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."

When a user sees a message like

"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"

please leave correct CRYST1 header only into a input pdb file.

For example, when a wrong CRYST1 header exists above a correct CRYST1 header, this message appeared.