# Data Processing Tutorials

## Case Studies

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th><th></th><th data-hidden data-card-cover data-type="image">Cover image</th><th data-hidden data-type="content-ref"></th><th data-hidden data-card-target data-type="content-ref"></th></tr></thead><tbody><tr><td><h3><a href="/pages/4DK1c0flbMqNyUuQPWgB">End-to-end processing of a motor-bound nucleosome part 1</a></h3></td><td>Processing EMPIAR-10739 including handling global pseudosymmetry, using 3DVA to guide classification strategies, separating low population classes, and local refinement of a flexible region.</td><td></td><td data-object-fit="contain"><a href="/files/2d2SKcIuX9f5COs9IQRd">/files/2d2SKcIuX9f5COs9IQRd</a></td><td></td><td><a href="/pages/4DK1c0flbMqNyUuQPWgB">/pages/4DK1c0flbMqNyUuQPWgB</a></td></tr><tr><td><h3><a href="/pages/3WJk4qRcDrSuOzCVmFAg">Processing of a motor-bound nucleosome part 2</a></h3></td><td>Processing EMPIAR-10739 including using 3DVA to guide classification strategies, separating low population classes, and local refinement of a flexible region.</td><td></td><td><a href="/files/8uu3Ar4VbSSbm9B4vp6T">/files/8uu3Ar4VbSSbm9B4vp6T</a></td><td></td><td></td></tr><tr><td><h3><a href="/pages/mjewEqrnK9WuE2Raf6R6">End-to-end processing of a ligand-bound GPCR</a></h3></td><td>Processing EMPIAR-10853 including Micrograph Denoising, Micrograph Junk Detector, Subset Particles by Statistic, Local Refinement and focussed 3D Classification to improve ligand density.</td><td></td><td><a href="/files/gcRBU5f29vP369F9yw5w">/files/gcRBU5f29vP369F9yw5w</a></td><td><a href="/pages/mjewEqrnK9WuE2Raf6R6">/pages/mjewEqrnK9WuE2Raf6R6</a></td><td></td></tr><tr><td><h3><a href="/pages/sPjOzQinmEGFBAjyLz8S">DkTx-bound TRPV1</a></h3></td><td>Processing EMPIAR-10059 in CryoSPARC v4.6 with a focus on particle curation, developing an intuition for when a domain may be blurred due to flexibility, and how to handle this type of flexibility.</td><td></td><td><a href="/files/bUAwx9ZHcxHgGzV7ARYM">/files/bUAwx9ZHcxHgGzV7ARYM</a></td><td><a href="/pages/sPjOzQinmEGFBAjyLz8S">/pages/sPjOzQinmEGFBAjyLz8S</a></td><td></td></tr><tr><td><h3><a href="/pages/k2zVBwZGu4WxnEDngKCT">Pseudosymmetry in TRPV5 and Calmodulin</a></h3></td><td>Processing EMPIAR-10256 with a focus on handling pseudosymmetry and 3D Classification parameter choices.</td><td></td><td><a href="/files/jGDoShTgWxL4AW3QNeEX">/files/jGDoShTgWxL4AW3QNeEX</a></td><td><a href="/pages/k2zVBwZGu4WxnEDngKCT">/pages/k2zVBwZGu4WxnEDngKCT</a></td><td></td></tr><tr><td><h3><a href="/pages/m6GUfEFLNzJhCrZhxwPO">End-to-end processing of an inactive GPCR</a></h3></td><td>Processing EMPIAR-10668 including Local Refinement, 3D Variability Analysis, 3D Flex and classification of continuous heterogeneity.</td><td></td><td><a href="/files/iVPSC48MJIELTU5Gzu4L">/files/iVPSC48MJIELTU5Gzu4L</a></td><td><a href="/pages/m6GUfEFLNzJhCrZhxwPO">/pages/m6GUfEFLNzJhCrZhxwPO</a></td><td></td></tr><tr><td><h3><a href="/pages/uSjph7wwSZP12yUe8mXH">End-to-end processing of encapsulated ferritin</a></h3></td><td>Processing EMPIAR-10716 with a focus on high-symmetry ab-initio reconstruction, local symmetry, non-point-group symmetry, symmetry expansion, and custom geometry operations.</td><td></td><td><a href="/files/mtKeNpiLp6AxKDOnObmg">/files/mtKeNpiLp6AxKDOnObmg</a></td><td><a href="/pages/uSjph7wwSZP12yUe8mXH">/pages/uSjph7wwSZP12yUe8mXH</a></td><td></td></tr><tr><td><h3><a href="/pages/2vRqETj7q0imlrns509A">Discrete and Continuous Heterogeneity in FaNaC1</a></h3></td><td>Processing a combined dataset of an ion channel with a focus on techniques for separating conformational states from a heterogeneous mixture.</td><td></td><td><a href="/files/tsuNYxF3GAEWWI59jUua">/files/tsuNYxF3GAEWWI59jUua</a></td><td></td><td></td></tr><tr><td><h3><a href="/pages/qOhy6Q0LrgULvhCazyRy">Picking-induced Orientation Bias in HA Trimer</a></h3></td><td>An analysis of the impact of data collection and particle picking techniques on orientation bias, including strategies for improving map quality and isotropy.</td><td></td><td><a href="/files/KAD2JAllQHA7oLSPcBkn">/files/KAD2JAllQHA7oLSPcBkn</a></td><td><a href="/pages/qOhy6Q0LrgULvhCazyRy">/pages/qOhy6Q0LrgULvhCazyRy</a></td><td></td></tr><tr><td><h3><a href="/pages/-MNjFTF5FhkP5zghzFtY">Yeast U4/U6.U5 tri-snRNP</a></h3></td><td>Processing EMPIAR-10073 with a focus on Local Refinement.</td><td></td><td><a href="/files/O2b6TG6YJT7zqLq4JpYt">/files/O2b6TG6YJT7zqLq4JpYt</a></td><td><a href="/pages/-MNjFTF5FhkP5zghzFtY">/pages/-MNjFTF5FhkP5zghzFtY</a></td><td></td></tr><tr><td><h3><a href="/pages/73gA7nYg30JfPluMiNVC">Exploratory data processing by Oliver Clarke</a></h3></td><td>Friendly, approachable introductions to cryoEM data processing in CryoSPARC with a focus on the exploratory, "try-it-and-see" nature of single-particle analysis. Kindly reproduced from Oliver Clarke, PhD, Assistant Professor of Physiology and Cellular Biophysics at Columbia University.</td><td></td><td><a href="/files/9BvUpoyA39335qu9ApHq">/files/9BvUpoyA39335qu9ApHq</a></td><td><a href="/pages/73gA7nYg30JfPluMiNVC">/pages/73gA7nYg30JfPluMiNVC</a></td><td></td></tr><tr><td><h3><a href="/pages/rLYf1CfmwVBS1dbAITXx">Tips for Membrane Protein Structures</a></h3></td><td>Helpful hints for processing cryo-EM data of membrane proteins.</td><td></td><td><a href="/files/wyJjwoFvWn8KB8t0Ti2v">/files/wyJjwoFvWn8KB8t0Ti2v</a></td><td><a href="/pages/rLYf1CfmwVBS1dbAITXx">/pages/rLYf1CfmwVBS1dbAITXx</a></td><td></td></tr><tr><td><h3><a href="/pages/gRLLQK0W1HuKs63dv8GH">Common CryoSPARC Plots</a></h3></td><td>A detailed description of the common plots that CryoSPARC makes across multiple job types.</td><td></td><td><a href="/files/L9NZoSXnRUsFlVu3TuIZ">/files/L9NZoSXnRUsFlVu3TuIZ</a></td><td><a href="/pages/gRLLQK0W1HuKs63dv8GH">/pages/gRLLQK0W1HuKs63dv8GH</a></td><td></td></tr></tbody></table>

