 |
 |
Dear all As it was already stated it is essential to use the same input file (after scaling and trancating) for all refinement sessions. Output mtz file in the absence of twinning has been scaled to account for anisotropic overall B values. It is modification of the data. In the twinning case output contains detwinned data. It is serious modification of the data and should not be used as input file for next refinement session. Output file in general is representation of the model and useful for model building but not for further refinement cycles. Regards Garib On 24 Jan 2013, at 11:30, Tim Gruene wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear , > of course you could ask Garib whether or not the output data were > modified by refmac5 - often they are, at least linearly scaled (which > would certainly do no harm), and unless you have read the refmac5 code > or Garib assures you I would not rely on it. > > Further trouble is that by using the output mtz-file, which contains > more data columns like the sigma-weighted coefficients for map > calculations, the e.g. GUI might accidentally pick the wrong one > overlooked by the user, especially if the user is less experienced. > > To always use the same input mtz-file you avoid such possibilities and > it also points a novice user to what refinement is actually doing. > > Best, > Tim > > On 01/24/2013 12:03 PM, Qixu Cai wrote: >> Dear Tim Gruene, >> >> >> >> 2013/1/24 Tim Gruene <[log in to unmask]> >> >> Dear Rajesh, >> >> first of all, a model is not "true" or "false", it can only be >> "better" or "worse". >> >> The explanation of what you observe depends on what you did: - did >> you use the identical and very same mtz-file as input to all three >> scenarios? Some people take the output mtz and use it as input to >> the next refinement cycle, which is a very, very, bad thing to do. >> >> >>> Is the F/SIGF columns of the output mtz of refmac5 still the same >>> as the F/SIGF columns of the input mtz? If they are the same, why >>> cann't I use the F/SIGF columns of the output mtz as input to the >>> next refinement? >> >>> Thanks for your reply. >> >> >> >> - did you ensure always the same set of reflections was used for >> Rfree when switching between programs? If not, your R/Rfree are >> meaningless. >> >> It may also be that combining phenix and refmac5 indeed resulted in >> a better mode - both programs have some substantial differences in >> how they work. >> >> Best, Tim >> >> On 01/24/2013 11:12 AM, rajesh harijan wrote: >>>>> Dear All, >>>>> >>>>> I am working on a perfectly twinned data in space group P31. >>>>> when I refine this data with phenix refine the R/Rfree is >>>>> 26.6/29.4 and average B-factor is 38. >>>>> >>>>> I did one test now..... I used phenix refined pdb and refine >>>>> with refmac5 and got R/Rfree of 26.2/29.7 and average >>>>> B-factor is 64. >>>>> >>>>> Now I used refmac5 refined pdb and refined with phenix again. >>>>> Now R/Rfree is 22.1/24.8 and average B-factor is 56. >>>>> >>>>> >>>>> My question is, why B-factor gone up now and R/Rfree reduced. >>>>> In which refined model should I believe in. If last refined >>>>> model is true then how should I reduce the B-factor? >>>>> >>>>> Thank you Rajesh >>>>> >> >>> >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFRARtHUxlJ7aRr7hoRAnvXAKCqUV5IHvKJShQHrN8/cCGmC4DDrACgw9gL > 6MGqgIDK4DJ2vcHtuzdWPBc= > =Pl4P > -----END PGP SIGNATURE----- Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: [log in to unmask] Web http://www.mrc-lmb.cam.ac.uk