Cryo_fit2 FAQ

Contents

How can I provide gaussian filtered maps?

  • For example, provide flexibile fitting a 4 Angstrom filtered map, 2 Angstrom filtered map, then non-filtered map.
  • Tools -> Volume Data -> Volume Viewer -> Tools -> Volume Filter -> (Set Width, e.g. 4,2) -> Filter
  • File -> Save map as -> (name a filtered map) -> Save

Is there a command line option for cryo_fit2 processing on multiple cores?

  • For example, phenix.cryo_fit2 nproc=40 model.pdb model.map resolution=3

My input (before cryo_fit2) and output (after cryo_fit2) pdb files have different molecule sizes

Although pdb text files show similar scales, input (before cryo_fit2) and output (after cryo_fit2) pdb files may show different molecule sizes in Pymol when Doo Nam used map that was made from phenix.map_box

Troubleshooting is ongoing.

In the meantime, please use UCSF chimera to visualize bio-molecules instead.

"RuntimeError: cctbx Error: Miller index not in structure factor map"

When a user sees above message, please consider to enter a correct resolution.

Doo Nam uses either EMDB reported resolution or phenix.mtriage derived resolution to properly run cryo_fit2.

"Sorry: Crystal symmetry mismatch between different files."

  • "Sorry: Crystal symmetry mismatch between different files.
  • (378, 378, 378, 90, 90, 90) P 1
  • (103.95, 91.35, 89.25, 90, 90, 90) P 1"
  • For example, when a wrong CRYST1 header exists above a correct CRYST1 header, this message appeared.