; Translational 3D refinement of selected structures.  Pawel A. Penczek 04/2002
; x51 - radius of the structure
;
x51=20
;  x52 - image size
x52=70

DO LB51 X71=1,6
RR X78
1,2,5,7,13,15

vm
rm -r refi{**X78}
vm
mkdir  refi{**X78}

cp
grp0.65/volf{***X78}
refi{**X78}/vol001

; X77 - number of projections in the group
UD N,X77
grp0.65/grp{****X78}
; do  projection alignment for 6 times and each time create a new 3D 
; reconstruction from the refined projections. The final projections
; will be in the directory refi{**X78}/tmp1/tmp****
; 
do lb1 x76=1,6
x86=x76+1
; use crosscorrelation to center 2D images
; calculate projections of 3D in the directions of original projections
pj 3q
refi{**X78}/vol{***x76}
x51
grp0.65/grp{****X78}
ang001
refi{**X78}/prj****
; calculate shifts
do lb5 x21=1,x77
ud ic,x21,x20
grp0.65/grp{****X78}

CC N
tlt/tls{****x20}
refi{**X78}/prj{****x20}
_5
pk x11,x12
_5
(1)
;
;
SH
tlt/tls{****x20}
refi{**X78}/tmp{****x20}
-x11,-x12
; store the shift parameters
sd x20,x11,x12
refi{**X78}/shifts{***x86}
lb5 
ud ice
grp0.65/grp{****X78}

sd e
shifts{***x86}
BP 3f
refi{**X78}/tmp****
grp0.65/grp{****X78}
ang001
*
refi{**X78}/ttvol{***x86}
fq np
refi{**X78}/ttvol{***x86}
refi{**X78}/vol{***x86}
(7)
(0.08,0.2)
; center 3D
;cg ph,x10,x11,x12,x21,x22,x23
;refi{**X78}/tvol{***x86}
;sh 3
;refi{**X78}/tvol{***x86}
;refi{**X78}/vol{***x86}
;-x21,-x22
;-x23
de
refi{**X78}/ttvol{***x86}
lb1
LB51
en d