PRIME is a scaling, post-refinement, and merging program that contains several features key to processing serial X-ray diffraction datasets, such as
- An advanced initial scaling algorithm, where each frame is corrected against the Wilson plot of the initial merged dataset.
- A classical post-refinement algorithm, where each frame's orientation vector, unit cell dimensions, reflection partiality, etc. are corrected against the merged dataset, which is subsequently updated using the post-refined frames.
- An adaptation of the Brehm-Diederichs algorithm to resolve indexing ambiguities
These features enable the assembly of complete datasets from relatively small sets of images (~ 1000 or less, sometimes as few as 100, depending on the crystal symmetry). PRIME has been developed in parallel with IOTA; users can thus generate a seamless data processing pipeline by reducing the raw diffraction images with IOTA and subsequently merging with PRIME.
PRIME can be run as a GUI or from the command-line; scripts can be used for both, interchangeably. The command-line mode is useful if the program is run remotely on servers that do not, for some reason, support graphics.
Please cite the following source article if using PRIME:
[1] Enabling X-ray Free Electron Laser Crystallography for Challenging Biological Systems from a Limited Number of Crystals. Uervirojnangkoorn M, Zeldin OB, Lyubimov AY, Hattne J, Brewster AS, Sauter NK, Brunger AT, Weis WI. Elife. 2015 Mar 17;4.
For an example of how the IOTA/PRIME pipeline was used to solve a structure from a small dataset, see
[2] Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex. Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Zhou Q, Zhao M, Brewster AS, Michels-Clark T, Holton JM, Sauter NK, Weis WI, Brunger AT. Elife. 2016 Oct 12;5.
For a report on resolving the indexing ambiguity in serial diffraction data, see
[3] Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns. Uervirojnangkoorn M, Lyubimov AY, Zhou Q, Weis WI, Brunger AT. Acta Crystallogr D Struct Biol. 2019 Feb 1;75(Pt 2):234-241.
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Work supported by the U.S. D.O.E under contract DE-AC03-76SF00515; and the National Institutes of Health, National Center for Research Resources, grant 2P41RR01209.