MANUAL OF SPIDER OPERATIONS

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

DC Determine tiltaxis - Goldfarb Version
DE DElete
DE A DElete
DF Density Foldover
DO start of DO loop
DR Density Reference
DR DIFF Density Reference - Error & DIFference between two volumes
DR ERR Density Reference - Error between two volumes
DU DUst
DU V DUst - with Value set

EC CL Extract Connected CLusters
EC CLOSE Extract Connected CLusters - merge CLOSE
EC FILTER Extract Connected CLusters - FILTER
EC SELECT Extract Connected CLusters - SELECTion
EC STAT Extract Connected CLusters - STATistics
ED Edge Detection
EN ENd
EN D ENd - Delete RESULTS file
EP Error Probability
EP TT T test

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

GOTO unconditional jumping command
GP Get Pixel value
GR GRaph an image row - in Results file
GR T GRaph an image row - on Terminal

HF Helical Fourier
HI HIstogram
HI D HIstogram - output in Document file
HI M HIstogram - masked area
HI T HIstogram - display on Terminal

IF conditional execution
IF_GOTO conditional jump
IF_THEN conditional execution of operation series
IN INsert
IN S INsert - and contrast Stretch
IP InterPolate
IP T Triangular InterPolation
IQ FI InQuire if a file exists
IQ REG InQuire if a Register's content is correct

LB# end of DO-loop
LD List Document file
LD T List Document file - on Terminal
LI LIst image values - in results file
LI D List image values - in Document file
LI R LIst Registers - in results file
LI RD LIst Registers - in Document file
LI RT List Registers - on Terminal
LI T List image values - on terminal
LI X List pixel values - in registers

MA MAsk - using circular radii
MA L MAsk - a line across image
MA X MAsk - 1D, in sample direction
MA Y MAsk - 1D, in row direction
MD MoDe
ME MEnu
MK MarKer
MK 3 MarKer 3D
MM Mask Multiplication
MM C Mask Multiplication - Continuous
MN MoNtage
MN S MoNtage with individual Scaling
MO MOdel image creation
MO 3 MOdel volume creation
MR MiRror - image or volume
MS Make empty inline Stack
MU MUltiply real or complex files
MU D Divide real or complex files
MU M Multiply 1st complex file by 2nd conjugated file
MU O MUltiply with arithmetic Or

NC New data/project extension
NK shriNK
NK M shriNK to Mask

OD Optical Density conversion
OR ORientation search - half circle used
OR 3A ORientation search - 3D, arbitrary center
OR 3DD Orientation search - two volumes by cross correlation
OR 3Q ORientation search - 3-D, Eulerian angles
OR F ORientation search - full circle used
OR FM ORientation search - Full circle, Find > one peak
OR M ORientation search - find More than one peak
OR P ORientation search - not Power of two

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

SA Sum Alignment
SA P Sum Alignment - Positive rotation and shift
SD Save Document
SD C Save Document - from Cluster file
SD E Save Document - End
SD NLM Save Document - from NonLinear Mapping
SD S Sort Document file according to one column
SD SHUFFLE Shuffle Document file
SE SEed fill an image
SH SHift - using bilinear interpolation
SH F SHift - using Fourier interpolation
SK StacK
SK R StacK - Replace
SL SLice image series
SP find the intensity of a SPot
SQ SQuare
SR Save/unsave Registers
ST SeT
SU SUbtract
SZ SqueeZes (Shears) an Image

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

UD Unsave Document
UD E Unsave Document - End
UD IC Unsave Document - In Core
UD ICE Unsave Document - In Core, End
UD N Unsave Document - get key Numbers
UD S Unsave Document - Sequential search

VM VMS spawn or Unix system call
VO Vector Operation
VO CEUL Vector Operation - Combine EULer rotations
VO EA Vector Operation - Even Angles doc. file
VO MD Vector Operation - angular doc. file from 'AP MD' output
VO RA Vector Operation - Rotate Angular document file

WI WIndow
WI B WIndow - using specified background
WT Lattice indexing
WT TV Lattice Indexing
WU square root - WUrzel
WV Window aVeraging
WV P Window aVeraging - over Patches
WV S Window aVeraging - Sequential document search