Cryo_fit2 FAQ

Contents

How can I provide gaussian filtered maps?

  • For example, flexibily fit with a 4 Angstrom filtered map. Then with the resultant atomic model and a 2 Angstrom filtered map, do flexible fitting. Then with the resultant atomic model and a non-filtered map, do final flexible fitting.
  • 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"

  • For example, 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"

  • The first line (378, ...) shows unit cell parameters from model.

  • The second line (103.95, ...) shows unit cell parameters from map.

  1. Just erase CRYST1 header information from an input pdb file. Then, provide that input file into cryo_fit2.
  • Cryo_fit2 will automatically extract CRYST1 header from map (both from original map and phenix.map_box derived map), and prepend (write at the first line) to the pdb file.
  1. (Alternatively) Just leave correct CRYST1 header only in an input pdb file.
  • For example, when a wrong CRYST1 header exists above a correct CRYST1 header, above error message appeared.