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Semi-automated selection of cryo-EM particles in RELION-1.3.

Scheres SH - J. Struct. Biol. (2014)

Bottom Line: Here, a semi-automated particle selection procedure is presented that has been implemented within the open-source software RELION.With only limited user-interaction, the proposed procedure yields results that are comparable to manual particle selection.Together with an improved graphical user interface, these developments further contribute to turning RELION from a stand-alone refinement program into a convenient image processing pipeline for the entire single-particle approach.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: scheres@mrc-lmb.cam.ac.uk.

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Improved GUI and workflow. (A) Screenshot of the new GUI in RELION-1.3. (B) Proposed workflow for semi-automated particle selection in RELION-1.3. After CTFs have been estimated for all micrographs, the particle selection procedure consists of five steps (numbered 1–5), as explained in more detail in Section 4.
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f0010: Improved GUI and workflow. (A) Screenshot of the new GUI in RELION-1.3. (B) Proposed workflow for semi-automated particle selection in RELION-1.3. After CTFs have been estimated for all micrographs, the particle selection procedure consists of five steps (numbered 1–5), as explained in more detail in Section 4.

Mentions: Apart from the new algorithms described above, RELION-1.3 also features an improved graphical user-interface (GUI). Whereas previous releases still relied on user input from the command-line, e.g. using linux-based “awk” commands to select particles from specific classes, all of the functionalities described in this paper may now be performed from the GUI. To that purpose, a new image display program has been developed that reads the RELION-specific metadata files in STAR format (Hall, 1991). This provides the user with a convenient tool to manually inspect micrographs and pick particles, display extracted particles in a given order, write out STAR files with particles from a selection of classes, or display aligned particles from any given class. Fig. 2 shows a screen shot of the new interface, as well as a schematic of the proposed semi-automated particle selection procedure that links together the auto-picking, sorting and reference-free 2D class averaging algorithms (Scheres, 2012b).


Semi-automated selection of cryo-EM particles in RELION-1.3.

Scheres SH - J. Struct. Biol. (2014)

Improved GUI and workflow. (A) Screenshot of the new GUI in RELION-1.3. (B) Proposed workflow for semi-automated particle selection in RELION-1.3. After CTFs have been estimated for all micrographs, the particle selection procedure consists of five steps (numbered 1–5), as explained in more detail in Section 4.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4318617&req=5

f0010: Improved GUI and workflow. (A) Screenshot of the new GUI in RELION-1.3. (B) Proposed workflow for semi-automated particle selection in RELION-1.3. After CTFs have been estimated for all micrographs, the particle selection procedure consists of five steps (numbered 1–5), as explained in more detail in Section 4.
Mentions: Apart from the new algorithms described above, RELION-1.3 also features an improved graphical user-interface (GUI). Whereas previous releases still relied on user input from the command-line, e.g. using linux-based “awk” commands to select particles from specific classes, all of the functionalities described in this paper may now be performed from the GUI. To that purpose, a new image display program has been developed that reads the RELION-specific metadata files in STAR format (Hall, 1991). This provides the user with a convenient tool to manually inspect micrographs and pick particles, display extracted particles in a given order, write out STAR files with particles from a selection of classes, or display aligned particles from any given class. Fig. 2 shows a screen shot of the new interface, as well as a schematic of the proposed semi-automated particle selection procedure that links together the auto-picking, sorting and reference-free 2D class averaging algorithms (Scheres, 2012b).

Bottom Line: Here, a semi-automated particle selection procedure is presented that has been implemented within the open-source software RELION.With only limited user-interaction, the proposed procedure yields results that are comparable to manual particle selection.Together with an improved graphical user interface, these developments further contribute to turning RELION from a stand-alone refinement program into a convenient image processing pipeline for the entire single-particle approach.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: scheres@mrc-lmb.cam.ac.uk.

Show MeSH