<table data-view="cards"><thead><tr><th></th></tr></thead><tbody><tr><td></td></tr></tbody></table>

## Data Processing

Alongside these tutorials, see: [**All Job Types in CryoSPARC**](/processing-data/all-job-types-in-cryosparc.md) and [**Tutorial Videos**](/processing-data/tutorial-videos.md)

### Files, Data and Import

{% content-ref url="/pages/-MM2Iwf9GZlJg-2WCA6n" %}
[Tutorial: Negative Stain Data](/processing-data/tutorials-and-case-studies/negative-stain-data.md)
{% endcontent-ref %}

{% content-ref url="/pages/-MM2JgV53bh37kaK6691" %}
[Tutorial: Phase Plate Data](/processing-data/tutorials-and-case-studies/phase-plate-data.md)
{% endcontent-ref %}

{% content-ref url="/pages/-MNf0RAgQryuEQo1LJej" %}
[Tutorial: EER File Support](/processing-data/tutorials-and-case-studies/tutorial-eer-file-support.md)
{% endcontent-ref %}

{% content-ref url="/pages/O7wX3crcWUMcxccpBwWT" %}
[Tutorial: EPU AFIS Beam Shift Import](/processing-data/tutorials-and-case-studies/tutorial-epu-afis-beam-shift-import.md)
{% endcontent-ref %}

