xmipp3.protocols.protocol_rotate_volume module

class xmipp3.protocols.protocol_rotate_volume.XmippProtRotateVolume(**kwargs)

Bases: EMProtocol

Rotates a 3D volume around the x, y, and z axes by specified angles. This protocol allows flexible repositioning of volumes for alignment, comparison, or visualization.

AI Generated

## Overview

The Rotate Volume protocol creates a rotated copy of a 3D volume.

This protocol is useful when a map needs to be reoriented for visualization, comparison, presentation, or compatibility with another workflow. It does not perform a full volume alignment against another reference. Instead, it applies a user-defined geometrical transformation to a single input volume.

The protocol supports two rotation modes:

• aligning a selected axis with the Z axis;

• rotating the volume by a specified number of degrees around a selected axis.

The output is a new volume containing the rotated map. The original input volume is not modified.

## Inputs and General Workflow

The input is a single 3D volume.

The protocol reads the input volume file and runs the Xmipp geometry transformation program. Depending on the selected mode, it either aligns the chosen axis with the Z direction or rotates the volume around the chosen axis by the requested angle.

The resulting rotated volume is written as an MRC file and registered in Scipion as a new output volume.

The output volume copies the metadata from the input volume, including the sampling rate.

## Input Volume

The Volume parameter defines the map to be rotated.

This volume can be any Scipion volume object. The protocol uses the file name of the selected volume and creates a new rotated file.

The input volume should already be the map that the user wants to reorient. The protocol does not search for an optimal alignment and does not compare the volume with another map.

## Rotation Mode

The Rotation mode parameter controls the type of transformation.

There are two options:

Align with Z rotates the volume so that the selected axis is aligned with the Z axis.

rotate applies a rotation by a user-defined number of degrees around the selected axis.

The first option is useful when the user wants a principal direction or known axis to be oriented along Z. The second option is useful for explicit manual rotations.

## Axis

The Axis parameter defines the axis used by the selected rotation mode.

The available options are:

• X axis;

• Y axis;

• Z axis.

In Align with Z mode, the selected axis is the direction that will be aligned with the Z axis.

In rotate mode, the selected axis is the axis around which the volume will be rotated.

## Degrees

The Degrees parameter is used only when the rotation mode is rotate.

It defines the rotation angle, in degrees, applied around the selected axis. For example, selecting the Z axis and 90 degrees rotates the volume by 90 degrees around Z.

Positive and negative angles can be used to rotate in opposite directions, depending on the convention of the underlying geometry transformation.

## Output Volume

The main output is outputVolume.

This output is the rotated version of the input volume. It is written as rotated_vol.mrc in the protocol working directory.

The output volume copies the input volume metadata and keeps the same sampling rate. This means that the physical pixel size of the map is preserved after rotation.

The output can be used in later protocols just like any other volume.

## Interpretation of the Result

The output should be interpreted as the same density map in a different orientation.

No new structural information is created. No refinement, filtering, masking, or validation is performed. The transformation only changes the spatial orientation of the volume.

Because interpolation may be involved during rotation, repeated rotations should be avoided when possible. If several rotations are needed, it is better to apply the intended final rotation once rather than repeatedly rotating the same volume.

## Practical Recommendations

Use this protocol when you need to reorient a volume manually.

Use Align with Z when a known axis should be placed along the Z direction.

Use rotate when you know the explicit angle and axis required.

Check the output visually after rotation to confirm that the map is oriented as expected.

Avoid using this protocol as a substitute for volume alignment. If the goal is to align two maps to each other, use a dedicated volume-alignment protocol.

Keep the original input volume unchanged and use the rotated output for downstream steps that require the new orientation.

## Final Perspective

Rotate Volume is a simple geometry utility for reorienting 3D maps.

For biological users, its value is practical: it helps prepare maps for visualization, comparison, figure generation, or workflows that expect a particular orientation.

The protocol should be understood as a manual transformation tool. It preserves the map content and sampling rate while producing a new volume in the selected orientation.

createOutputStep()

rotateStep()