That sounds like the bug in Phenix.refine v1.8 that a few of us encountered - updating to the latest release will help.
Actually wasn't so much a bug but a "feature", albeit not the best one imaginable. Anyone using older v1.8 versions should update. --- Phil Jeffrey Princeton On Nov 2, 2012, at 6:41 AM, "Demetres D. Leonidas" <ddleoni...@bio.uth.gr> wrote: > Dear Tim, > > this affects all atoms and yes I did reset the B-factors to 20.00 prior to > refinement. I have not tried REFMAC but now I will give it a try since phenix > does not seem to do the job. > > best > > Demetres > > > On 2/11/2012 1:34 μμ, Tim Gruene wrote: >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> Dear Demetres, >> >> does this affect all atoms, or only a few selected ones? >> >> Did you compare with refmac5 (for e.g. input script errors), or did >> you reset the B-factors to a reasonable value (e.g. 20-30) prior to >> refinement? pdbset can do this conveniently. >> >> Best, >> Tim >> >> On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote: >>> Hello, >>> >>> I am experiencing a weird problem with B factor refinement >>> (individual, isotropic) in phenix.refine (1.8.1.-1168) and a >>> structure at 1.9 A resolution. The ADP values after the refinement >>> are very very low, less than 2 and sometimes 0. I am getting the >>> same result with and without optimization of the X-ray/ADP weight. >>> Has anyone else noticed that and is there a workaround ? >>> >>> Demetres >>> >> - -- 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/ >> >> iD8DBQFQk6+vUxlJ7aRr7hoRAvCZAKDxzmLYV74HKanTuoNiqLEu6AmlRwCgkVQs >> Q+SZVN6ISb0X38ZekG119/s= >> =xKhB >> -----END PGP SIGNATURE----- > > -- > ----------------------------------------------- > Dr. Demetres D. Leonidas > Associate Professor of Biochemistry > Department of Biochemistry & Biotechnology > University of Thessaly > 26 Ploutonos Str. > 41221 Larissa, Greece > --------------------------------------------- > Tel. +302410 565278 > Tel. +302410 565297 (Lab) > Fax. +302410 565290 > E-mail: ddleoni...@bio.uth.gr > http://www.bio.uth.gr > -----------------------------------------------
