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ME - MEnu

(02/19/98)

PURPOSE

Prints out the mnemonic for each operation. A listing of about 15 operations will be displayed at the terminal at one time. Type <Return> to continue listing or '*' to return to ".OPERATION".

USAGE

.OPERATION: ME
 

Operation Description

AC Auto-Correlation (mp) AC MS Auto-Correlation, Masked and normalized (mp) AC N Auto-Correlation - Normalized (mp) AD ADd images AD M ADd images using Multipliers AP CA Alignment Program - Classification and Alignment AP MD Alignment Program - 3D projection alignment. (mp) AP MQ Alignment Program - 3D projection/Multi-reference alignment. AP MR Alignment Program - Multi-reference alignment AP RA Alignment Program - Rotational Alignment (mp) AP SA Alignment Program - Shift Alignment (mp) AP SR Alignment Program - Shift and Rotational alignment (mp) 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 picking, Windowing.

BC Box Convolution BL BLank BP 3 iterative (ART) Back Projection--3D BP 3D Back-Projection - 3D using three Eulerian angles (mp) BP 3E Calculate Back Projection using 3 Euler angles BP CTF 3D Reconstruction with CTF correction || BP GW Weighting of projections for weighted Back Projection BP GW3 Weighting of projections for weighted Back Projection BP MEM2 2D Maximum Entropy Method Reconstruction BP R2 R**2 weighting of the series of 2D images BP RP 3D Iterative Reconstruction With Constraints || BP S2 2D Single-tilt Iterative Reconstruction With Constraints BP W2 2D Filtered Weighted Back Projection BP WX Weighted Back Projection BP WY Weighted Back Projection BP XY Simple Back Projection for single axis & conical tilting.

CA MAP Correspondence Analysis--nonlinear MAPping 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 VIS Correspondence Analysis, Create VISual map CC Cross-Correlation (mp) CC C Correlation Coefficient and Euclidean distance CC N Cross-Correlation, Normalized CE Contrast Enhancement CE FIT Contrast Enhancement, FIT the histogram CE GNC Contrast Enhancement using Graduated Non-Convex CE MED Contrast Enhancement using Median Filtering CE OD Contrast Enhancement, adjust Optical Densities CF Construct Fourier CF 3 Construct 3-D Fourier 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 (mp) CI Confidence Interval CL CLA Correspondence Analysis -- CLAssification 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 (mp) CN N CoNvolution - Normalized (mp) CO COntours into contour storage file CP CoPy CP FROM ASCII CoPy FROM ASCII text file to SPIDER File CP FROM MRC CoPy MRC format File to SPIDER File CP FROM PDB Copy a PDB file to SPIDER format CP FROM PE Copies Perkin Elmer disk file to SPIDER CP FROM RAW CoPy RAW Image to SPIDER CP FROM SF3 Copies a 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 into Editable file 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 Copies a 3D SPIDER Fourier file to simple format CP TO SGI CoPy a SPIDER file to SGI format CP TO TARGA CoPy a Spider file to Targa format CP TO TIFF CoPy to a TIFF file CP TO VAX CoPy a Unix file to Vax SPIDER CP TO VV CoPy 3D file to Voxel-View format CS DI GD Plot Contour Storage File on Gould Plotter CS DI PL Convert Contour Storage Metafile to HPGL CS DI PO Converts Contour Storage File to Postsript CS DI TX Plots Contour Storage File on Tektronix Plotter CS DI VT Display Contour Storage File on VT125/240 CS MV Contour Storage MoVie.BYU interface CS MVVT Contour Storage MoVie.BYU interface CS TH Contour Storage THinning CV REPL projection onto ConVex sets, projector Replace

DE DElete DE A DElete DF Density Foldover DO start of DO loop DR Density Reference DR DIFF Difference and error calculation between two volumes DR ERR Error Calculation Between Two 3D Volumes DU DUst DU V DUst with Value

