Here are command procedures of some programs from the MRC package.
They are tested under OpenVMS AXP Operating System, Version 6.2
All users at the EMBL : please see what
conventions were used !
$ ============================= $ AUTOCORRL $ ============================= $! LABEL FOR 26x26 BOX IN CENTRE $ run /nodebug prog:LABEL grid_0.FLT 1 grid_box.FLT 488,513,488,513 $! Mitte -12 +13 26x26 image necessary for AUTOCORRL ! $ $ ASSIGN/USER grid_box.FLT IN $ ASSIGN/USER grid_box.COR OUT $ run /nodebug prog:AUTOCORRL 20Go back to top of virus and image processing
boximage
$!================================ $! BOXIMAGE $!================================ $ ASSIGN/USER_MODE grid_0.FLT IN $ ASSIGN/USER_MODE grid_ref.FLT OUT $ run /nodebug prog:BOXIMAGE 4 ! NOVERT, VERTEX COORDS GIVEN IN GRID UNITS RELATIVE TO (0,0) ORIGIN. 0 0 ! ORIGIN FOR LATER USE (E.G. IN FOURIER TRANSFORM) 500 500 ! VERTEX COORDINATES IN GRID STEPS WRT CORNER (0,0) 500 540 540 540 540 500
convert_microd
$!=============================================================== $! Convert_microd $!=============================================================== $run/nodebug prog:convert_microd grid_0 m 0 N 500 1200
emref
$! =============================================================== $! emref $! =============================================================== $ run /nodebug prog2:emref 0 2 212 96 2 0 190 -138 1 0 96.0 -68. 3 0 284.0 -204. 1 -1 -10. -116. 1 -2 -118 -164 2 -1 82 -186 2 -2 -23 -234 2 -3 -130 -280 2 -4 -236 -328 2 1 296 -88 2 2 402 -40 3 -1 178 -252 3 -2 72 -300 3 -3 -34 -348 0 1 106 48 0 3 320 144 -1 1 10 116 -1 2 118 164 -1 3 224 212 -2 3 130 280 -2 4 236 328 -2 5 342 376 -3 3 34 348 -2 2 24 232
fftrans
$!============== $! FFTRANS $!============== $ ASSIGN/USER grid_0.mrc IN $ ASSIGN/USER grid_0.fft OUT $ $ RUN /nodebug prog:FFTRANS $
histo
$!================================================================= $! HISTO $!================================================================= $ ASSIGN/USER grid_0.MRC IN $ ASSIGN/USER grid_histo.PLT PLOT $ RUN/nodebug prog:HISTO 0 999 0 999 0 $!
label
$!============== $! Label $!============== $!------------------------------------------------------------------------------ $ RUN/nodebug prog:LABEL grid_0.MRC 4 ! option 4 for LABEL : Averaging grid_red.mrc 2,2 ! # of pixels averaged in X and Y $ $!------------------------------------------------------------------------------
masktran
$! ======================================= $! MASKTRAN $! ======================================= $ ASSIGN/USER grid_0.fft IN $ ASSIGN/USER grid_0.MSK OUT $ Run /nodebug prog:MASKTRAN 2 T ! ISHAPE= 1(CIRC),2(GAUSS CIRC),OR 3(RECT) HOLE, IAMPLIMIT(T or F) 9 ! RADIUS OF HOLE IF CIRCULAR, X,Y HALF-EDGE-LENGTHS IF RECT. 94.994 -68.146 106.406 48.016 -2 2 -2 2 500 1 !A/BX/Y,IH/IKMN/MX,RMAX,ITYPE 1 0 2 0 3 0 1 -1 1 -2 2 -1 2 -2 2 -3 2 -4 2 1 2 2 3 -1 3 -2 3 -3 0 1 0 2 0 3 -1 1 -1 2 -1 3 -2 3 -2 4 -2 5 -3 3 -2 2
mmbox
