In addition to the automatically launched processes of autoindexing and integration/scaling, users may request that RAPD reindex a snapshot or pair of snapshots or reintegrate and data run. Reindexing allows the user to define several parameters such as the expected spacegroup, change the method used for strategy determination, and add additional images to the indexing. Reintegration currently allows the user to define a subset of frames from a data collection run to be reintegrated and scaled. Also, a user may request that RAPD merge to data sets together or for RAPD to launch protocols for SAD or MR structure phasing. Merging of two data sets is accomplished by the CCP4 program scala. SAD phasing consists of running the ShelX suite, followed by phenix.autobuild if RAPD believes a anomalous phasing substructure has been identified. MR allows the user to submit either a PDB code or upload a .pdb structure file to be used as an molecular replacement search model. The MR pipeline utilizes the CCP4 program Phaser.