case, a manual alignment can be used. However, it is not advisable,
and a map-model difference map may be best.
6.9 Docking
Note 15: A graphical interface for AutoDock Vina is implemented
in Chimera.
Note 16: This can be done using the “scoring functions” module in TEMPy; however, a simulated density map must first be
calculated at a suitable resolution using the TEMPy “structure
blurrer” module.
6.10 Jwalk
Note 17: The Jwalk web server: http://jwalk.ismb.lon.ac.uk/
jwalk/
Note 18: The format for uploading a list is each link on a single
line of a text file. Each link has the format “residue A|chain|residue
B|chain|” (e.g., 52|A|129|A| is a link between residue 52 of chain |A
to residue 129 of chain A).
Note 19: The MNXL web server: http://mnxl.ismb.lon.ac.uk/
mnxl/.
Acknowledgments
We are grateful for funding from the Wellcome Trust (209250/Z/
17/Z and 208398/Z/17/Z) and the Medical Research Council
Doctoral Training Programme (UCL). We thank the Topf group
and CCP-EM team for their help with software development.
References
1. Moult J, Fidelis K, Kryshtafovych A et al
(2018) Critical assessment of methods of protein structure prediction (CASP)-round XII.
Proteins Struct Funct Bioinforma 86:7–15
2. Webb B, Sali A (2014) Comparative protein
structure modeling using MODELLER. Curr
Protoc Bioinformatics 47:5.6.1–5.6.32
3. Pettersen EF, Goddard TD, Huang CC et al
(2004) UCSF chimera?A visualization system
for exploratory research and analysis. J Comput
Chem 25:1605–1612
4. Wriggers W, Milligan RA, McCammon JA
(1999) Situs: a package for docking crystal
structures into low-resolution maps from Electron microscopy. J Struct Biol 125:185–195
5. Topf M, Lasker K, Webb B et al (2008) Protein
structure fitting and refinement guided by
Cryo-EM density. Structure 16:295–307
6. Tama F, Miyashita O, Brooks CL (2004) Flexible multi-scale fitting of atomic structures into
low-resolution Electron density maps with
elastic network Normal mode analysis. J Mol
Biol 337:985–999
7. 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 184:226–236
8. Herzik MA, Fraser JS, Lander GC (2019) A
multi-model approach to assessing local and
global Cryo-EM map quality. Structure
27:344–358.e3
9. Roseman AM (2000) Docking structures of
domains into maps from cryo-electron microscopy using local correlation. Acta Crystallogr
D Biol Crystallogr 56:1332–1340
10. Vasishtan D, Topf M (2011) Scoring functions
for cryoEM density fitting. J Struct Biol
174:333–343
11. Joseph AP, Lagerstedt I, Patwardhan A et al
(2017) Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy. J Struct
Biol 199:12–26
12. Hryc CF, Jeong H-H, Fei X et al (2017) Subunit conformational variation within individual
220
Tristan Cragnolini et al.
and a map-model difference map may be best.
6.9 Docking
Note 15: A graphical interface for AutoDock Vina is implemented
in Chimera.
Note 16: This can be done using the “scoring functions” module in TEMPy; however, a simulated density map must first be
calculated at a suitable resolution using the TEMPy “structure
blurrer” module.
6.10 Jwalk
Note 17: The Jwalk web server: http://jwalk.ismb.lon.ac.uk/
jwalk/
Note 18: The format for uploading a list is each link on a single
line of a text file. Each link has the format “residue A|chain|residue
B|chain|” (e.g., 52|A|129|A| is a link between residue 52 of chain |A
to residue 129 of chain A).
Note 19: The MNXL web server: http://mnxl.ismb.lon.ac.uk/
mnxl/.
Acknowledgments
We are grateful for funding from the Wellcome Trust (209250/Z/
17/Z and 208398/Z/17/Z) and the Medical Research Council
Doctoral Training Programme (UCL). We thank the Topf group
and CCP-EM team for their help with software development.
References
1. Moult J, Fidelis K, Kryshtafovych A et al
(2018) Critical assessment of methods of protein structure prediction (CASP)-round XII.
Proteins Struct Funct Bioinforma 86:7–15
2. Webb B, Sali A (2014) Comparative protein
structure modeling using MODELLER. Curr
Protoc Bioinformatics 47:5.6.1–5.6.32
3. Pettersen EF, Goddard TD, Huang CC et al
(2004) UCSF chimera?A visualization system
for exploratory research and analysis. J Comput
Chem 25:1605–1612
4. Wriggers W, Milligan RA, McCammon JA
(1999) Situs: a package for docking crystal
structures into low-resolution maps from Electron microscopy. J Struct Biol 125:185–195
5. Topf M, Lasker K, Webb B et al (2008) Protein
structure fitting and refinement guided by
Cryo-EM density. Structure 16:295–307
6. Tama F, Miyashita O, Brooks CL (2004) Flexible multi-scale fitting of atomic structures into
low-resolution Electron density maps with
elastic network Normal mode analysis. J Mol
Biol 337:985–999
7. 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 184:226–236
8. Herzik MA, Fraser JS, Lander GC (2019) A
multi-model approach to assessing local and
global Cryo-EM map quality. Structure
27:344–358.e3
9. Roseman AM (2000) Docking structures of
domains into maps from cryo-electron microscopy using local correlation. Acta Crystallogr
D Biol Crystallogr 56:1332–1340
10. Vasishtan D, Topf M (2011) Scoring functions
for cryoEM density fitting. J Struct Biol
174:333–343
11. Joseph AP, Lagerstedt I, Patwardhan A et al
(2017) Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy. J Struct
Biol 199:12–26
12. Hryc CF, Jeong H-H, Fei X et al (2017) Subunit conformational variation within individual
220
Tristan Cragnolini et al.