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PS just checked an example, and the the refmac input and output F and SIGF are in fact NOT the same and have been subjected to something more than linear scaling. This was using refmac version 5.5.0109, admittedly not the newest one. So using the refmac output mtz as input for the next run is wrong as Tim states, although it is probable that in practice the resulting differences may not be noticeable. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 24 Jan 2013, at 12:03, Qixu Cai wrote: > Dear Tim Gruene, > > > > 2013/1/24 Tim Gruene <[log in to unmask]> > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > 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/ > > iD8DBQFRAQ56UxlJ7aRr7hoRAsJmAJ9RcS1Bp7g53LwiTm1ZMAVAICHXAACfdWgD > FlLHo/1euT/BIeSW7EhrvHo= > =w9IY > -----END PGP SIGNATURE----- >