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Cryo-EM density maps adjustment for subtraction, consensus and sharpening
Journal of Structural Biology ( IF 3.0 ) Pub Date : 2021-08-29 , DOI: 10.1016/j.jsb.2021.107780
E Fernández-Giménez 1 , M Martínez 2 , R Sánchez-García 2 , R Marabini 3 , E Ramírez-Aportela 2 , P Conesa 2 , J M Carazo 2 , C O S Sorzano 4
Affiliation  

Electron cryomicroscopy (cryo-EM) has emerged as a powerful structural biology instrument to solve near-atomic three-dimensional structures. Despite the fast growth in the number of density maps generated from cryo-EM data, comparison tools among these reconstructions are still lacking. Current proposals to compare cryo-EM data derived volumes perform map subtraction based on adjustment of each volume grey level to the same scale. We present here a more sophisticated way of adjusting the volumes before comparing, which implies adjustment of grey level scale and spectrum energy, but keeping phases intact inside a mask and imposing the results to be strictly positive. The adjustment that we propose leaves the volumes in the same numeric frame, allowing to perform operations among the adjusted volumes in a more reliable way. This adjustment can be a preliminary step for several applications such as comparison through subtraction, map sharpening, or combination of volumes through a consensus that selects the best resolved parts of each input map. Our development might also be used as a sharpening method using an atomic model as a reference. We illustrate the applicability of this algorithm with the reconstructions derived of several experimental examples. This algorithm is implemented in Xmipp software package and its applications are user-friendly accessible through the cryo-EM image processing framework Scipion.



中文翻译:

用于减法、一致和锐化的冷冻电镜密度图调整

电子低温显微镜(cryo-EM)已成为解决近原子三维结构的强大结构生物学仪器。尽管从低温 EM 数据生成的密度图数量快速增长,但仍然缺乏这些重建之间的比较工具。目前比较低温电磁数据衍生体积的建议基于将每个体积灰度调整到相同比例来执行映射减法。我们在这里提出了一种在比较之前调整体积的更复杂的方法,这意味着调整灰度级和光谱能量,但在掩模内保持相位完整,并将结果强加为严格正数。我们建议的调整将卷保留在相同的数字框架中,允许以更可靠的方式在调整后的卷之间执行操作。这种调整可以是多个应用程序的初步步骤,例如通过减法进行比较、地图锐化或通过选择每个输入地图的最佳解析部分的共识来组合体积。我们的开发也可以用作使用原子模型作为参考的锐化方法。我们通过几个实验示例的重建来说明该算法的适用性。该算法在 Xmipp 软件包中实现,其应用程序易于用户通过低温 EM 图像处理框架 Scipion 访问。我们的开发也可以用作使用原子模型作为参考的锐化方法。我们通过几个实验示例的重建来说明该算法的适用性。该算法在 Xmipp 软件包中实现,其应用程序易于用户通过低温 EM 图像处理框架 Scipion 访问。我们的开发也可以用作使用原子模型作为参考的锐化方法。我们通过几个实验示例的重建来说明该算法的适用性。该算法在 Xmipp 软件包中实现,其应用程序易于用户通过低温 EM 图像处理框架 Scipion 访问。

更新日期:2021-09-01
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