How can I provide gaussian filtered maps?

• Many people in flexible fitting field know that often providing gaussian filtered maps results in better fitting.

• 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.

• UCSF Chimera can generate these filtered maps.

• 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?

• Note that using multiple cores for cryo_fit2 is only useful when explore=True
• Like other PHENIX applications, specify nproc

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

• If nproc is not specified, cryo_fit2 will use 'available number of cores'/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, consider to enter a correct resolution.

• 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."

• Sometimes, Doo Nam observed,

• "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.

• Solutions

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.

2. (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.

When cryo_fit2 is useful?

• To model dynamic conformational change, cryo_fit2 is useful.
• To simply fit to cryo-EM map, cryo_fit seems to be useful when initial cc_mask and cc_box < 0.6. When initial cc_mask and cc_box >= 0.6, phenix.real_space_refine tends to do similar fitting with faster speed.