### Preprocessing

{% content-ref url="/pages/-MNeA4BFZRumxWAGw8dk" %}
[Tutorial: Patch Motion and Patch CTF](/processing-data/tutorials-and-case-studies/tutorial-patch-motion-and-patch-ctf.md)
{% endcontent-ref %}

{% content-ref url="/pages/m2ZKPnYFV34AIV6sIefG" %}
[Tutorial: Float16 Support](/processing-data/tutorials-and-case-studies/tutorial-float16-support.md)
{% endcontent-ref %}

### Particle Picking

{% content-ref url="/pages/-MNeDNqIMQeFUtOTFpvN" %}
[Tutorial: Particle Picking Calibration](/processing-data/tutorials-and-case-studies/tutorial-particle-picking-calibration.md)
{% endcontent-ref %}

{% content-ref url="/pages/cSD5FBtQRcgoYTmHkjWX" %}
[Tutorial: Blob Picker Tuner](/processing-data/tutorials-and-case-studies/tutorial-blob-picker-tuner.md)
{% endcontent-ref %}

### Helical Reconstruction

{% content-ref url="/pages/-MNekGUdpWzfm6xme2fe" %}
[Tutorial: Helical Processing using EMPIAR-10031 (MAVS)](/processing-data/tutorials-and-case-studies/case-study-empiar-10031-mavs.md)
{% endcontent-ref %}

### 3D Refinement

{% content-ref url="/pages/-MZ-Mm2KJuLeZJ-8NCvi" %}
[Tutorial: Maximum Box Sizes for Refinement](/processing-data/tutorials-and-case-studies/performance-metrics.md)
{% endcontent-ref %}

{% content-ref url="/pages/-MNdq-d6IKp2p3NX\_b87" %}
[Tutorial: CTF Refinement](/processing-data/tutorials-and-case-studies/tutorial-ctf-refinement.md)
{% endcontent-ref %}

{% content-ref url="/pages/nsV1YOZcx5U2geBUT0ap" %}
[Tutorial: Ewald Sphere Correction](/processing-data/tutorials-and-case-studies/tutorial-ewald-sphere-correction.md)
{% endcontent-ref %}

{% content-ref url="/pages/EFRgNeFzebTiZ7rzBN1U" %}
[Tutorial: Symmetry Relaxation](/processing-data/tutorials-and-case-studies/tutorial-symmetry-relaxation.md)
{% endcontent-ref %}

{% content-ref url="/pages/BlTU0FWtTYObbHEhP0F9" %}
[Tutorial: Orientation Diagnostics](/processing-data/tutorials-and-case-studies/tutorial-orientation-diagnostics.md)
{% endcontent-ref %}

{% content-ref url="/pages/9Hdb2qihpbWXTMd2NEub" %}
[Tutorial: BILD files](/processing-data/tutorials-and-case-studies/tutorial-bild-files.md)
{% endcontent-ref %}

### Local Refinement

{% content-ref url="/pages/-MM26XPCiAGx3PYLvmk\_" %}
[Tutorial: Mask Creation](/processing-data/tutorials-and-case-studies/mask-selection-and-generation-in-ucsf-chimera.md)
{% endcontent-ref %}

### Conformational Variability

{% content-ref url="/pages/3ytGpVHpfQKk7d22drrF" %}
[Tutorial: 3D Classification](/processing-data/tutorials-and-case-studies/tutorial-3d-classification.md)
{% endcontent-ref %}

{% content-ref url="/pages/-MNpORbZunrx-oW5myhV" %}
[Tutorial: 3D Variability Analysis (Part One)](/processing-data/tutorials-and-case-studies/tutorial-3d-variability-analysis-part-one.md)
{% endcontent-ref %}

{% content-ref url="/pages/-MNux9zxgGymFEewpZ3m" %}
[Tutorial: 3D Variability Analysis (Part Two)](/processing-data/tutorials-and-case-studies/tutorial-3d-variability-analysis-part-two.md)
{% endcontent-ref %}

{% content-ref url="/pages/tJUJijPRuOI8t3kB0MNV" %}
[Tutorial: 3D Flexible Refinement](/processing-data/tutorials-and-case-studies/tutorial-3d-flexible-refinement.md)
{% endcontent-ref %}

{% content-ref url="/pages/63kKkK7nvLpPDmOx6PEI" %}
[Tutorial: 3D Flex Mesh Preparation](/processing-data/tutorials-and-case-studies/tutorial-3d-flex-mesh-preparation.md)
{% endcontent-ref %}


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