| AC | Auto Correlation |
| AC MS | Auto Correlation - Masked and normalized |
| AC N | Auto Correlation - Normalized |
| AD | ADd images |
| AD M | ADd images - using Multipliers |
| AP CA | Alignment Program - Classification and Alignment |
| AP MD | Alignment Program - 3D projection alignment. |
| AP MQ | Alignment Program - 3D projection / Multi reference alignment |
| AP MR | Alignment Program - Multi-reference alignment |
| AP RA | Alignment Program - Rotational Alignment |
| AP SA | Alignment Program - Shift Alignment |
| AP SR | Alignment Program - Shift and Rotational alignment |
| AR | ARithmetic operation |
| AS | Average images - find & save variance |
| AS AD | Add to an existing average - find variance. |
| AS DC | Average images - find & save variance, from doc. file |
| AS F | Average images - find statistics & Q factor map |
| AS R | Average images - find & save variance, better |
| AT IT | Automatic particle picking - intermediate program. |
| AT PK | Automatic particle picking - peak search |
| AT SA | Automatic particle picking - statistical parameters. |
| AT WN | Automatic particle selection |
| |
|
| BC | Box Convolution |
| BL | BLank |
| BP 3 | Back Projection - 3D, iterative (ART) |
| BP 3D | Back Projection - 3D, using Euler angles, || |
| BP 3E | Back Projection - 3D, using Euler angles |
| BP CTF | Back Projection - 3D, CTF correction, || |
| BP GW | Back Projection - weighted, arbitrary geometry |
| BP GW3 | Back Projection - weighted, arbitrary geometry, 3 angles |
| BP MEM2 | Back Projection - 2D maximum entropy method |
| BP R2 | Back Projection - 2D, weighting of the image series |
| BP RP | Back Projection - 3D, iterative, with constraints, || |
| BP S2 | Back Projection - 2D, single tilt iterative, with constraints |
| BP W2 | Back Projection - 2D, filtered weighted |
| BP WX | Back Projection - weighted, X |
| BP WY | Back Projection - weighted, Y |
| BP XY | Back Projection - simple for single axis & conical tilting |
| |
|
| CA | Correspondence Analysis - prepare sequential file |
| CA 3 | Correspondence Analysis - create 3-D volume |
| CA E | Correspondence Analysis - prepare sequential file |
| CA M | Correspondence Analysis - Map |
| CA MAP | Correspondence Analysis - nonlinear MAPping |
| CA R | Correspondence Analysis - Reconstitute images |
| CA S | Correspondence Analysis - find Solution |
| CA SI | Correspondence AnalysiS - Initialize |
| CA SM | Correspondence Analysis - Factor Map |
| CA SME | Correspondence Analysis - Factor Map and Eigen Values |
| CA SR | Correspondence Analysis - full Reconstitution of images |
| CA SRD | Correspondence Analysis - Reconstitute Differential images |
| CA SRI | Correspondence Analysis - Reconstitute Importance images |
| CA SRP | Correspondence Analysis - PCA reconstitution |
| CA VAR | Correspondence Analysis - Variance |
| CA VIS | Correspondence Analysis - Create VISual map |
| CC | Cross Correlation |
| CC C | Cross Correlation Coefficient |
| CC N | Cross Correlation - Normalized |
| CE | Contrast Enhancement |
| CE FIT | Contrast Enhancement - FIT the histogram |
| CE GNC | Contrast Enhancement - Graduated Non Convex restoration |
| CE MED | Contrast Enhancement - using Median Filtering |
| CE OD | Contrast Enhancement - adjust Optical Densities |
| CG | Center of Gravity |
| CG 3 | Center of Gravity - radius of gyration |
| CG 3S | Center of Gravity - Solid body option |
| CG PH | Center of Gravity - PHase approximation |
| CI | Confidence Interval |
| CL CLA | CLAssification - Clusters |
| CL CLAF | CLassification - Fuzzy |
| CL HC | CLassification - Hierarchical Clustering |
| CL HD | CLassification - Hierarchical clustering, calculate classes |
| CL HE | CLassification - Hierarchical clustering, create docfiles |
| CL KM | CLassification - K Means clustering |
| CN | CoNvolution |
| CN N | CoNvolution - Normalized |
| CO | COntours into contour storage file |
| CO S | COntours into STERECON storage files |
| CP | CoPy |
| CP FIX | CoPy to FIX a malformed stack |
| CP FROM ASCII | CoPy ASCII text file to SPIDER format |
| CP FROM MRC | CoPy MRC format File to SPIDER File |
| CP FROM PDB | Copy PDB file to SPIDER format |
| CP FROM PE | Copy Perkin Elmer disk file to SPIDER format |
| CP FROM RAW | CoPy RAW Image to SPIDER |
| CP FROM SF3 | Copy 3D simple Fourier file to SPIDER format |
| CP FROM SHORT | CoPy SHort header file to SPIDER file |
| CP FROM TERM | CoPy terminal input to SPIDER file |
| CP FROM TR | Copy old TR file to SPIDER format |
| CP FROM VAX | CoPy VAX SPIDER file to a Unix SPIDER file |
| CP TO ASCII | CoPy SPIDER file to ASCII text format |
| CP TO BRIX | CoPy SPIDER volume to BRIX file for O input |
| CP TO MRC | CoPy SPIDER file TO MRC format file |
| CP TO POST | CoPy SPIDER file to a POSTscript file |
| CP TO RAW | CoPy SPIDER file to a 8-bit raw image |
