Dear Reza, you can do this kind of precise magnification calibration by fine-scaling the cryo-EM map with respect to your atomic model using for example Chimera. Try varying the scales by increments of 0.01 of the pixel size and check for the best cross-correlation between the cryo-EM map and a map calculated from the atomic model. Btw, we noticed that the quality of this fine calibration is also visible in the geometry quality of the atomic model under refinement (Ramachandran outliers etc.), e.g. when using Phenix, Buster etc.
See for example methods section in https://www.ncbi.nlm.nih.gov/pubmed/29143818 Best regards, Bruno From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Reza Khayat Sent: 24 February 2018 21:38 To: [email protected] Subject: [ccp4bb] EM voxel size correction Hi, Has anyone established a robust method to calibrate the pixel/voxel size of a cryo-EM image reconstructions using a known PDB? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031
