10. The N available GPUs are typically numbered from 0 to (N-1).
The command “nvidia-smi” can be used to see which NVIDIA GPUs are available on your computer.
11. The minimum amount of MPI processes to use in (multi-body)
refinement in RELION is 3 because each of the gold-standard
half-sets is executed on a different MPI worker, and one process is reserved for the master. Provided you have enough
RAM, you may increase the number of MPI processes. It is
best to keep the total number of MPI processes an odd number, so that equal amounts of MPI workers work on both
halves of the data.
12. The total amount of required RAM is difficult to predict. An
important part of the required RAM scales linearly with the
number of bodies, but this changes to quadratic scaling if all
bodies overlap with each other. For this example, the RAM
requirements were up to 13 GB for the workers and approximately 6 GB for the master.
13. Using even more threads than available cores on your computer may lead to further, minor speed-ups, as not all threads
will always be occupied at the same time.
14. Multi-body refinement does not write out a single map that
somehow combines the individual bodies, as such map would
not represent the heterogeneity in the data (also see Notes 19
and 20).
15. STAR files with the modulation transfer function for commonly used detectors can be downloaded from the RELION
Wiki. In the example shown here, the data were collected on a
K2 detector at 300 kV.
16. In the “Post-processing” job-type, resolution estimation
within a mask region is performed using high-resolution phase
randomization [12]. In the FSC plot of the output “logfile.
pdf” (Fig. 3), the FSC between the two unmasked half-maps is
shown in green. The FSC between the two half-maps to which
the solvent mask has been applied is shown in blue. Typically,
the blue curve has higher FSC values than the green curve.
There are two reasons for this. Firstly, by removing noise from
the solvent, and from errors in the subtraction of the other
bodies, application of the solvent mask improves the signal-tonoise ratio of the half-maps. Secondly, because application of
the solvent mask comprises a multiplication operation in
real-space, Fourier-space components from different spatial
frequencies will be mixed together through convolution. In
particular, mixing of larger and better-correlating Fourier components at lower spatial frequencies with smaller and worsecorrelating components at higher spatial frequencies will lead
to an inflation of the FSC curve. Application of the
156
Takanori Nakane and Sjors H. W. Scheres
The command “nvidia-smi” can be used to see which NVIDIA GPUs are available on your computer.
11. The minimum amount of MPI processes to use in (multi-body)
refinement in RELION is 3 because each of the gold-standard
half-sets is executed on a different MPI worker, and one process is reserved for the master. Provided you have enough
RAM, you may increase the number of MPI processes. It is
best to keep the total number of MPI processes an odd number, so that equal amounts of MPI workers work on both
halves of the data.
12. The total amount of required RAM is difficult to predict. An
important part of the required RAM scales linearly with the
number of bodies, but this changes to quadratic scaling if all
bodies overlap with each other. For this example, the RAM
requirements were up to 13 GB for the workers and approximately 6 GB for the master.
13. Using even more threads than available cores on your computer may lead to further, minor speed-ups, as not all threads
will always be occupied at the same time.
14. Multi-body refinement does not write out a single map that
somehow combines the individual bodies, as such map would
not represent the heterogeneity in the data (also see Notes 19
and 20).
15. STAR files with the modulation transfer function for commonly used detectors can be downloaded from the RELION
Wiki. In the example shown here, the data were collected on a
K2 detector at 300 kV.
16. In the “Post-processing” job-type, resolution estimation
within a mask region is performed using high-resolution phase
randomization [12]. In the FSC plot of the output “logfile.
pdf” (Fig. 3), the FSC between the two unmasked half-maps is
shown in green. The FSC between the two half-maps to which
the solvent mask has been applied is shown in blue. Typically,
the blue curve has higher FSC values than the green curve.
There are two reasons for this. Firstly, by removing noise from
the solvent, and from errors in the subtraction of the other
bodies, application of the solvent mask improves the signal-tonoise ratio of the half-maps. Secondly, because application of
the solvent mask comprises a multiplication operation in
real-space, Fourier-space components from different spatial
frequencies will be mixed together through convolution. In
particular, mixing of larger and better-correlating Fourier components at lower spatial frequencies with smaller and worsecorrelating components at higher spatial frequencies will lead
to an inflation of the FSC curve. Application of the
156
Takanori Nakane and Sjors H. W. Scheres