5.9 CCP-EM
The CCP-EM software suit comprises a large number of tools to fit,
assess, and refine cryo-EM map and structural models. Some of
TEMPy tools and scores, Flex-EM, and RIBFIND are available as
part of it [83]. An overview of these tools for cryo-EM fitting and
assessment can be found in Fig. 12.
6 Notes
6.1 Resolution
Note 1: Multiple definitions of resolution exists and are commonly
used: the Rayleigh resolution, the crystallographic resolution, or
the Full-Width at Half-Maximum (FWHM); more variants exist,
and do not generally agree [84] (also, see Table above). In addition,
the exact definition of resolution for a cryo-EM map is not simply
an experimental parameter, but also a function of the reconstruction quality [85]. The use of a mask or other preprocessing on the
map will also alter its estimated resolution.
These variety of approaches cannot be easily reconciled, and the
reported numerical value of the resolution should be considered in
the context of the definition and criterion of resolution used, and
the method used to compute it.
6.2 Density Map
Preprocessing
Note 2: Methods from 2D image processing can be applied to 3D
density maps generated from cryo-EM, in order to enhance their
contrast, trace contours, segment the map, or remove background
noise. This can be used in conjunction with the scoring methods
described above to obtain better estimates when comparing maps
and models.
Fig. 12 Overview of our cryo-EM fitting and assessment tools and workflow
CryoEM Density Fitting and Validation
217
The CCP-EM software suit comprises a large number of tools to fit,
assess, and refine cryo-EM map and structural models. Some of
TEMPy tools and scores, Flex-EM, and RIBFIND are available as
part of it [83]. An overview of these tools for cryo-EM fitting and
assessment can be found in Fig. 12.
6 Notes
6.1 Resolution
Note 1: Multiple definitions of resolution exists and are commonly
used: the Rayleigh resolution, the crystallographic resolution, or
the Full-Width at Half-Maximum (FWHM); more variants exist,
and do not generally agree [84] (also, see Table above). In addition,
the exact definition of resolution for a cryo-EM map is not simply
an experimental parameter, but also a function of the reconstruction quality [85]. The use of a mask or other preprocessing on the
map will also alter its estimated resolution.
These variety of approaches cannot be easily reconciled, and the
reported numerical value of the resolution should be considered in
the context of the definition and criterion of resolution used, and
the method used to compute it.
6.2 Density Map
Preprocessing
Note 2: Methods from 2D image processing can be applied to 3D
density maps generated from cryo-EM, in order to enhance their
contrast, trace contours, segment the map, or remove background
noise. This can be used in conjunction with the scoring methods
described above to obtain better estimates when comparing maps
and models.
Fig. 12 Overview of our cryo-EM fitting and assessment tools and workflow
CryoEM Density Fitting and Validation
217