xmipp3.protocols.protocol_resolution_monogenic_signal module
- class xmipp3.protocols.protocol_resolution_monogenic_signal.XmippProtMonoRes(**args)[source]
Bases:
ProtAnalysis3DAssigns local resolution values to each voxel within a given 3D map, providing detailed insight into regional map quality. This aids in interpreting structural data by highlighting areas of varying resolution.
AI Generated
## Overview
The Local MonoRes protocol estimates the local resolution of a 3D cryo-EM map using the monogenic-signal approach.
Global resolution values summarize the reconstruction with a single number, but cryo-EM maps often have regions with different levels of detail. A rigid core may be well resolved, while flexible domains, peripheral regions, or poorly ordered parts may be resolved at lower resolution. Local MonoRes addresses this by assigning a local-resolution value to each voxel inside a mask.
The result is a 3D local-resolution map. Each voxel value represents the estimated resolution, in angstroms, at that position. Lower numerical values indicate better local resolution, while higher numerical values indicate poorer local resolution.
The protocol can estimate local resolution from a single full map or from two half maps. When half maps are used, the noise estimation can be performed from the difference between the two halves.
## Inputs and General Workflow
The protocol can work in two main modes:
using a single input volume;
using two half volumes.
The user may provide a binary mask. If no mask is provided, the protocol generates an approximate mask automatically by smoothing and thresholding the input volume.
The protocol then runs the Xmipp monogenic-signal local-resolution program over the selected resolution range. The output local-resolution map is registered in Scipion as a volume. A Chimera-oriented resolution map and a histogram of resolution values are also generated.
## Use Half Volumes
The Would you like to use half volumes? option controls whether the protocol uses one full map or two half maps.
If this option is disabled, the protocol estimates local resolution from the selected full map.
If this option is enabled, the protocol uses two half maps. This allows the noise estimation to be based on the difference between independently reconstructed halves, which is often preferable for validation-oriented local resolution analysis.
Use half maps when they are available and correctly associated with the reconstruction.
## Half Maps Stored with the Input Volume
When half-volume mode is enabled, the Are the half volumes stored with the input volume? option controls how the half maps are provided.
If this option is enabled, the user selects Input Half Maps, which is a volume object containing associated half-map file names. The protocol reads the two half maps from that volume.
If this option is disabled, the user must explicitly provide Volume Half 1 and Volume Half 2.
In both cases, the two half maps should have the same box size, sampling rate, origin, orientation, and processing state.
## Input Volume
When half-volume mode is disabled, the Input Volume parameter defines the map to be analyzed.
This map should be a reconstruction with a correct sampling rate and origin. The sampling rate is required to express local-resolution values in angstroms.
The map should be reasonably preprocessed for local-resolution analysis. Extremely noisy maps, maps with strong artifacts, or maps with inappropriate masking can produce unreliable local-resolution estimates.
## Binary Mask
The Binary Mask parameter defines the region in which local resolution is estimated.
The mask separates specimen from background. If the user provides a mask, the protocol binarizes it using the selected mask threshold. If no mask is provided, the protocol creates an approximate mask automatically by applying a Gaussian filter to the input volume and thresholding the result.
A good mask should include the molecular density while excluding solvent and irrelevant background. If the mask is too tight, it may remove real density. If it is too loose, background noise may affect the local-resolution estimate.
## Mask Threshold
The Mask threshold parameter is used when the provided mask is not already binary.
Mask values below the threshold are converted to 0, and values above the threshold are converted to 1. This creates the binary mask used by MonoRes.
The default threshold is 0.5, which is appropriate for many masks whose values range between 0 and 1.
If the input mask has a different intensity convention, the threshold may need to be adjusted.
## Automatic Mask Generation
If no mask is provided, the protocol generates one automatically.
It applies a real-space Gaussian-like low-pass filter to the input volume, then uses a threshold based on a fraction of the maximum filtered value. The result is binarized and used as the analysis mask.
This automatic mask is useful for quick analysis, but a carefully prepared user mask is usually preferable for final reporting.
Users should inspect the generated mask when possible, especially for maps with weak density, flexible regions, or strong background artifacts.
## Exclude Area
The Exclude Area parameter allows the user to provide an additional mask for a region that should be excluded from local-resolution estimation.
