Whereas the Warp model for a movie or tilt series describes the non-linear deformation of the entire particle ensemble and its environment, it is unclear whether this deformation gradient stays continuous throughout a single particle, i. e. if the protein structure is subject to the same compression and shearing as the ice around it. Many recent high-resolution maps were reconstructed using particles extracted from dose-weighted averages produced by MotionCor29 (link). The tool assumes the deformation gradient to be continuous in all parts of the image, and will thus deform images of particles and ice in the same way. This will be beneficial if the underlying physical model is indeed continuous. However, it also distorts the CTF locally without passing any knowledge of the distortion to downstream processing tools. In case of a strong local change in the motion direction, this will result in an artifact similar to lens astigmatism.
Warp assumes a continuous deformation field when exporting dose-weighted averages of whole 2D movies, i. e. each pixel will be shifted according to the grid interpolants at that exact position. This has the benefit of uniformly sharper images for visual inspection and particle picking. For particle and sub-tomogram extraction, however, the entire particle image will be shifted uniformly according to the grid interpolants at the particle’s center. This keeps the CTF true to its fitted analytical description, but makes the assumption that the protein is more rigid than the surrounding ice and thus deforms less due to BIM. For whole-tomogram reconstruction, a hybrid approach is pursued: the local volumes are produced using the same procedure as sub-tomogram extraction, but the combined volume is largely continuous depending on how small the local volumes were.
Dose weighting in Warp adds a B-factor of -4 Å2 per 1 e-/Å2 of dose, similar to a heuristic published previously7 . While a different heuristic is used in MotionCor29 (link) and Unblur7 , the accuracy of both approaches is of decreased significance as data-driven re-weighting is likely to be performed using an approach like the “particle polishing” in RELION 3.0.
Warp assumes a continuous deformation field when exporting dose-weighted averages of whole 2D movies, i. e. each pixel will be shifted according to the grid interpolants at that exact position. This has the benefit of uniformly sharper images for visual inspection and particle picking. For particle and sub-tomogram extraction, however, the entire particle image will be shifted uniformly according to the grid interpolants at the particle’s center. This keeps the CTF true to its fitted analytical description, but makes the assumption that the protein is more rigid than the surrounding ice and thus deforms less due to BIM. For whole-tomogram reconstruction, a hybrid approach is pursued: the local volumes are produced using the same procedure as sub-tomogram extraction, but the combined volume is largely continuous depending on how small the local volumes were.
Dose weighting in Warp adds a B-factor of -4 Å2 per 1 e-/Å2 of dose, similar to a heuristic published previously7 . While a different heuristic is used in MotionCor29 (link) and Unblur7 , the accuracy of both approaches is of decreased significance as data-driven re-weighting is likely to be performed using an approach like the “particle polishing” in RELION 3.0.
