune Way > Gaithersburg, MD 20878 > USA > Phone: (301)398-5851 > www.medimmune.com > > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > Behalf Of Ian Tickle > Sent: Wednesday, November 08, 2006 1:26 PM > To: [EMAIL PROTECTED] > Cc: [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 *** > > > > 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. The Company accepts no liability or responsibility > for any onward transmission or use of emails and attachments > having left the Astex Therapeutics domain. Unless expressly > stated, opinions in this message are those of the individual > sender and not of Astex Therapeutics Ltd. The recipient > should check this email and any attachments for the presence > of computer viruses. Astex Therapeutics Ltd accepts no > liability for damage caused by any virus transmitted by this > email. E-mail is susceptible to data corruption, > interception, unauthorized amendment, and tampering, Astex > Therapeutics Ltd only send and receive e-mails on the basis > that the Company is not liable for any such alteration or any > consequences thereof. > > > > 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. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof.
