7. If your protein of interest undergoes post translational processing, the canonical sequence reported on UniProt may be
different to the true experimental mass. Additional sequence
information can be found on UniProt for characterized entries.
8. Identified subcomplexes can be used to determine the connectivity based on its internal constituents. Start from the smallest
subcomplex and build up a network of additional subunits.
9. While density maps can be opened in PyMOL, the graphics
viewer Chimera is better suited for visualizing density maps and
possessed advanced functions for fitting structures into
maps, etc.
10. Structures can be fitted into density maps using Chimera’s “Fit
in Map” function. Open both the map and structures in Chimera. “Fit in Map” can be accessed from the Volume Viewer
window when a map file is open, under the “Tools” tab. You
may need to manually move the structure in close proximity of
the map file for better fitting.
11. The calculate_density.sh script can be opened using any text
editor. You will need to replace the “python¼”/anaconda2/
bin/python” line with the path to python for IMP on your
own system.
12. GMMs can be calculated for electron density maps as a sum of
three-dimensional gaussians. The shape of a structure in PDB
format can also be converted into a simulated volume, and
likewise converted into a GMM. The fit between each subunit
GMM can then be rapidly calculated against the GMM of the
complex. Consult the IMP documentation for more information on how GMMs are used.
13. The number of residues that are represented by a single bead is
set in the “topology.txt” file under “bead_size.”
14. See IMP documentation at: https://integrativemodeling.org/
talks/dec_2016_workshop/IMP%20software%20introduc
tion%20and%20tutorial.pdf for additional information on replica exchange simulations.
15. See IMP documentation at: https://integrativemodeling.org/
talks/dec_2016_workshop/Modeling%20of%20the%
20Nup84%20complex.pdf for more information on scoring
functions.
16. Consult the PyMOL documentation for the “Align” function:
https://pymolwiki.org/index.php/Align.
17. CCS can be calculated through four different metrics, these are
the projection approximation (PA), projection superposition
approximation (PSA) [48], exact hard sphere scattering
(EHSS), and trajectory method (TM or TJM). These metrics
vary in accuracy and computational speed see also [19].
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Andy M. Lau and Argyris Politis
different to the true experimental mass. Additional sequence
information can be found on UniProt for characterized entries.
8. Identified subcomplexes can be used to determine the connectivity based on its internal constituents. Start from the smallest
subcomplex and build up a network of additional subunits.
9. While density maps can be opened in PyMOL, the graphics
viewer Chimera is better suited for visualizing density maps and
possessed advanced functions for fitting structures into
maps, etc.
10. Structures can be fitted into density maps using Chimera’s “Fit
in Map” function. Open both the map and structures in Chimera. “Fit in Map” can be accessed from the Volume Viewer
window when a map file is open, under the “Tools” tab. You
may need to manually move the structure in close proximity of
the map file for better fitting.
11. The calculate_density.sh script can be opened using any text
editor. You will need to replace the “python¼”/anaconda2/
bin/python” line with the path to python for IMP on your
own system.
12. GMMs can be calculated for electron density maps as a sum of
three-dimensional gaussians. The shape of a structure in PDB
format can also be converted into a simulated volume, and
likewise converted into a GMM. The fit between each subunit
GMM can then be rapidly calculated against the GMM of the
complex. Consult the IMP documentation for more information on how GMMs are used.
13. The number of residues that are represented by a single bead is
set in the “topology.txt” file under “bead_size.”
14. See IMP documentation at: https://integrativemodeling.org/
talks/dec_2016_workshop/IMP%20software%20introduc
tion%20and%20tutorial.pdf for additional information on replica exchange simulations.
15. See IMP documentation at: https://integrativemodeling.org/
talks/dec_2016_workshop/Modeling%20of%20the%
20Nup84%20complex.pdf for more information on scoring
functions.
16. Consult the PyMOL documentation for the “Align” function:
https://pymolwiki.org/index.php/Align.
17. CCS can be calculated through four different metrics, these are
the projection approximation (PA), projection superposition
approximation (PSA) [48], exact hard sphere scattering
(EHSS), and trajectory method (TM or TJM). These metrics
vary in accuracy and computational speed see also [19].
238
Andy M. Lau and Argyris Politis