On Sun, Jan 13, 2013 at 11:38 AM, CPMAS Chen
I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To my surprise, the absolute electron density on the 2Fo-Fc map is quite different.
The electron density maps (or coefficients) generated by Phenix are not on an absolute scale, and the values displayed by Coot are more or less irrelevant. The scaling method changed significantly between 1.6.4 and 1.8, so I'm not surprised that the map levels did too.
By the way, is there a simple way to keep only F and SIGF column of the autoxds generated truncate.mtz via phenix? the GUI does not allow to reduce columns. I normally use IMEAN and SIGIMEAN to do refinement, but this may not be necessary as it is pointed in the maillist, since the intensity is already transformed to amplitude after truncation in autoxds.
I can specify labels by xray_data.labels = "F, SIGF", but apparently phenix treats it as containing anomalous data. the following is extracted from the refine pdb file
MIN(FOBS/SIGMA_FOBS) : 1.16 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.11 REMARK 3 NUMBER OF REFLECTIONS : 143207 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247
Also, in the auto generated def file, xray_data.labels = "F, SIGF, DANO, SIGDANO"
This is intentional - why would you want to throw out information? However, you can always use either the reflection file editor (in the latest builds) or the French & Wilson GUI to convert IMEAN to F. -Nat