if they are the same, there is in principle no problem. (you can quickly check using "mtzdump") but, just to make sure, I always use the exact same scaled and truncated mtz-file for all refinements of any particular structure. Then there is no doubt at all...and it is in fact easer, i.e. one less file-name to edit in the GUI or script you use.
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 <t...@shelx.uni-ac.gwdg.de> > -----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----- >