| CP TO SF3 | Copy SPIDER 3D Fourier file to simple format |
| CP TO SGI | CoPy SPIDER file to SGI format |
| CP TO TARGA | CoPy SPIDER file to Targa format |
| CP TO TIFF | CoPy SPIDER file to a TIFF format |
| CP TO VAX | CoPy SPIDER Unix file to Vax SPIDER format |
| CP TO VV | CoPy SPIDER volume to Voxel View format |
| CS DI GD | Contour display - on Gould plotter |
| CS DI PL | Contour display - convert to HPGL |
| CS DI PO | Contour display - convert to Postscript |
| CS DI VT | Contour display - on VT125/240 terminal |
| CS MV | Contour Storage - MoVie.BYU interface |
| CV REPL | projection onto ConVex sets - projector Replace |
| |
|
| FC | File Contouring |
| FC E | File Contouring - External contour levels |
| FD | Filter according to a Document file |
| FF | Fourier Filter |
| FF B | Fourier Filter - Bar, ky direction |
| FF BX | Fourier Filter - Bar, kx direction |
| FF PLOT | Fourier Filter - design filter |
| FF S | Fourier Filter - restore Surface topography |
| FI | File Information |
| FI A | File Information - Multiple files |
| FI N | File Information - Do not halt if file not found |
| FI X | File Information - place header values in registers |
| FP | Fourier interPolation |
| FQ | Filter - Quick |
| FQ NP | Filter - Quick, No Padding |
| FR | File Read |
| FS | Find Statistics |
| FS M | Find Statistics - within Mask |
| FT | Fourier Transform |
| |
|
| PA | PAtch |
| PD | PaD |
| PF | Graph (ProFile) an image row - to contour storage file |
| PJ 3 | ProJect - 3D volume |
| PJ 3E | ProJect - 3D volume using Eulerian angles, fast |
| PJ 3Q | ProJect - 3D volume using Eulerian angles |
| PJ 3T | ProJect - 3D volume using internal Threshold |
| PJ AT | ProJect 3D volume using exponential ATtenuation |
| PJ COL | ProJected surface - COLoring |
| PJ CYL | ProJect - 3D volume onto CYLinder |
| PJ INTER | ProJected Surface - INTERlace two surface representations |
| PJ SHAD | ProJected Surface - cosine SHADing |
| PJ ST | ProJected Surface - Creation |
| PK | PeaK search |
| PK 3 | PeaK search - 3D |
| PK 3D | PeaK search - 3D, output to doc. file |
| PK C | PeaK search - Center of gravity |
| PK D | PeaK search - output to doc. file |
| PK DC | PeaK search - Center of gravity, output to Doc. file |
| PL | Plot doc. file data into CNT meta-file |
| PL FIT | FIT PoLynomial to document file data |
| PL HI | PLot HIstogram - from document file |
| PP L | Put Points in image - from doc. file Listing |
| PP LL | Put Lines in image - from doc. file Listing |
| PP P | Put Points in image - from doc file, alters neighbors |
| PP V | Put height image into Volume |
| PR | overPRint image - to results file |
| PR P | overPRint Power spectrum - to results file |
| PR T | overPRint image - to Terminal |
| PS | Pick Slice - Y (xz planes) |
| PS A | Pick Slice - Arbitrary direction |
| PS X | Pick Slice - X, (yz planes) |
| PS Z | Pick Slice - Z, (xy planes) |
| PT | create PaTtern or Mask file |
| PW | PoWer spectrum |
| PW L | PoWer spectrum - Log10 |
| |
|
| RA | RAmp |
| RA GN | Gaussian contrast Normalization |
| RC | Real Convolution |
| RE | REturn |
| RF | R Factor |
| RF 3 | Phase Residual & Fourier shell correlation, 3D |
| RF SN | Spectral SNR of images |
| RM | Radon transforM suite of programs. |
| RO | ROtational average - single line output |
| RO I | ROtational average - 2D Image output |
| RP | Replace Pixel value |
| RR | Read Register |
| RT | RoTate - image or volume, use average as background |
| RT 3 | RoTate - volume, slow |
| RT 3A | RoTate - volume, around arbitrary center |
| RT 3D | RoTate - volume, fast |
| RT 90 | RoTate - image or volume, by 90, 180, or 270 degrees |
| RT B | RoTate - image or volume, supply Background |
| RT C | RoTate - image, around arbitrary center, for small files |
| RT M | RoTate - image or volume, use minimum as background |
| RT SQ | RoTate - image or volume, Shift, use Quadratic interpolation |
| |
|
| TF | Transfer Function - defocus dependent |
| TF C | Transfer Function - Complex |
| TF C3 | Transfer Function - Complex 3D |
| TF CT | Transfer Function - phase flipping, Complex, Ternary |
| TF CT3 | Transfer Function - Complex, Ternary 3D |
| TF CTF | Transfer Function - CTF correction |
| TF D | Transfer Function - Display |
| TF DDF | Transfer Function - Determine DeFocus and amplitude contrast |
| TF DEV | Transfer Function - Determine EnVelope function |
| TF DNS | Transfer Function - determine and Delete NoiSe background |
| TF FL | Transfer function - Flip sign of Fourier transform |
| TF MFL | Transfer Function - Make FiLter file for 'TF FL' |
| TH | THreshold |
| TH C | THreshold - Change a value |
| TH F | THreshold - set a Fixed value |
| TH M | THreshold - and create Mask |
| TM | TiMe |
| TP | Three dimensional Plot |
| TT | Sets image TiTle |
| |
|