Software

The advent of cryo-EM’s “Resolution Revolution” came in the early 2010’s: thus, only a decade later, the field remains relatively immature. Alongside wet lab strategies to aid in the sample-preparatory stages of cryo-EM structure determination, we also actively develop our own software to address specific problems that come up during our work.

Local resolution

“Variable local resolution is a perennial issue in cryo-EM, structures. The interpretable resolution of structures frequently varies substantially within the reconstructed density. We have developed software to aid in determining the local resolution over the map, and then to filter by it after the fact, in order to allow the safest possible interpretation of the available data.”

Image compression

“We provide an efficient C program to compress gain referenced 32-bit float K2 or K3 image stacks back into MRC mode 101 (4-bit) data, in order to save space when archiving. The method requires the original gain reference, although a (statistically minutely unsafe) mechanism by which the gain reference can be estimated by taking the minimum positive value from a long series of images has previously been proposed, which may be used in extremis.”

CTF Analysis

Check the quality of collected  EM data following CTF estimation (with either gCTF or CTFFIND4). Displays interactive scatterplots to subset micrographs (based on resolution, defocus, astigmatism and CC score), allows checking of what proportion of the total data fits your subset and will save a star file with your selected data.