SPIDER 3D Projection Matching Using Samrefine.py

Procedure:

(1) Make a new working folder, for example, called "samrefine", and go into it.
(2) Link or copy the particle stack in the current folder. Note that this stack must contain white particles on black background,
and in SPIDER format (*.dat). If not sure, please read about particle stack preparation.
(3) Make a folder called "cycle_000", and go into it. Link or copy the 3D initial model in SPIDER format, and name it as "3Dvol_000.dat".
(4) Go back into the main working folder, run "samrefine.py setup", and input all the parameters.
(The number of input "theta steps for ref.proj" must >= total cycle number!
The following inputs will run for 2 cycles: cycle_001 with a theta step of 25, and cycle_002 with a theta step of 20.)

>>>> PLEASE INPUT GENERAL SETTINGS
**** (0)Alignment;(1)Ali&Rec;(2)Reconstruction : 1
**** How many CPU to use? (0: all) : 2
**** Particle image stack (no extension) : stack_fixs5_n1
**** Pixel size (A) : 3.46
**** First particle for refinement : 1
**** Last particle for refinement : 1000
**** First refinement cycle : 1
**** Last refinement cycle : 2

>>>> PLEASE INPUT REFERENCE SETTINGS
**** Theta steps for ref.proj. in every cycle (e.g. 15,10, ...) : 25,20
**** Projection theta MIN (e.g. 0.0) : 0
**** Projection theta MAX (e.g. 90.0) : 90
**** Projection phi MIN (e.g. 0.0) : 0
**** Projection phi MAX (e.g. 359.90) : 359.9
**** CTF on ref.proj.? (0/1/2:No/individual/film_avg; negative:*TFC*TFCT) : 0
**** Defocus file (no extension) :

>>>> PLEASE INPUT ALIGNMENT SETTINGS
**** First rotation alignment ring : 4
**** Last rotation alignment ring : 25
**** Ring skip (1: no skip) : 1
**** XY scan scale (0: no XY scan) : 2
**** XY scan step (also serves as XY-CC range limit) : 1
**** How many with high APCC to get XYCC? (1=< X <=(xyscale*2+1)**2) : 1

>>>> PLEASE INPUT TRANSLATION_CC SETTINGS
**** Particle mask radius for XY-CC : 28
**** Particle mask COS edge for XY-CC : 4
**** Low pass radius for XY-CC (A) (0: skip) : 0
**** High pass radius for XY-CC (A) (0: skip) : 0

>>>> PLEASE INPUT GENERAL RECONSTRUCTION SETTINGS
**** Image stack for reconstruction (no extension) (*:same for alignment) : *
**** Particle selection ("*" for all;"INT_list";"?.dat";"?.plt") : *
**** Reconstruction method (BPCG/BP3F/BP3G/FREALIGN) : BP3F
**** Symmetry doc file (*: no symmetry) : *
**** Calculate resolution? (y/n) : y
**** Filter output volume? (y/n) : y
**** FERMI high-pass stop,pass bands(A) (e.g. 100.0,50.0) (0,0: skip) : 0,0
**** FERMI low-pass pass,stop bands(A) (e.g. 15.0,10.0) (0,0: skip) : 40,30

>>>> PLEASE INPUT "BPCG" RECONSTRUCTION SETTINGS (hit ENTER to skip inputs if not using BP_CG)
**** "BPCG" Reconstruction radius :
**** "BPCG" Reconstruction mode (1,2 or 3) :
**** "BPCG" Reconstruction lambda (2000,500 or 100) :

(5) Run "samrefine.py run".