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Copy file name to clipboardExpand all lines: doc/quickstart/matching/constrained.rst
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@@ -115,11 +115,11 @@ To integrate orientational constraints, we need to ensure the template used for
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--sampling-rate 6.8 \
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--lowpass 15 \
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--box-size 60 \
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--align-axis 2 \
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--invert-contrast \
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--flip-axis
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--align-axis 2
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.. note::
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For NA we need to provide the ``--flip-axis`` flag due to the handedness of the alignment problem. When aligning a protein structure to a principal axis, the algorithm determines the orientation based on the distribution of mass around the center. However, this can result in two possible orientations that are 180° apart - the protein could point "up" or "down" along the chosen axis.
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In some cases we need to provide the ``--flip-axis`` flag due to the handedness of the alignment problem. When aligning a protein structure to a principal axis, the algorithm determines the orientation based on the distribution of mass around the center. However, this can result in two possible orientations that are 180° apart - the protein could point "up" or "down" along the chosen axis.
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After alignment, your templates should look similar to what is shown here, with the transmembrane region pointing in the direction of negative z and the extracellular domain pointing in direction of z
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mask_type="tube",
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shape=(60,60,60),
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symmetry_axis=2,
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base_center=(29,29,23.5),
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center=(29,29,23.5),
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inner_radius=0,
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outer_radius=10,
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height=37
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You can also constrain the rotational search to account for properties like template symmetry. For instance for the C3 symmetric HA, try replacing ``--angular-sampling 10`` with ``--cone-angle 180 --cone-sampling 10 --axis-symmetry 3``.
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The output of constrained template matching is a pickle file containing the score space and identified orientations. We can explore the score space in the ``preprocessor_gui.py`` using the **Import Pickle** button. Shown below is a comparison of HA and NA matching using constrained and unconstrained matching, respectively. Note the increase in peak sharpness and decreased contribution of the membrane density in constrained matching. Achieving more uniform matching scores for HA would require a more stringently created mask. In essence, HAs orthogonal to the missing wedge score lower, because applying a wedge mask to the template density stretches the template, and pushes a considerable amount outside the mask. Alternatively, background correction could be performed, for instance using ``--background-correction phase-scrambling``.
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The output of constrained template matching is a pickle file containing the score space and identified orientations. We can explore the score space in the ``preprocessor_gui.py`` using the **Import Pickle** button. Shown below is a comparison of HA and NA matching using constrained and unconstrained matching, respectively. Note the increase in peak sharpness and decreased contribution of the membrane density in constrained matching.
Copy file name to clipboardExpand all lines: doc/quickstart/postprocessing/motivation.rst
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@@ -108,7 +108,7 @@ In all cases, the tool will report statistics for foreground, background, and no
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> Background mean 0.089, std 0.023, max 0.234
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> Normalized mean 0.067, std 0.078, max 0.298
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Since the background of the individual entities may differ, we can also compare SNR-like cross-correlations instead, using ``--snr``. This is also useful when comparing the scores across an entire dataset.
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Since the background of the individual entities may differ, we can also compare SNR-like cross-correlations instead, using ``--snr``. This is also useful when comparing scores across an entire dataset.
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Local Optimization and Refinement
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Details for Developers
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----------------------
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The output of ``match_template.py`` is a `pickle <https://docs.python.org/3/library/pickle.html>`_ file. All but the last element will correspond to the return value of a given :doc:`analyzer </reference/analyzer/base>`'s merge method. The file can be read using :py:meth:`load_pickle <tme.matching_utils.load_pickle>`. For the default analyzer :py:class:`MaxScoreOverRotations <tme.analyzer.MaxScoreOverRotations>` the pickle file contains
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The output of ``match_template.py`` is a `pickle <https://docs.python.org/3/library/pickle.html>`_ file containing a tuple. All but the last element will correspond to the return value of a given :doc:`analyzer </reference/analyzer/base>`'s merge method. The file can be read using :py:meth:`load_pickle <tme.matching_utils.load_pickle>`. For the default analyzer :py:class:`MaxScoreOverRotations <tme.analyzer.MaxScoreOverRotations>` the pickle file contains
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- **Scores**: An array with scores mapped to translations.
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- **Offset**: Offset informing about shifts in coordinate sytems.
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- **Rotations**: An array of optimal rotation indices for each translation.
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- **Rotation Dictionary**: Mapping of rotation indices to rotation matrices.
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- **Scores**: Score for each position in the target.
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- **Offset**: Coordinate system shift.
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- **Rotations**: Optimal rotation index for each translation.
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- **Rotation Dictionary**: Dictionary mapping rotation indices to rotation matrices.
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- **Sum of Squares**: Sum of squares of scores for statistics.
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- **Metadata**: Coordinate system information and parameters for reproducibility.
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However, when you use the `-p` flag the output structure differs
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- **Translations**: A numpy array containing translations of peaks.
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- **Rotations**: A numpy array containing rotations of peaks.
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- **Scores**: Score of each peak.
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- **Details**: Additional information regarding each peak.
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- **Translations**: Peak position.
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- **Rotations**: Rotation matrix describing template orientation at peak.
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- **Scores**: Score at peak.
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- **Details**: Additional properties of peak.
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- **Metadata**: Coordinate system information and parameters for reproducibility.
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References
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----------
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.. [1] Heymann, J.B.; Chagoyen, M.; Belnap, D.M. Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology. J Struct Biol 2005, 151, 196-207.
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.. [1] Heymann, J.B.; Chagoyen, M.; Belnap, D.M. Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology. J Struct Biol 2005, 151, 196-207.
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