Flow chart for processing helical particles 
July 15, 1996 
 
 
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	program	 command		control		output	
	Information 
		parameters		file		file 
______________________________________________________________________________ 
DENSITOMETRY       PDS 
	PDS2MRC 
 
DISPLAY 
	LABEL or AXCHGMRC                               ID.rot          swap axes
	MRCDISP 
	XDISP                                                           display 
image
	XDISPH								display fft	
        PRNIMG                                          prnimg.ps       print 
image or fft
        MRCTOGIF                                        ID.gif          change 
to gif for printing
                                                                          on 
poster printer
 
FFT	 
	HFT  	 box:130x1024		ID.box		ID.fft,ID.prj 
     		 fft:256x1024 
	 | HLXBOX			ID.box		ID.imb		box the image 
	 | FFTRANS							fft 

	HFTOUT  	 print, examine phases and adjust roughly to determine 
 			center of particle 
 
REPEAT DISTANCE 
	ACF				ID.acf 
		print IDacf.log and determine repeat distance 
		criteria for true peak:	higher orders present peak lies along axis 
of particle. 
		1st and 2nd images consistent signal along high order ll maximal 
		extract ll if necessary (HLXS) 
		determine 2-fold residual if necessary 
 
SELECTION RULE 
	MATHCAD (on PC)			[1,0;n,l] 
					[0,1;n,l] 
	SRCHAID	 selection rule         ID.sra          ID.src                 
          SRCH                          ID.src                          phase 
residuals
 
EXPECTATION FOR LL 
	NLTABL besselmax rastersize     		ID.id, ID.tbl	extent of ll 
                above 2 parameters should be specified on the command line
                                                 ID.id used by other
                                                 programs - check it carefully
 
CTF DETERMINATION 
	SCTRAVGFT			ID.fft		ID.ctf		 
	  (CTFAVG)			ID.ctf		ID.avg,ctfavg.ps 
	PLTCTFX	pltctf.def		ID.ctf		ctffit.log,ctf.ps  
defocus,astig
 
PARTICLE WIDTH AND CENTER AND OMEGA TILT 
	PRJPLT						ID.prj,prjplt.out	particle width 
	HFT       width by n(rpts)	ID.box 		ID.fft 
 
        HLXS     omega,dx=0,0		hlxs.cnt	IDhlx.log 
        SRCHAID	 n,l,peak pos		ID.sra		ID.src	 
        SRCH				ID.src		srch.log	omega and dx 
 
TWO-FOLD ORIGIN 
submit HLXS		omega,dx	hlxs.cnt			ll for 2f srch 
	HLXFL     	extent of ll	ID.hlx		ID.nea,ID.far 
	NFAVG				ID.avg 
	H2FLD	phi, z			twofold.cnt	ID.2fd	residual 
 
COMMON ORIGIN FOR INDEPENDENT IMAGES 
	HRENUM	old/new (n,l)		ID.ren 
	HLXFIT	oldID.2fd		ID.fit		phi,z,Rscale 
		ID.avg					fit residual 
	HLX2FLD	phi,z from HFIT	ID.2fd	 		refined phi,z 
 
EXTRACT ALL LL 
	MKHLXCNT	        	ID.id		IDw.hlx 
	HLXFL				IDw.hlx	 	IDw.nea,IDw.far 
	NFAVG						IDw.avg 
	HRENUM	old/new (n,l)		IDw.ren 
	LLPRX2						IDwpr.log	ll lengths 
	 obsolete: llpr					IDw.edt		xwindow on 
screen 
         obsolete:HLXTBL n,l,ctf			IDw.edt	HEDIT template 
	HLXEDT				IDw.edt		IDw.new			 
 
APPLY SCALES AND CORRECTIONS 
	HLPASS	w2=4,excl. equator			IDw.lps	(2nd img only) 
	HCTFCOR	rpt,ctf zero,amp ctrst			IDw.lpc	(equator only) 
		     	 1st image:			IDw.cor	(equator only) 
	HLX2FLD	check corrected data for shift of 2f origin		final 
phi,z 
	HADDCTF	dfmax,dfmin, angle	haddctf.cnt	IDwt.nea,far	ctf info 
added to coln 
										phase reversed 
	HDIVCTF	dfmax,dfmin, angle	hdivctf.cnt	Idwt.cor	ctf corrected 
 
AVERAGE 1ST AND 2ND IMAGES 
	HLXAVG	"N" weight		ID1x2avg.cnt	ID1x2.lpc 
			ID2: scale = 2.2 (equator: 1), phi, z 
			ID1: scale = 1.0, phi z 
	 
HLX2FLD	rpt				ID1x2.2fd (for map)phi,z 
			check averaged data for slight shift of 2f origin 
	LLPR		print out averaged data		ID1x2pr.log	save output 
	LLPRX2 
 
AVERAGE INDEPENDENT IMAGES 
	HLXAVG	phi,z			hlxavg.cnt	?.lpc 
		weight images according to length of tube 
		Rscale, "F" or "N" weighting for individual ll. 
	HLX2FLD	rpt					?.2fd (for map) 
	LLPR						?pr.log 
	LLPRX2 
 
DRAW UNIT CELLS 
	LGLST				lglst.cnt	lglst.dat	edit .dat fot gnuplot 
	GNUPLOT					plot mean radial density distribution 
	HCELLPRM			ID.id		cell parameters  
	MATHCAD(on PC)							draw unit cell 
 
REFINEMENT 
	HBOXREFN	pitch,tilt,y shift	hboxrefn.cnt	hbox.out 
	HCTFREFN						refine ctf according to ll data 
	HAVGREFN	phi, z			havgrefn.cnt	havg.out	common 
2fd origin 
 
REVERSE TRANSFORM 
	HLXFB				hlxfb.cnt	ID.lg?	 
 
SECTIONS 
	HCLND				cylindrical sections 
	HX				x sections 
	HPSEC 
	HHRZ				horizontal sections