-----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 <t...@shelx.uni-ac.gwdg.de> > > 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-----