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

FC File Contouring FC E File Contour--External contour levels FD Filter according to a Document file FF Fourier Filter (mp) FF B Fourier Filter/Bar (ky direction) FF BX Fourier filter (kx direction) FF PLOT Design of Filter FF S Fourier Filter--restore Surface topography FI File Information FI A File Information (Multiple files) FI N File Information - No stop if file not found FI X23,X24 place FIle header values in specified registers FP Fourier interPolation (mp) FQ Filter Quick (mp) FQ NP Filter Quick, No Padding (mp) FR File Read FS Find Statistics FS M Find Statistics within Mask FT Fourier Transform (mp)

GF General Filter for quasi-optical Fourier Filtration GF C General Filter (Condensed Fourier) GOTO unconditional jumping command GR GRaph GR T GRaph, plot file 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 jump in batch mode IN INsert IN S INsert and contrast Stretch IP InterPolate IP T Triangular InterPolation

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 doc. 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 X11,X12.. List pixel values in registers

MA MAsk using circular radii MA L Mask a line MA X 1-D MAsking in sample direction MA Y 1-D MAsking in row direction MD MoDe ME MEnu MK MarKer MK 3 MarKer 3D MM Mask Multiplication MM C Mask Multiply--Continuous MN MoNtage MN S MoNtage with individual Scaling MO MOdel MO 3 3-D MOdel creation MR MiRror MS Make 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 Code NK shriNK NK M shriNK to Mask

OR 2 Orientation search for rotation angles in 2D. (mp) OR 2M Orientation search - 2D, multiple peaks. (mp) OR 3A ORientation Search in 3D (Eulerian Angles), arbitrary center OR 3Q ORientation Search in 3D (Eulerian Angles) (mp)

PA PAtch PD PaD PF ProFile image 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 COL COLour surface representation PJ CYL ProJect onto CYLinder PJ INTER ProJect -- INTERlace two surface representations PJ SHAD ProJect -- cosine SHADing of surface representation PJ ST ProJect -- Surface represenTation PK PeaK search PK 3 PeaK search in 3D PK 3D PeaK search in 3d. stores output in Document file PK C PeaK search--Center of gravity PK D PeaK search using Document file PK DC PeaK search + Center of gravity + Document 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 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 -- xz planes PS A Pick Slice -- Arbitrary direction PS X Pick Slice X -- yz planes PS Z Pick Slice -- xy planes PT create PaTtern or Mask file PW PoWer spectrum PW L PoWer spectrum Log10

RA RAmp RC Real Convolution RD ReDuce transform RD D Reduce transform -- use reflection files RD L ReDuce transform - List only RE REturn RF R-Factor RF 3 Phase Residual & Fourier Shell correlation in 3D (mp) RF SN Spectral SNR of Images RM Radon transforM suite of programs. RO ROtational average (single line output) RO I ROtational average 2-D Image output RR Read Register RT RoTate, use average as background RT 3 RoTate a volume, slow RT 3A RoTate a volume around an arbitrary center RT 3D RoTate a volume, fast RT 90 RoTate volume by 90, 180, or 270 degrees RT B RoTate, supply Background RT C Rotate, center selected by user (for small files) RT M Rotate, use minimum as background RT SQ RoTate and 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 (mp) 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 for phase flipping -- Complex, Ternary TF CT3 Transfer Function -- Complex, Ternary 3D TF CTF Transfer Function -- CTF correction TF D Transfer Function -- Display TF DDF Determine DeFocus and amplitude contrast TF DEV Transfer Function -- Determine EnVelope function TF DNS Transfer Function -- determine and Delete NoiSe background TF FL Flip the sign of Fourier transform according to CTF TF MFL Transfer Function -- Make FiLter file for TF FL TH THreshold TH C THreshold--Change a value TH F THreshold--Fixup constant TH M THreshold and create Mask TM TiMe TP Three-dimensional Plot TT 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 key numbers UD S Unsave Document--Sequential search

VM VMS spawn or Unix system call VO EA Vector Operation -- Even Angles docfile VO MD Vector Operation -- angular docfile 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

NOTES

  1. Operations marked by '(mp)' use parallel code on multiprocessor SGI computers.

  2. For a more up-to-date listing use your WWW viewer on the HTML documentation..

SUBROUTINES

NUMENU

CALLER

DRIV1

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