<input file>

Get info/stats on this file

<input file>

Source file

<output file>

Destination file

[shrink=<div>]

Shrinks the image by an integral scaling factor, median filter

[scale=<factor>]

Rescales the image, generally used with clip=

[clip=<x,y,z[,xc,yc,zc]>]

Make the output have this size, no scaling

[fftclip=<x,y,z>]

Make the output have this size, rescaling by padding FFT

[rot=<alt,az,phi>]

Rotate the volume, angles in degrees

[rotspin=<n1,n2,n3,angle>]

Rotate the volume around axis (n1,n2,n3) by angle degrees

[trans=<dx,dy,dz>]

Translate the volume, before the rotation

[posttrans=<dx,dy,dz>]

Translate the volume, after the rotation

[center]

Centers volume using center of mass

[acfcen]

Centers volume using cross correlation with mirrored model

[apix=<A/pix>]

Specify the Angstr/pixel for S scaling

[origin=<x,y,z>]

Set the coordinates for the pixel (0,0,0)

[lp=<filt r>]

Gaussian lowpass filter, r in angstroms if apix defined, pixels if undef

[hp=<filt r>]

Arctan highpass filter

[tlp=<filt r>]

Gaussian/artan mix lowpass

[unhp=<filt r>]

Undoes the hp= filter

[filefilt=<file>]

Applies a filter defined by an x/y text file

[rfilt=<type>[,<val1>[,<val2>[,<val3>]]]]

Apply one of a variety of real-space filters

[blfilt=<sigma spa,sigma den,iter,localwidth>]

Apply bilateral filtering

[normfilt=<thr,filt>]

This filter attempts to perform a 'local normalization' so low density and high density features will be on a more even playing field in an isosurface display. Thr is an isosurface threshold at which all desired features are visible, filt is a normalization size similar to an lp= value

[axialfilt=<filt r>]

This filter applies a correction for cases where reconstructions with many 'side' views have produced an asymmetric resolution. Specify the gaussian resolution in the z direction.

[flip]

Mirrors the object across the x-y plane

[yflip]

Mirrors the object across the x-z plane

[sym=<c?,icos,etc>]

Applies the specified symmetry to the map

[mask=<radius>]

Applies a circular mask at the given radius

[imask=<radius>]

Applies an inside mask at the given radius

[automask=<thr1>,<thr2>]

Tries to mask out only interesting density

[automask2=<rad>,<thr>,<N>]

Same goal as automask

[maskfile=<file>]

Multiplies the input by the specified file using pixel indices(must be same size)

[maskfile2=<file>]

Multiplies the input by the specified file using pixel coordinates instead of pixel indices (can be different size) and use the original cube

[maskfile3=<file>]

Multiplies the input by the specified file using pixel coordinates instead of pixel indices (can be different size) and use the smaller cube of the two

[maskval=<int>]

Value to be used in a multi-valued masks

[mask1file=<file>]

This will take a file containing a set of masks and apply the first mask to the image

[maskresample=<ref file>]

Resample the input mask file to use the <ref file> apix, origin and size

[maskmerge=<mask file2>]

Merge the second mask file to the first mask

[cut1stquad]

Cut the first quad frin the map

[norm]

Normalizes the output, mean->0 sigma->1

[bin=<thresh>]

use the threshold value to turn the 3D map into a binary map

[bin2]

Turn any non-zero values into 1 to create a binary map

[mult=<constant>]

Scales the densities in the output

[add=<constant>]

Adds a constant to the densities

[noise=<level>]

Adds flatband noise at specified absolute level

[signoise=<sig mult>]

Same, but level in terms of sigma

[setsf=<SF file>]

Sets the structure factor based on a 1D x/y text file, must specify apix

[calcsf=<output>]

This will calculate a radial structure factor for the current 3D model and write it to the specified output file, must specify apix.

[icos5fTo3f]

Rotate the map from icos 5 fold view to 3 fold view

[icos3fTo5f]

Rotate the map from icos 3 fold view to 5 fold view

[icos5fTo2f]

Rotate the map from icos 5 fold view to 2 fold view

[icos2fTo5f]

Rotate the map from icos 2 fold view to 5 fold view

[icos5fhalfmap]

The input is the icos 5f top half map generated by the "tophalf" option

[tophalf]

The output only keeps the top half map to save some memory

[icos5fhalf2full]

Generate full map from the icos5f half map

[vtk]

Output should be in VTK format

[df3]

Output in df3 format (POVRAY)

[em]

Output should be in EM format.

[amira]

Output should be in AMIRA format, not MRC

[amiralabel]

Output should be in AMIRA labelField format

[amirashort]

Output should be in AMIRA short data type format

[amirabyte]

Output should be in AMIRA byte data type format

[rawiv]

Output should be in RawIV format, not MRC

[xplor]

Output should be in XPLOR format, not MRC

[icos]

Output should be in ICOS format, not MRC

[spider]

Output should be in Spider format, not MRC. Warning, this is a spider stackfile, and Spider may not be able to read stacks of 3D images. spidersingle is a better choice

[spidersingle]

Output should be in single-image Spider format, not MRC

[imagic]

Output is an IMAGIC file

[mrc8bit]

Output an 8 bit MRC image

[pif]

Output to a PIF (Purdue Image Format) file

[hdf]

Output to a HDF5 (Hierarchical Data Format) file

[png]

Output to a PNG (Portable Network Graphics) file

[gwin=<radius>]

Apply a Gaussian radial falloff, r is 1/e width

[edgenorm]

Normalize the image based on the mean value at the edge of the box

<input 1>

Input 1 to compare/process

<input 2>

Input 2 to compare/process

[apix=<A/pix>]

Specify the Angstr/pixel for S scaling

[fsc=<out>]

Fourier shell correlation

[phase=<out>]

mean phase difference (not residual!)

[snr=<out>]

Relative signal to noise ratio between 2 images.

[rfactor=<out>]

R factor between inputs

[rms=<thresh>]

RMS variation above threshold

[rdiv=<out>]

Radial plot of input 1/input 2

[rdivf=<out>]

Radial plot of input 1/input 2 in Fourier space

[diffmap[=<~binary thr>]]

Generates a difference map in "diffmap.mrc"

[sum=<output>]

Adds input files

[pha1amp2=<out>]

Makes a new image with the phases from image 1 and the amplitudes from image2

[anim=<frames>]

Generates linearly interpolated intermediates between two maps

[animorph=<frames>,<vecfile>[,<start #>]]

Generates a linear morphing of one map into another based on a vector file