thepowerOfXmipp

Author: albertmena

docs/index.rst

@@ -90,8 +90,9 @@ the main repository is required and also the installation of the plugins.
     :hidden:
     :caption: Others
 
+    thePowerOfXmipp
     listOfPublications
-    enhancingXmipp
     history
+    enhancingXmipp
     contact
     license

docs/thePowerOfXmipp.rst

@@ -0,0 +1,99 @@
+.. _thePowerOfXmipp:
+
+===============================
+Importance of Xmipp in Cryo-EM
+===============================
+
+Xmipp is a key software suite in the image processing workflow for cryo-electron microscopy (cryo-EM) single-particle analysis. Its modular protocols and deep integration with Scipion enable users to handle the complexity of cryo-EM data and achieve high-resolution 3D reconstructions.
+
+This page highlights the relevance of Xmipp through two concrete examples: **ClpC1P1P2** and **HER2-TZB**. In both cases, Xmipp protocols played a critical role in various stages of data processing, from preprocessing and particle selection to final 3D refinement and validation.
+
+.. contents::
+   :local:
+   :depth: 2
+
+-------------------------
+Xmipp Contributions at a Glance
+-------------------------
+
+- Robust CTF estimation and correction protocols
+- Automated and deep learning-based particle picking
+- Advanced 2D classification and 3D reconstruction tools
+- Postprocessing with deep learning (e.g., `emhancer`)
+- Flexible integration of masks, volumes, and structural validation
+
+=========================
+Example: ClpC1P1P2 Project
+=========================
+
+.. admonition:: Project Summary
+
+   - **Protein**: *[To be completed]*
+   - **Final Resolution**: *[To be completed]*
+   - **Number of Movies**: *[To be completed]*
+   - **EMDB ID**: *[To be completed]*
+   - **Resolution Method**: *[To be completed]*
+   - **Xmipp Version**: *[To be completed]*
+
+.. rubric:: Protocols Used
+
+- **CTF Estimation and Consensus**:
+  - `CTFConsensus`
+- **Particle Picking**:
+  - `ConsensusPicking`
+- **Micrograph Quality Control**:
+  - `DeepMicrographScreen`
+- **3D Postprocessing**:
+  - `XmippProtDeepVolPostProc`
+  - `emhancer`
+- **Masking**:
+  - `Create3DMask`
+
+=======================
+Example: HER2-TZB Project
+=======================
+
+.. admonition:: Project Summary
+
+   - **Protein**: *[To be completed]*
+   - **Final Resolution**: *[To be completed]*
+   - **Number of Movies**: *[To be completed]*
+   - **EMDB ID**: *[To be completed]*
+   - **Resolution Method**: *[To be completed]*
+   - **Xmipp Version**: *[To be completed]*
+
+.. rubric:: Protocols Used
+
+- **CTF Correction**:
+  - `XmippProtCTFCorrectWiener2D`
+- **Volume Processing and Refinement**:
+  - `XmippProtAlignVolumeParticles`
+  - `XmippProtReconstructFourier`
+  - `XmippProtPreprocessVolumes`
+  - `XmippProtFilterVolumes`
+  - `XmippProtMaskVolumes`
+  - `XmippProtMonoRes`
+  - `XmippProtStructureMap`
+  - `XmippProtSubtractProjection`
+- **Particle Handling**:
+  - `XmippProtCropResizeParticles`
+- **3D Visualization and Validation**:
+  - `XmippProtCompareAngles`
+  - `XmippProtCompareReprojections`
+  - `XmippProtConsensusClasses`
+  - `XmippProtCreateGallery`
+  - `XmippProtCreateMask3D`
+  - `XmippProtFSO`
+- **Postprocessing**:
+  - `emhancer`
+- **Model Integration**:
+  - `XmippProtConvertPdb`
+
+======================
+Conclusion
+======================
+
+The two projects above exemplify how Xmipp provides a comprehensive toolbox that supports end-to-end cryo-EM workflows. From CTF correction to final volume polishing and validation, Xmipp’s protocols are critical in producing reliable, reproducible, and high-quality structural data.
+
+Future developments in Xmipp continue to incorporate state-of-the-art techniques such as deep learning, automation, and hybrid modeling to push the boundaries of cryo-EM analysis.
+