coot_tutorial - I2PC/scipion-courses GitHub Wiki

  • activate ccp4 commands: type in terminal -> source /home/ubuntu/scipion_model_building/ExternalSoftware/ccp4/ccp4-8.0/bin/ccp4.setup-sh
  • open coot: type in terminal -> coot
  • load data tutorial: calculate -> Load tutorial model and data (sometimes is in Extensions)
  • delete second map (display manager)
  • calculate map to sharpen/blur
  • set_show_intermediate_atoms_rama_markup(1) (polyhedral)
  • set_show_intermediate_atoms_rota_markup(1) (sphere)
  • set_do_coot_probe_dots_during_refine(1) (dot)

  • Edit preference

    • set sphere radius in which 3D map is shown: edit -> map parameters -> map radius -> 16
    • change steps: general - smooth recentering- 10
    • verbose icos: general - refinement tool bar - icos and text

  • Navigation:

    • Left-mouse Drag Rotate view
    • Middle-mouse Centre on atom // shit
    • Right-Mouse Drag Zoom in and out
    • Scroll-wheel Forward Increase map contour level
    • Scroll-wheel Backward Decrease map contour level
    • Shift Left-Mouse Label Atom

  • Set background color to white (good for papers): Edit → Background Colour → White

  • Go To Residue: CTRL-G 23A (goes to residue 23 in chain A)

  • You can toggle spin and rock the view with: CTRL-R

  • Validate:

  • RC constrains

  • Fix: 89A, 41A

  • calculate -> model (icon with text)

  • set all constrains

  • Icon:

    • Real space refine
    • Rigid body
    • Rotamer
    • Mutate
    • Add residue

  • validate: ramachandran, rotamer, density probe

  • calculate -> map sharpening ====== Assignment

  • load data tutorial: calculate -> Load tutorial model and data (sometimes is in Extensions)

  • open validate, ramachandran, rotamer, density probe

  • fix problem (real space refine zone, rotamers, mutate/delete)