How to Make an Animation using Chimera

Tom Goddard
August 27, 2012
Bay Area cryoEM Meeting, Santa Cruz

Show how to create an animation to show a morph between two conformations of a ParM filament, morphing both the EM maps and fit molecular models. Use EMDB maps 5128, 5129 and PDB models 1mwm, 1mwk in ADP bound and unbound states.

Map Morph

  • Align maps 5128 and 5129.
  • Requires flipping one map end-to-end.
  • Use Fit in Map dialog.
  • Use Morph Map dialog to morph.
  • Grids of two maps must align.
  • vop resample #1 ongrid #0
  • Morph Map dialog Play.
  • Resize graphics window and Record.
  • windowsize 384 512
  • Playback in a movie player.
  • Use player loop option.
  • Make it slower by adding more frames.
  • Morph Map Options, step 0.02 gives 51 frames.
  • Record movie and playback.

Molecule Morph

  • Fetch 1mwm and 1mwk
  • Delete B chains.
  • Select / Chain / B, Actions / Atoms / Delete
  • Sequence based structure alignment.
  • MatchMaker dialog, match #5 to #4.
  • Note ADP ligand in 1mwm.
  • Morph Conformations dialog.
  • Add 1mwm, 1mwk and 1mwm to return to start, Create.
  • Play morph.
  • Simple domain motion.
  • Show ADP ligand.
  • Show 1mwm, select and hide ribbon.
  • Select ADP, Actions / Atom / show only.
  • Show as spheres.
  • Record movie. MD Movie File / Record.

Combined Map and Molecule Morph

  • Use commands to morph map and molecule at same time.
  • Fit 1mwm in emd 5128, ADP bound
  • Fit 1mwk in emd 5129, unbound
  • Play molecule and map morphs with commands

    coordset #6 1,100

    vop morph #0,2 start 0 playstep 0.01 frames 100 model #3

  • Run both commands separated by a semicolon.
  • Use command file movie1.cmd for movie recording.

    movie record
    coordset #6 1,100 ; vop morph #0,2 ...
    wait 100
    movie encode ~/Desktop/morph.mp4 roundtrip true

  • Use movie2.cmd with "movie record" after morph
    commands assure first frame of movie is at start of morph.
  • Show animation command examples web page.

Symmetric Molecule Morph

  • Create molecule symmetric copies.
  • Find map symmetry
    measure symmetry #0 helix 20,180,opt min .95
    gives rise per subunit 24.18 Angstroms,
    angle per subunit 165.3 degrees,
    center grid point 50,50,94
  • Make symmetric copies
    sym #6 group h,24.2,165.3,12,-6 coord #0
  • Color copies
    rainbow model #7 ; color pink #6
  • Display as spheres, no ribbon
    display #6,7 ; repr sphere #6,7 ; ~ribbon #6,7
  • Morphing original molecule does not update symmetric copies.
  • Update copies symmetric with
    mcopy #6 #7 set x.
  • Enable shadows.
  • Record movie with movie3.cmd
  • To update coordinates on every movie frame
    perframe "mcopy #6 #7 set x" frames 100
  • Recording takes a few minutes.
  • Large size movie

Symmetric Morph Movie - Large Size