Hi Aaron, this is because Refmac reports residual B-factors in ATOM records and the TLS component is stored in PDB file header that is ignored when you run phenix.refine (slides #30-36): http://www.phenix-online.org/presentations/neutron_japan_2009/phenix_japan_p... It is not a problem if you run an equivalent refinement in phenix.refine, since within a macro-cycle or two it will be equilibrated. Pavel. On 1/18/10 6:47 PM, Bart, Aaron G wrote:
Greetings,
I am fairly new to crystallography, and have just started to use Phenix for structural refinement. I am currently working on a 2.8A structure that was run through multiple rounds of rigid body refinement via Refmac and manual revision using Coot. I eventually got stuck where large portions of my molecule had very poor density and the rwork and rfree stayed around 0.3. I then performed a TLS refinement which resulted in better density, and tried running it through phenix.refine with default ADP settings, as well as simulated annealing. It worked beautifully, however when I looked at the log file for the refinement, phenix was reporting a starting rwork and rfree that represented my first stage of refinement in refmac, 0.38/0.44. My question is, is phenix somehow neglecting the refinement that was done in refmac?
Regards -Aaron _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb