Abstract
The MRC binary file format is widely used in the three-dimensional electron microscopy field for storing image and volume data. Files contain a header which describes the kind of data held, together with other important metadata. In response to advances in electron microscopy techniques, a number of variants to the file format have emerged which contain useful additional data, but which limit interoperability between different software packages. Following extensive discussions, the authors, who represent leading software packages in the field, propose a set of extensions to the MRC format standard designed to accommodate these variants, while restoring interoperability. The MRC format is equivalent to the map format used in the CCP4 suite for macromolecular crystallography, and the proposal also maintains interoperability with crystallography software. This Technical Note describes the proposed extensions, and serves as a reference for the standard.
Highlights
Electron cryo-microscopy is a rapidly advancing technique in structural biology
To maintain compatibility with the software library for electron density maps used by the Collaborative Computational Project No 4 (CCP4) in macromolecular crystallography (MX) (Winn et al, 2011), agreement between the two communities was reached in 1982 on a shared format specification
The authors intend to adopt these extensions to the MRC/CCP4 format, and make the required changes to the following packages: CCP4, MRC library, Xplore3D, EPU, Amira/Avizo, IMOD, UCSFTomo, EMAN2, Appion and XMIPP
Summary
Electron cryo-microscopy is a rapidly advancing technique in structural biology. Together with advances in sample preparation and in instrumentation, there are increasing efforts in software. To maintain compatibility with the software library for electron density maps used by the Collaborative Computational Project No 4 (CCP4) in MX (Winn et al, 2011), agreement between the two communities was reached in 1982 on a shared format specification An update to this format was agreed in 2000 to include a machine stamp in the file header, to aid file portability. This divergence has come about as a result of the desire to record more metadata in the header, as well as to minimize the disk space taken up by the ever-increasing image sizes Since these modifications were not coordinated, it has reached a point today that some of the variants, in particular those output from some image acquisition software packages, cannot be read by other packages. The format update is being supported by changes to the MRC and CCP4 software libraries
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