Cryo_fit1 FAQ
- 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.
- 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