xmipp3.protocols.protocol_normalize_strain module

class xmipp3.protocols.protocol_normalize_strain.XmippProtNormalizeStrain(**args)

Bases: ProtAnalysis3D

Normalize the local strain and rotations amongst several runs.

AI Generated

## Overview

The Normalize Strain protocol prepares consistent visualizations for several previous volume-strain analyses.

Volume-strain analysis can produce maps describing local deformation and local rotation between two volumes. When several strain calculations are performed, for example for different maps, different conformational transitions, or different processing conditions, each run may have its own numerical range of strain or rotation values.

If each result is visualized with an automatically chosen color scale, the same color may represent different numerical values in different runs. This can make comparisons misleading.

The purpose of this protocol is to normalize the visualization ranges across several strain-analysis runs. It finds the global minimum and maximum values across all selected runs and writes ChimeraX command files that use the same color scale for all of them.

The protocol does not recompute strain or local rotations. It only harmonizes the visualization of existing results.

## Inputs and General Workflow

The input is a set of previous Xmipp volume strain protocol runs.

For each selected run, the protocol reads the strain and local-rotation result maps produced by that run. It computes the overall minimum and maximum values across all selected runs.

It then creates ChimeraX command files for each run. These files open the corresponding final volume and the associated strain or local-rotation map, and apply a common rainbow color scale using the global minimum and maximum values.

This produces comparable visualizations across all selected strain analyses.

## Input Strain Calculations

The input strain calculations parameter should contain several completed Xmipp volume-strain runs.

Each selected run is expected to contain the standard output files generated by the strain protocol, including:

• the final volume used for visualization;

• the local-rotation map;

• the strain map.

This protocol assumes that those files already exist. If one of the selected runs is incomplete or does not contain the expected output files, the normalization cannot be performed correctly.

The selected runs should be comparable in biological and processing terms. For example, they may correspond to different conformational transitions of the same molecular system or to different reconstructions analyzed with the same strain workflow.

## Local Rotation Normalization

The protocol first normalizes the visualization of the local rotation maps.

For all selected runs, it reads the local-rotation result volume and determines the global minimum and maximum values. These values define a common color range for all local-rotation visualizations.

The resulting ChimeraX files make it possible to inspect local rotation across different runs using the same color scale.

This is important because local rotations can otherwise appear artificially larger or smaller depending only on the automatic scaling used in the viewer.

## Strain Normalization

The protocol also normalizes the visualization of the strain maps.

As with local rotation, it reads the strain result volume from each selected run and computes the overall minimum and maximum values across all runs. These global limits are then used to generate ChimeraX visualization commands.

This makes strain patterns visually comparable. A given color corresponds to the same strain value in all selected runs.

This is particularly useful when comparing whether one conformational change shows stronger local deformation than another, or whether strain is localized in similar regions across different analyses.

## ChimeraX Output Files

For each selected strain-analysis run and for each quantity, local rotation and strain, the protocol writes a ChimeraX command file.

Each command file opens the corresponding final volume and the associated strain or local-rotation map. The scalar map is hidden as a separate volume and used to color the final volume surface with a common color scale.

The color map is a rainbow scale, applied over the global minimum and maximum range computed from all selected runs. Colors are reversed so that the visual convention is consistent with the command generated by the protocol.

These ChimeraX files are the main practical output of the protocol.

## Why Common Color Scaling Matters

Common color scaling is essential when comparing several scalar maps.

If two strain maps are displayed with independent automatic scales, a red region in one map may correspond to a very different numerical value from a red region in another map. This can lead to incorrect visual conclusions.

By forcing all selected runs to use the same minimum and maximum range, this protocol makes visual comparison more meaningful.

The protocol is therefore especially useful for figures, reports, qualitative comparisons, and exploratory interpretation of multiple strain analyses.

## Interpretation of the Results

The protocol does not change the underlying strain or local-rotation values. It only changes how they are visualized.

After normalization, differences in color intensity between runs more directly reflect differences in the numerical values of the corresponding scalar maps.

However, interpretation still requires care. Stronger colors may reflect larger computed strain or rotation, but the biological meaning depends on the quality of the input volumes, the reliability of the deformation analysis, and the validity of comparing the selected runs.

## Practical Recommendations

Use this protocol after running several volume-strain analyses that you want to compare visually.

Select only runs that are biologically and methodologically comparable. Mixing unrelated systems or very different processing conditions may make the common scale difficult to interpret.

Use the generated ChimeraX command files to produce consistent figures across all selected runs.

Remember that this protocol normalizes visualization ranges, not the data themselves. The original strain and local-rotation maps remain unchanged.

Inspect both the strain and local-rotation visualizations. They describe different aspects of the deformation field and may highlight different regions.

## Final Perspective

Normalize Strain is a visualization-normalization protocol for comparing several previous strain-analysis results.

For biological users, its main value is interpretability. It ensures that color differences across multiple strain or local-rotation maps correspond to a shared numerical scale rather than to independent viewer settings.

This makes the protocol particularly useful when preparing comparative figures, evaluating multiple conformational transitions, or presenting strain analysis results in a consistent and visually reliable way.

normalize(what)