;b87.pam runs ok on spider4.308 ;3D projection alignment program derived from ;file:/net/saba/usr/people/pawel/mosaic/batch.html b86.pam 8/26/99 ;adapted by M. Samso on 8/26/99 for the following: ;MD SET MP, BP RP instead of BP 32F, ;changed sequence of angular steps : first round 4 degrees instead of 2; ;modified all @ali procedures and @lang for 4-fold symmetry ;cut the last BP RP since all our 3Ds are already done that way, ;the last if--gotolb71 moved down ; gives an output of % angles that moved more than 1.5 degrees MD TR OFF ; file info turned off MD VB OFF MD SET MEM 900 ;MD ;SET MP ;8 ; ;vm ;echo "Program started"|Mail $USER ; ; !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ; In this refinement program it is NOT assumed that preliminary angular ; document files exist. ; !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ; Procedures used: ; Makeselsort ; ; x78=1 ; x51 - radius of the structure x51=24 ; x52 - image size x52=75 ; x58 - image center x58=38 ; x54 - first radius for APMD x54=5 ; the CCF file is windowed to prevent too large shifts of projections. ; Shift allowed is +-x55, input images are padded x55=6 ; x66 - number of defocus groups x66=1 x76=1 x86=0 ; x62 - total number of particles x62=1529 ;goto lb87 ; create dummy transformation files for the first step. DO LB17 j=1,x62 sd x0,x86,x86,x86,x86 refi/transx76 LB17 sd e refi/transx76 ; ; copy all the projections from file data to dala vm cp refi/data.$DATEXT refi/dala.$DATEXT ; ; prepare document files @Makeselect[x62] refi/select refi/selectodd refi/selecteven ; ; do 3D projection alignment DO LB1 i=1,8 x76=x0 x86=x0+1 ; ; BELOW - particular sequence of angular steps, can be modified !!! RR x41 4.0,2.0,2.0,2.0,2.0,1.5,1.5,1.5 ; Restrict angular search RR x42 15.0,15.0,5.0,5.0,5.0,5.0,5.0,5.0 ; ; count how many changed x47=0 ; ; Get all the input projections CP refi/dala@ _8@ x62 ; ; x62 - number of images ; x52 - image size ; x58 - image center ; x55 - allowed shift ; x51 - object radius ; x41 - theta step ; x42 - range of angular search if(x76.eq.1) then ; x62 - number of images ; x52 - image size ; x58 - image center ; x55 - allowed shift ; x51 - object radius ; x41 - theta step @ali3dapmd4s[x62,x52,x58,x55,x51,x41] refi/volx76 refi/data@**** _8@**** refi/apmdx86 refi/anglesx86 refi/transx76 refi/transx86 refi/angvoea refi/selvoea endif if(x76.eq.2) then ; check mirrored positions only during second iteration @alr3dapmd4s[x62,x52,x58,x55,x51,x41,x42] refi/volx76 refi/data@**** _8@**** refi/apmdx86 refi/anglesx76 refi/anglesx86 refi/transx76 refi/transx86 refi/angvoea refi/selvoea endif if(x76.gt.2) then @aln3dapmd4s[x62,x52,x58,x55,x51,x41,x42] refi/volx76 refi/data@**** _8@**** refi/apmdx86 refi/anglesx76 refi/anglesx86 refi/transx76 refi/transx86 refi/angvoea refi/selvoea endif ; ;vm ;Mail -s "APMD{***x86" $USER