Hi Engin, 1) phenix.refine writes total B-factors into PDB file. If TLS is used, then there are ANISOU records that contains total atomic B. The ATOM records in this case contain the isotropic equivalent of ANISOU (and NOT residual B, as Refmac outputs). 2) When you do group B-factors refinement, the original B-factors are not reset. For example, if your starting B-factors BEFORE group B refinement are 5,6,7, then after group B refinement they can be 7,8,9 (if refined group B is 2) or 2,3,4 (if refined group B is "-3"). 3) The total B-factor used in phenix.refine: Utotal = Ulocal + Utls + Ucryst where Ulocal can be refined individually for each atom or as a group (in group B refinement is chosen). This is explained in details in phenix.refine documentation: http://www.phenix-online.org/documentation/refinement.htm see section "Refinement of atomic displacement parameters (commonly named as ADP or B-factors)". For an illustration you can have a look at the slides #28-32: http://cci.lbl.gov/~afonine/aca2008_knoxville_neutron/ Pavel. On 12/16/2008 12:08 PM, Engin Ozkan wrote:

Dear phenixbb people,

I am performing group ADP refinement and TLS at the same time. At the end, the total B factors in the pdb are not identical within residue groups.

ATOM 7 N ILE A 11 23.863 6.894 77.827 1.00151.81 A N ANISOU 7 N ILE A 11 20044 20245 17393 -796 -2448 -568 A N ATOM 8 CA ILE A 11 23.647 6.312 76.502 1.00149.93 A C ANISOU 8 CA ILE A 11 19407 19827 17732 -699 -2577 -541 A C ATOM 9 CB ILE A 11 24.451 7.060 75.423 1.00142.17 A C ANISOU 9 CB ILE A 11 18258 18757 17003 -502 -2834 -817 A C ATOM 10 CG2 ILE A 11 24.819 6.135 74.260 1.00140.21 A C ANISOU 10 CG2 ILE A 11 17760 18301 17213 -445 -3136 -730 A C ATOM 11 CG1 ILE A 11 23.648 8.266 74.929 1.00141.20 A C ANISOU 11 CG1 ILE A 11 17949 18698 17002 -369 -2502 -1103 A C ATOM 12 CD1 ILE A 11 22.184 7.945 74.630 1.00147.23 A C ANISOU 12 CD1 ILE A 11 18421 19495 18025 -392 -2156 -1014 A C ATOM 13 C ILE A 11 24.000 4.831 76.450 1.00152.71 A C ANISOU 13 C ILE A 11 19772 20013 18238 -798 -2860 -201 A C ATOM 14 O ILE A 11 24.895 4.377 77.158 1.00153.29 A O ANISOU 14 O ILE A 11 20114 20074 18055 -857 -3135 -9 A O

I would like to know if the refinement was truly grouped B-factor refinement - I am suspecting the residual B-factors might be grouped, but I haven't checked for that. Could anyone, maybe Pavel, confirm that is the case? Is there anyplace in the log files I could see the number of B groups?

Thanks,

Engin _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb