How long does it take to run cryo_fit?

How to generate and record movie?

Generate_record_movie_by_cryo_fit1

I see an error message at my 1_make_gro step.

• If a user sees "Fatal error: Atom xx in residue xx xxx was not found in rtp entry xx with xx atoms while sorting atoms." on his/her screen,
  • please remove/fix wrong atoms. Running real_spaace_refine via phenix GUI will show which atoms need to be removed/fixed.

I see an error message at my 8_cryo_fit step.

• If a user sees "Fatal error: A charge group moved too far between two domain decomposition steps. This usually means that your system is not well equilibrated" in his/her md.log file,
  • using macOS 10.13.6 helped rather than using Ubuntu 16.04. Maybe macOS has better numerical stability.
  • One gromacs expert suggested to try smaller time_step_for_cryo_fit.
  • However but for Doonam, simply using macOS solved the problem.
• If a user sees "Fatal error: Number of grid cells is zero. Probably the system and box collapsed." in his/her md.log file,
  • step_8 may be full of stepxb_nx.pdb.
  • Most likely, this means that initial cc is too low for MD simulation.
  • When Doonam ran real_space_refine first, then run real_space_refined atomic model in cryo_fit, it was solved.
  • Alternatively, UCSF Chimera's 'fit in map' or UCSF ChimeraX's isolde may improve initial cc.
  • Less likely, but still a possible case is when the map weight is too high, lowering emweight_multiply_by may help.
• If a user sees "step 0 correlation coefficient: nan" in his/her md.log file,
  • this often indicates that the initial atomic model is not placed into a cryo-EM map.
  • Try dock_in_map or UCSF Chimera's fit in map