Hi Ralf, in fact, phenix.refine outputs information about refined f' and f'' in ready-to-PDB-deposit format under RAMARK 3 prefix. For eample: REMARK 3 REMARK 3 ANOMALOUS SCATTERER GROUPS DETAILS. REMARK 3 NUMBER OF ANOMALOUS SCATTERER GROUPS : 2 REMARK 3 ANOMALOUS SCATTERER GROUP : 1 REMARK 3 SELECTION: name BR REMARK 3 fp : -0.8792 REMARK 3 fdp : 5.8029 REMARK 3 ANOMALOUS SCATTERER GROUP : 2 REMARK 3 SELECTION: name CO REMARK 3 fp : 0.0000 REMARK 3 fdp : 0.0000 REMARK 3 I hope this information is preserved when such structures get deposited into PDB -:) Pavel. On 1/20/10 9:44 PM, Ralf W. Grosse-Kunstleve wrote:
Do I understand correctly that there is no way to force refine to skip the serial in the output pdb file name, i.e. foo.pdb, not foo_001.pdb?
Yes, that's true. The main reason is that the same run writes foo_001.eff foo_002.def When I implemented this I thought the serial numbers are the only practical way to keep things straight. Later we added storage of refined f' and f" to the .def file (since there is no place in the .pdb file that would survive passes through external programs). Because of this the serial numbers seem even more important to me. Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb