How to generate and record movie by cryo_fit1?

Contents

Pymol (confirmed with version 2.2.2)

  1. [command] cd output/trajectory
  2. [command] load trajectory.gro, mytraj
  3. [command] load_traj traj.xtc, mytraj
  4. Click salmon color play button (triangle) in right bottom to play

(reference) https://pymolwiki.org/index.php/Load_Traj

UCSF Chimera (confirmed with version 1.13 and 1.14)

  1. [menu] Tools -> MD/Ensemble analysis -> MD Movie -> Trajectory format = GROMACS
  2. Run input (.tpr) = output/trajectory/for_cryo_fit.tpr
  3. Trajectory (.xtc) = output/trajectory/traj.xtc
  4. OK
  5. (optional)
  • [menu] Tools -> Depiction -> Rainbow -> OK
  • [menu] File -> Open -> .../user.mrc (set opacity into 50%)
  • [menu] Presets -> Publication 1
  1. (in MD Movie) click black play button to play
  2. (in MD Movie) File -> Record Movie, to record as .mp4 file

UCSF ChimeraX (confirmed with version 0.7 and 0.8 (2018-08-14))

  1. [menu] File -> Open -> .../output/cryo_fitted_chain_recovered_cleaned_for_real_space_refine_molprobity.pdb
  2. [command] rainbow
  3. [menu] File -> Open -> .../user.map (set opacity into 50%)
  4. [command] cd <user_path>/output/trajectory
  5. [command] open traj.xtc structureModel #1

(note) Specified structure and coordinates should have the same number of atoms, if these are mismatched, Doo Nam recommends to use UCSF Chimera instead

  1. [command] coordset slider #1
  2. Click black play button to play
  3. Click red record button to record movie as .mp4 file

VMD (confirmed with version 1.9.3)

  1. [menu] File -> New Molecule -> Browse -> (.../user.map) -> Load
  2. [menu] Graphics -> Representation -> Draw -> Solid Surface
  3. [menu] Graphics -> Representation -> Material -> Transparent
  4. [menu] Graphics -> Representation -> Show -> Isosurface
  5. [menu] File -> New Molecule -> Browse -> (output/trajectory/trajectory.gro) -> Load

Note