be taken with such samples, and the maps, along with 3D
FSCs, should be carefully inspected. It would be better to
alter the orientation distribution (e.g., through tilting) and
obtain a less anisotropic map.
21. For new structures, an external reference standard does not
exist, and the model must be derived from the density. The
model would be refined into the density, which would accordingly improve map-model FSC. In such a case, an analysis
comparing differences between half-map and map-model
FSCs is less likely to yield insight into any potential overfitting. The user is advised to take care when interpreting anisotropic maps, and preferably, improve the orientation
distribution and obtain a less anisotropic map.
Acknowledgments
The authors acknowledge the input from Yong Zi Tan. Molecular
graphics and analyses were performed with the USCF Chimera
package (supported by NIH P41 GM103311). This work was
supported by the Pioneer Fund to C.Z. and by grants DP5
OD021396, U54 GM103368, and R01 AI136680 of the National
Institutes of Health, grant MCB-1933864 from the National Science Foundation, and the Margaret T. Morris Foundation to D.L.
Author Contributions: S.A. performed analyses and wrote sections
for directional resolution. C.Z. performed analyses and wrote sections
for local resolution. P.R.B. develops and maintains the 3D FSC code
and helped with writing and analyses. D.L. guided and supervised the
analyses and helped with writing. All authors contributed to manuscript preparation and review.
References
1. Vinothkumar KR, Henderson R (2016) Single
particle electron cryomicroscopy: trends, issues
and future perspective. Q Rev Biophys 49:e13.
https://doi.org/10.1017/
S0033583516000068
2. Cheng Y, Grigorieff N, Penczek PA, Walz T
(2015) A primer to single-particle cryo-electron microscopy. Cell 161(3):438–449.
https://doi.org/10.1016/j.cell.2015.03.050
3. Lyumkis D (2019) Challenges and opportunities in cryo-EM single-particle analysis. J
Biol Chem 294(13):5181–5197. https://doi.
org/10.1074/jbc.REV118.005602
4. Cardone G, Heymann JB, Steven AC (2013)
One number does not fit all: mapping local
variations in resolution in cryo-EM
reconstructions.
J
Struct
Biol
184
(2):226–236. https://doi.org/10.1016/j.jsb.
2013.08.002
5. Harauz GavH M (1986) Exact filters for general geometry three dimensional reconstruction. Optik 73:146–156
6. Tan YZ, Baldwin PR, Davis JH, Williamson JR,
Potter CS, Carragher B, Lyumkis D (2017)
Addressing preferred specimen orientation in
single-particle cryo-EM through tilting. Nat
Methods 14(8):793–796. https://doi.org/
10.1038/nmeth.4347
7. Penczek PA (2002) Three-dimensional spectral
signal-to-noise ratio for a class of reconstruction algorithms. J Struct Biol 138(1–2):34–46
Local and Directional Resolution in Cryo-EM Maps
185
FSCs, should be carefully inspected. It would be better to
alter the orientation distribution (e.g., through tilting) and
obtain a less anisotropic map.
21. For new structures, an external reference standard does not
exist, and the model must be derived from the density. The
model would be refined into the density, which would accordingly improve map-model FSC. In such a case, an analysis
comparing differences between half-map and map-model
FSCs is less likely to yield insight into any potential overfitting. The user is advised to take care when interpreting anisotropic maps, and preferably, improve the orientation
distribution and obtain a less anisotropic map.
Acknowledgments
The authors acknowledge the input from Yong Zi Tan. Molecular
graphics and analyses were performed with the USCF Chimera
package (supported by NIH P41 GM103311). This work was
supported by the Pioneer Fund to C.Z. and by grants DP5
OD021396, U54 GM103368, and R01 AI136680 of the National
Institutes of Health, grant MCB-1933864 from the National Science Foundation, and the Margaret T. Morris Foundation to D.L.
Author Contributions: S.A. performed analyses and wrote sections
for directional resolution. C.Z. performed analyses and wrote sections
for local resolution. P.R.B. develops and maintains the 3D FSC code
and helped with writing and analyses. D.L. guided and supervised the
analyses and helped with writing. All authors contributed to manuscript preparation and review.
References
1. Vinothkumar KR, Henderson R (2016) Single
particle electron cryomicroscopy: trends, issues
and future perspective. Q Rev Biophys 49:e13.
https://doi.org/10.1017/
S0033583516000068
2. Cheng Y, Grigorieff N, Penczek PA, Walz T
(2015) A primer to single-particle cryo-electron microscopy. Cell 161(3):438–449.
https://doi.org/10.1016/j.cell.2015.03.050
3. Lyumkis D (2019) Challenges and opportunities in cryo-EM single-particle analysis. J
Biol Chem 294(13):5181–5197. https://doi.
org/10.1074/jbc.REV118.005602
4. Cardone G, Heymann JB, Steven AC (2013)
One number does not fit all: mapping local
variations in resolution in cryo-EM
reconstructions.
J
Struct
Biol
184
(2):226–236. https://doi.org/10.1016/j.jsb.
2013.08.002
5. Harauz GavH M (1986) Exact filters for general geometry three dimensional reconstruction. Optik 73:146–156
6. Tan YZ, Baldwin PR, Davis JH, Williamson JR,
Potter CS, Carragher B, Lyumkis D (2017)
Addressing preferred specimen orientation in
single-particle cryo-EM through tilting. Nat
Methods 14(8):793–796. https://doi.org/
10.1038/nmeth.4347
7. Penczek PA (2002) Three-dimensional spectral
signal-to-noise ratio for a class of reconstruction algorithms. J Struct Biol 138(1–2):34–46
Local and Directional Resolution in Cryo-EM Maps
185