| CP FROM ASCII | [Copy ASCII text file to SPIDER file] |
| CP FROM CCP4 | [Copy CCP4 format File to SPIDER file] |
| CP FROM EMI | [Copy EMISPEC format file to SPIDER file] |
| CP FROM MRC | [Copy Old MRC format file to SPIDER file] |
| CP FROM NIK | [Copy Nikon Coolscan format file to SPIDER file] |
| CP FROM PDB | [Copy PDB file to SPIDER format] |
| CP FROM RAW | [Copy Raw Image to SPIDER file] |
| CP FROM TERM | [Copy Terminal input to SPIDER image/volume] |
| CP FROM VAX | [Copy VAX SPIDER file to a Unix SPIDER file] |
| CP FROM XP | [Copy X-PLOR ASCII file to 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 CCP4 | [Copy SPIDER file To CCP4 format file] |
| CP TO MRC | [Copy SPIDER file To MRC format file] |
| CP TO OPEND | [Copy SPIDER file To Opposite Byte Endian] |
| CP TO POST | [Copy SPIDER image to a POSTscript image] |
| CP TO RAW | [Copy SPIDER file to a 8-bit raw image] |
| CP TO TIFF | [Copy SPIDER file to a TIFF format] |
| CP TO XPLOR | [Copy SPIDER volume to X-PLOR format] |
.CCP4 OUTPUT FILE NAME: ccpout
[Enter name for CCP4 format output file.]
.ENTER DATA LENGTH FOR CCP4 FILE (8 OR 32 BITS): 32
[Can create either a CCP4 MODE=0 file containing 8 bit
integer values or CCP4 MODE=2 file containing 32 bit
floating point values with currrent machine byte-ordering.]
.ENTER STARTING X,Y, & Z OF CCP4 IMAGE: <CR>
[Default value for Start:((NX/2)+ 1, (NY/2)+1),
(NZ/2)+1
(+1 ADDED ONLY IF AXIS LENGTH IS ODD)
Enter <CR> if you want to use the default values.]
.ENTER ANGSTROMS/PIXEL FOR X, Y, & Z AXIS: 12.0, 12.0, 5.0
[Angstrom/pixel scale will be be multiplied by the
number of pixels in each axis to get the cell dimensions.]
.ENTER X,Y & Z ORIGIN OF CCP4 IMAGE: <CR>
[Default value for origin:((NX/2)+ 1, (NY/2)+1),
(NZ/2)+1
(+1 ADDED ONLY IF AXIS LENGTH IS ODD)
Enter <CR> if you want to use the default values.]
NOTES
; fit_ccp4_to_pdb.spi ; ; THIS PROCEDURE ORIENTS AND SHIFTS A SPIDER VOLUME THAT HAS BEEN CONVERTED TO ; A BRIX VOLUME BY "CP TO BRIX" AND HAS BEEN USED (THE BRIX VOLUME) TO ; FIT A PDB STRUCTURE USING "O" OR REAL SPACE REFINEMENT (RSR). THE OUTPUT ; OF THIS PROCEDURE IS A CCP4 VOLUME WHICH IS AT THE CORRECT LOCATION AND ; ORIENTATION AS THAT OF THE FITTED PDB STRUCTURE. THIS CAN BE VISUALIZED ; USING "O" OR "CHIMERA" OR "PYMOL". ; ALTERNATIVELY, ; (1) ONE CAN ALSO ORIENT AND SHIFT THE FITTED PDB FILE TO FIT THE CCP4 ; VOLUME WHICH IS GENERATED FROM THE UNROTATED AND UNSHIFTED SPIDER VOLUME, ; WHICH CAN BE VISUALIZED BY USING "O" OR "CHIMERA" OR "PYMOL". USE PROCEDURE ; "fit_pdb_to_ccp4.spi" IN THE SPIDER PROCEDURE DIRECTORY"spider/proc/". ; (2) ONE CAN USE "CP TO BRIX" TO CONVERT THE UNROTATED AND UNSHIFTED ; SPIDER VOLUME TO A BRIX VOLUME WHICH CAN BE USED TO VISUALIZE THE ; FITTED PDB STRUCTURE IN "O" OR "CHIMERA" OR "PYMOL". ;;;;;;;;;;;;;;;;;;;;;;;BEGINING OF INPUT PARAMETERS;;;;;;;;;;;;;;;;;;; FR L ?INPUT SPIDER VOLUME NAME ?[input] vol_spi FR L ?OUTPUT CCP4 VOLUME NAME ?[output] vol_ccp4.ccp4 ;PIXEL SIZE "[ps]" [ps] = 2.82 ;DATA LENGTH FOR CCP4 FILE "[len]" [len] = 32 ;;;;;;;;;;;;;;;;;;;;;;;END OF INPUT PARAMETERS;;;;;;;;;;;;;;;;;;;;;;;;; ; ROTATE THE VOLUME SO THAT X = Y, Y = X AND Z = -Z RT 3D [input] _1 90, 0, 0 RT 3D _1 _2 0,180,0 RT 3D _2 _3 180,0,0 ; FIND NX, NY AND NZ FI [NX],[NY],[NZ] [input] 12,2,1 ; FIND THE CENTER IN PIXELS, FOR EVEN DIMENSION, IT IS NX/2 ETC.. ; FOR ODD DIMENSION, IT IS (NX/2 + 1) ETC.. [xc] = INT([NX]/2 ) [yc] = INT([NY]/2 ) [zc] = INT([NZ]/2 ) [x] = ([NX] - 2*[xc]) + [xc] [y] = ([NY] - 2*[yc]) + [yc] [z] = ([NZ]- 2*[zc]) + [zc] ; CALCULATE THE CENTER IN ANGSTROMS [xa] = [x] * [ps] [ya] = [y] * [ps] [za] = [x] * [ps] ; CREATE THE CCP4 FILE ; NOTE: FOR DISPLAY, "CHIMERA" READS THE ORIGIN WHEREAS "O" READS THE STARTING ; POINTS OF XYZ. ORIGIN IS GIVEN IN ANGSTROMS, STARTING POINTS ARE GIVEN IN PIXELS. CP TO CCP4 _3 [output] [len] -[x],-[y],-[z] [ps],[ps],[ps] -[xa],-[ya],-[za] EN