Instruct virtual course on Single Particle Analysis by CryoEM 2020 - I2PC/scipion-courses GitHub Wiki

Image Processing for Single Particle Analysis

• Theory. Although not necessary for performing the practice, you may find useful the following theoretical explanations about the operations being performed: Slides

  1. Basic image processing operations
  2. Micrograph acquisition and related ideas
  3. Particle selection and pruning
  4. Initial volume
  5. Random Conical Tilt
  6. 3D Reconstruction
  7. Validation
  8. 3D Heterogeneity
  9. Resolution

• Practice. For the practical work, we will use a few micrographs of apoferritin to reconstruct a 3A resolution structure of this macromolecule. If you have your own machine, you will need to install Scipion3 with the Xmipp, Cistem, Relion, Sphire, GCTF, and CryoSparc plugins (you will need to install the CryoSparc binaries before installing the plugin). You will find an explanation of the different parts of the workflow at:

  1. From movies to micrographs
  2. From micrographs to particles
  3. From particles to initial volume
  4. Particle classification and structure refinement
  5. Map enhancement

Tutorial PDF

Paper with an example workflow

You may download the solved project from here

Model Building Course Material

• Presentation

  • PPT presentation (model building)
  • Scipion model building tutorial

• Practical working sessions (General modeling workflow)

  1. Map Preprocessing
  2. From sequence to Model
  3. Rigid Fitting
  4. Flexible fitting - validation
  5. Chain merge & symmetrization
  6. Analysis: contacts

• Data resources and IDs

  • BlastP (search for homologues)
  • Human haemoglobin
    • 3D map: emd_3488.map, available directory Data
    • sequence:
      • alpha subunit: UniProt ID P69905 (Homologous sequences: P01958, P01948, P81023, P83134)
      • beta subunit: UniProt ID P68871 (Homologous sequences: P02062, P02057, G1U9Q8, P83133)
    • PDB reference: 1pbx (antartic fish: Pagothenia bernacchii)

• Coot Tutorial

  • 3D map
  • atomic model

• ChimeraX Tutorial

• EMDB submission link

  • Haemoglobin in PDB: ID 5ni1
    • Haemoglobin PDB full validation report

• Contacts AD type V (Zhou)

Model Building Agenda