Rossmann's Lab

CUTPIFMAP

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.

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

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

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

If you meet any bugs or problems of the programs, please email xc@purdue.edu.