$! ========================= $! MMBOX $! ========================= $Run /nodebug prog2:MMBOX grid_0.fft 1234 , grid *** INITIAL LATTICE *** Y ! Use grid units? Y ! Generate grid from lattice? N ! Generate points from lattice? 2 0 25 5 5 20 20 ! IPIXEL,IOUT,NUMSPOT,NOH,NOK,NHOR,NVERT 500. 500. ! XORIG,YORIG 30. 500. 0 50.0 60.0 50. 90. ! RINNER,ROUTER,IRAD,ACELL,BCELL,WIDTH,ABANG 94.817 -68.246 106.181 47.823 ! lattice
mmlatref
$!================================================ $! MMLATREF $!================================================ $ run/nodebug prog:MMLATREF grid_0.fft 151295 Grid_0 LATTICE Y ! Use grid units? Y ! Generate grid from lattice? N ! Generate points from lattice? 1 0 25 5 5 20 20 ! IPIXEL,IOUT,NUMSPOT,NOH,NOK,NHOR,NVERT 30. 500. 500. 500. ! RINNER,ROUTER,XORIG,YORIG 20 10. 0 ! NCYCLES,FSHIFT,ILIST for lattice param refn 95.0 -68.000 106.375 48.00 ! lattice
ptone
Bug report : Ptone was not able to recognize the logical "PTONE". This is fixed now. It does not anymore try print the postscript file on a printer from within the program. You have to print it seperately. PTONE produces nonstandard postsript. Printers which nonetheless recognize the file as a postscript file will print it properly, others will print it as an ascii file. (Jan 17, 1996) $!============== $!PTONE : generates postscript file from mrc file $!============== $ $! Define Output file : $ ASSIGN/USER grid_fft.ps ptone $ RUN/nodebug prog2:PTONE grid_0.FFT 0 999 0 999 ! coordinates of TONE output 40 60 ! min, max levels for TONING 12.05 ! width of output in cm $!------------------------------------------------------------------------------
quadsercha
$!============================================================== $! Quadsercha $!============================================================== $ ASSIGN/USER grid_box.map PROFILE $ ASSIGN/USER grid_prof.DAT PROFDATA $ ASSIGN/USER grid_quad.plt ccplot $ run /nodebug prog:QUADSERCHA 0,20 ! IPASS,NRANGE grid_cor.cor 1000,1000 ! SIZE OF TRANSFORM (ISIZEX, ISIZEY) 94.812 -68.231 106.506 47.896 ! lattice -25,25,-25,25 ! NUMBER UNIT CELLS TO SEARCH 3,3 ! RADIUS OF CORR SEARCH 500 500 ! POSN OF START SEARCH ORIGIN 0,0 IS ORIGIN N ! YES/NO FOR DETAILED PRINTOUT 40. , 40. , 0.0 ! RADLIM IN PROFILE GRID UNITS
trilogd
Bug report : Several bugs had to be fixed to make it run on the VMS Alpha machines.(eb Jan 16, 1996) $!============================================================== $! Trilogd $!============================================================== $ ASSIGN/USER grid_histo.PLT PLOTIN $ ASSIGN/USER grid_histo.PS PLOTOUT $ RUN/nodebug prog:TRILOGD $
twofile
$! ============================================ $! TWOFILE $! ============================================ $! Multiply two files together : FILE1 * Complex Conjugate of FILE2 $! ICOMB = 2 $! First image on stream 1 (IN1) $! Second image on stream 2 (IN2) $! Product output on stream 3 (OUT) $! $ ASSIGN/USER grid_0.MSK IN1 $ ASSIGN/USER grid_ref.FFT IN2 $ ASSIGN/USER grid_cor.FFT OUT $ run /nodebug prog:TWOFILE 2 ! ICOMB = 2 2 0 0 500 500 ! IORIGIN,OXA,OYA,OXB,OYB ORIGIN SHIFTS TO FFT'S.
Author: Eckart Bindewald
Last Updated: January 17, 1996