Hi, I am using the latest version of phenix 1.8.1-1168 for the MacOSX and I see a similar behaviour with the B-factors. Which version do you suggest to update to?
There might be a problem with over-refinement and one workaround might be to limit the Rfree-R=0.05, but your Rfree will likely to increase. Your B-factors will make more sense though. Cheers, Joao On 02/11/2012 10:54, "Jeffrey, Philip D." <pjeff...@princeton.edu> wrote: >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 >> ----------------------------------------------- > Contact and registered office address: Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX. The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please make no use of its contents and contact the sender.
