Dear PhenixBBer, 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. https://www.dropbox.com/s/prs0z8ayb73kg9k/Screenshot_sigma.png At the same sigma level(1.5), the absolute density of the violet map is 0.32e/A^3 (phenix-dev-1266), while that of the blue map is 0.01e/A^3(phenix-1.6.4-486). Besides the different phenix used, there is no other difference on the data and model used. Sam encountered a similar problem on the density. http://phenix-online.org/pipermail/phenixbb/2012-December/019226.html 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" Or there is a work round for this issue? Thanks! -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************