This is an advanced option. It may be useful when a particular part of the map, such as an artifact, contaminant, or region outside the biological molecule, should not influence the analysis.
The exclusion mask should be used carefully, because excluding biologically relevant density may bias the local-resolution interpretation.
## Resolution Range
The Resolution Range parameters define the range of resolutions tested by MonoRes.
The range is given in angstroms:
High defines the high-resolution end of the search;
Low defines the low-resolution limit;
Step defines the spacing between tested resolution values.
The protocol validates that a low-resolution limit is provided.
The step size controls how finely the resolution range is sampled. A smaller step gives finer resolution estimates but increases computation time. If no step is provided, the protocol uses a default value of 0.5 Å.
## Significance
The Significance parameter controls the statistical hypothesis tests used by MonoRes.
The default value is 0.95. This value determines how strict the method is when deciding whether signal at a given resolution is significant.
A higher significance level is more stringent. A lower value is more permissive, but may be more sensitive to noise.
Most users should start with the default value.
## Noise Estimation from Half Maps
When half maps are used, the Use noise inside protein? option controls how the noise distribution is estimated.
When enabled, the noise distribution is estimated inside the protein region by using the difference between the two half maps. This is recommended because it uses the independent half-map information to characterize noise in the region of interest.
If disabled, noise estimation follows the alternative behavior of the underlying MonoRes program.
For most half-map workflows, the recommended setting is to keep this option enabled.
## Gaussian Noise Assumption
The Consider noise gaussian? option tells the protocol to assume that the noise in the map follows a Gaussian distribution.
This assumption is often approximately reasonable, but it may not always hold. Noise in cryo-EM maps can be affected by reconstruction, masking, filtering, preferred orientation, and other processing effects.
This is an advanced option. Users should enable it only when they want the Gaussian-noise assumption used explicitly by the MonoRes calculation.
## Output Resolution Volume
The main output is resolution_Volume.
This output is a 3D volume where voxel values represent local resolution in angstroms. It is assigned the sampling rate and origin of the input map or half maps.
The volume can be visualized directly or used to color a cryo-EM map according to local resolution.
Lower values indicate regions estimated to have better local resolution. Higher values indicate regions estimated to have poorer local resolution.
## Chimera-Oriented Resolution Map
The protocol also produces a Chimera-oriented local-resolution map internally.
This version is used to compute the minimum and maximum resolution values reported in the protocol summary. It may also be useful for visualization depending on the workflow.
The summary reports the highest and lowest estimated local resolution values. Here, “highest resolution” corresponds to the smallest angstrom value.
## Histogram
The protocol creates a histogram of local-resolution values inside the output mask.
The histogram summarizes the distribution of resolution values across the map. This is useful because two maps may have the same global resolution but very different local-resolution distributions.
For example, one map may have a small well-resolved core and large poorly resolved regions, while another may have more uniform resolution throughout the structure.
## Interpreting the Local-Resolution Map
The local-resolution map should be interpreted as a spatial map-quality estimate.
Regions with better local resolution usually correspond to more rigid, well-ordered, and better-supported parts of the structure. Regions with worse local resolution may correspond to flexible domains, low occupancy, weaker alignment signal, preferred-orientation effects, or lower local particle support.
Local resolution should not be interpreted in isolation. It should be compared with the original density, half-map agreement, global FSC, map-model fit, and biological knowledge.
## Practical Recommendations
Use half maps when available, especially for validation-oriented analysis.
Provide a good binary mask for final analyses. Automatic masks are convenient, but user-defined masks are usually more reliable.
Set the low-resolution limit to cover the expected poorest local resolution in the map.
Use a step size of 0.5 Å as a practical starting point. Use smaller steps only when finer sampling is needed.
Keep the default significance value at first.
Inspect the output resolution map together with the original density. Check whether flexible, peripheral, or poorly ordered regions show worse local resolution, as expected.
Be cautious near mask boundaries, weak density, and regions affected by post-processing artifacts.
## Final Perspective
Local MonoRes is a local-resolution estimation protocol based on the monogenic signal.
For biological users, its main value is that it shows how map quality changes across the reconstruction rather than reducing the entire map to a single global resolution number.
The output local-resolution map is useful for interpreting structural features, identifying flexible or poorly resolved regions, guiding model building, and communicating regional confidence in a cryo-EM map.