How long does it take to run cryo_fit?

How to enlarge map box size?

• Doo Nam uses relion_image_handler to change map box size.
• For example, relion_image_handler --i user.mrc --new_box 370 --o user_box_size_370.mrc
• However, relion_image_handler derived mrc file may not go through cryo_fit's automatic mrc to sit map format conversion properly.
• Therefore, please use situs map2map to convert your mrc format map to situs format map. You can convert by "map2map user.mrc user.sit" then enter 1 for "Convert to classic Situs (auto)*". Then, provide this user.sit file to your cryo_fit. For example, phenix.cryo_fit user.pdb user.sit
• When Doo Nam provided situs made sit map file, the cryo_fit ran smoothly again.

How to generate and record movie?

• Generate_record_movie_by_cryo_fit1

How to improve initial cc?

• dock_in_map or UCSF Chimera's 'fit in map' or UCSF ChimeraX's isolde may improve initial cc.

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 "Fatal error: A charge group moved too far between two domain decomposition steps. This usually means that your system is not well equilibrated" at my 8_cryo_fit step.

• 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 Doo Nam, simply using macOS solved the problem.

I see "Fatal error: Number of grid cells is zero. Probably the system and box collapsed." at my 8_cryo_fit step.

• step_8 may be full of stepxb_nx.pdb.
• Most likely, this means that initial cc is too low for MD simulation.
• When Doo Nam ran real_space_refine first, then run real_space_refined atomic model in cryo_fit, it was solved.
• Alternatively, improve initial cc by fitting initial atomic model into a map (see "How to improve initial cc?" in this FAQ)
• Less likely, but still a possible case is when the map weight is too high, lowering emweight_multiply_by may help.

I see "step 0 correlation coefficient: nan" at my 8_cryo_fit step.

• This often indicates that the initial atomic model is not placed into a cryo-EM map.
• Improve initial cc by fitting initial atomic model into a map (see "How to improve initial cc?" in this FAQ)

I see "step 0 correlation coefficient: nan" and "Range checking error: Explanation: During neighbor searching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again." at my 8_cryo_fit step.

• When a user didn't use phenix.map_box, relion_image_handler or gaussian filtering, it means that the map dimensions need to be larger. (see "When cryo_fit's automatic mrc to sit map format conversion may not work properly?" in this FAQ).

• Like other MD simulations, gromacs need enough map box size to cover the atomic model to run (ziggle and wiggle). Refer Waters seems to be out of the box

• For example, stuck-out red oxygen atoms outside the right edge of the box are the problem.

• 

• In order to run any MD simulation (including cryo_fit), a box should be large enough like

• 

• Make map box size larger (see "How to enlarge map box size?" in this FAQ), and run cryo_fit again. You can check map box size by VMD. Alternatively, remove sticking out atoms if these are unnecessary, then run cryo_fit again.

• For protein modeling, I would use cryo_fit2 which is not limited by box size requirement. Most of the time, it better fits than cryo_fit1 in terms of fitting and geometry preservation anyway.

I see "User's provided atomic model had 0.0 cc" in my cryo_fit.overall_log.

• If a user didn't use phenix.map_box, relion_image_handler or gaussian filtering, it means that literally user's provided atomic model has no correlation to map to start with.
• See "How to improve initial cc?" in this FAQ, and provide initially aligned atomic model to cryo_fit.

When cryo_fit's automatic mrc to sit map format conversion may not work properly?

• As Doo Nam have been used for more than 16 MRC format maps (mostly EMDB downloaded one) so far, cryo_fit's automatic mrc to sit map format conversion works perfectly for all cases (map origins are 0,0,0 or negative values or positive values). However, when a user used a particular map region ("boxed map") by phenix.map_box or changed map size by relion_image_handler, or gaussian filtered map by UCSF Chimera, cryo_fit's automatic mrc to sit map format conversion may not work properly.
• Therefore, please use situs map2map to convert your mrc format map to situs format map. You can convert by "map2map user.mrc user.sit" then enter 1 for "Convert to classic Situs (auto)*". Then, provide this user.sit file to your cryo_fit. For example, phenix.cryo_fit user.pdb user.sit
• When Doo Nam provided situs made sit map file, the cryo_fit ran smoothly again.