; USED TO ROTATE (AS PER SPIDER EULERIAN ANGLE CONVENTION)  AND TRANSLATE 
; PDB CO-ORDINATES. PREPARE OUTPUT VOLUMES TO BE VISUALIZED USING PACKAGE "O".

; BIMAL RATH, OCT'03


; MAKE A BRIX MAP_FILE FROM THE SPIDER DENSITY MAP
cp to brix
large_vol         ; input vol.
large_vol_brix    ; output vol.
1.83              ; pixel size
n                 ; don't change default unit cell size

; CALL THE PYTHON PROGRAM "pdbfit.py" TO DO THE ROTATION. phi, theta AND psi
; ARE THE EULERIAN ANGLES AS DETERMINED BY THE SIGNATURE SEARCH PROCEDURES.
; motif.pdb AND motif_rt.pdb ARE THE INPUT AND OUTPUT VOLUMEs. 


vm
pdbfit.py motif.pdb  motif_rt.pdb rot=phi,theta,psi centercoord

; CALL THE PYTHON PROGRAM "pdbfit.py" TO DO THE TRANSLATION. x, y AND z
; ARE DETERMINED IN THE FOLLOWING WAY:
;
; IF THE POSITION OF THE MOTIF INSIDE THE LARGE VOLUME IS FOUND (BY THE SIGNATURE
; SEARCH PROCEDURES) TO BE AT x1, y1, and z1;  THE DIMENSION OF THE LARGE
; VOLUME IS x2, y2 and z2 ; AND PIXEL SIZE IS p, THEN
;
;                         x = (x1 - (INT(x2/2)+1))*p
;                         y = (y1 - (INT(y2/2)+1))*p
;                         z = (z1 - (INT(z2/2)+1))*p
;
; motif_rt.pdb ARE THE INPUT AND OUTPUT VOLUMEs. 
vm
pdbfit.py motif_rt.pdb motif_fit.pdb trans=x,y,z

; NOW ONE CAN USE "O" TO VISUALIZE LARGE VOLUME(large_vol_brix) AND FITTED MOTIF
; (motif_fit.pdb). 

en