Function of the program:   Cut the pifmap by radius or by input Row, Column, or Section numbers At the edge of cut, it can apply soft cut of Gaussian function.

Purpose of the program:   Remove the center nucleic acid to generate shell density. Change map dimensions for new reconstructions.

Usage of the program:

• Usage: cutpifmap [option] inFile outFile

• Options:

  Options	explanations
  -imin[imum] inside_minimum_radiu	inside minimum radiu in voxel,default 0
  -imax[imum] inside_maximum_radiu	inside maximum radiu in voxel, If not input, no inside shell will be cut
  -omin[imum] outside_minimum_radiu	outside minimum radiu in voxel If not input, no outside shell will be cut
  -omax[imum] outside_maximum_radiu	outside maximum radiu in voxel, default radiu of the map
  -q	working quitely,without intermediate output
  -s	Soft edge cut using the default pameter,also see -e Default soft_cut_step=3.0;edge_cut_weight=0.000001
  -e soft_cut_step edge_cut_weight	Soft cut parameters,after soft_cut_step grids(voxel) the weight drops to edge_cut_weight
  -f fill_value	fill the cut with the fill_value,default 0.0
  -t dimension	global (x,y,z) truncate the map to the dimension
  -xmin[imum] X(row)_minimun	Truncate start with X(row)_minimun
  -xmax[imum] X(row)_maximun	Truncate end with X(row)_maximun
  -ymin[imum] Y(col)_minimun	Truncate start with Y(col)_minimun
  -ymax[imum] Y(col)_maximun	Truncate end with Y(col)_maximun
  -zmin[imum] Z(sec)_minimun	Truncate start with Z(sec)_minimun
  -zmax[imum] Z(sec)_maximun	Truncate end with Z(sec)_maximun
  -h	Print the help, no calculation

• Example for CUTPIFMAP:

  cut inside nucleic acid and outside empty noise:	cutpifmap -imax 40 -omin 60 final.map final_cut.map
  Do a global truncation of the map:	cutpifmap -t 300 final.map final_cut.map
  Do a truncation of the map:	cutpifmap -xmin 175 -xmax 275 -ymin 106 -ymax 256 -zmin 245 -zmax 285 final.map final_cut.map
  X-plor SF -> PIFMAP:	mapfft -B -x -p 3.00 -d 251 map.xpl map.pif