Appion

Example of SIMPLE command: 
runSimpleCluster.py --stack=34 --projectid=248 --expid=7146 --runname=simpletest2 --description="test2" --nproc=12 --jobtype=partalign --timestamp=t1 --minp=5 --ncls=15 --mw=500

name of form: runSIMPLEClusterAndOrigami.php, under "Ab Initio Reconstruction", titled "SIMPLE Common Lines" 

Left side of form – keep the same as runCL2DAlign.php
Right side of form: 
Limiting parameters
____ “unbinned clip diameter” ; default value = size of stack in pixels ; help = Clip the unbinned boxsize ; --commandval = --clip ; minval = 2 ; maxval = size of stack
____ “particle binning” ; default value = 1 ; help = Binning of the image.  This takes any integer value, but powers of 2 are recommended. Binning quickly shrinks the image to help make the processing faster ; commandval = --bin
____ “number of particles” ; default value = number of particles in stack ; help = number of particles to use ; commandval = --num-part ; minval = 10 ; maxval = number of particles in stack
Pre-processing parameters
Checkbox “Center Stack” ; default value = checked ; help = center the stack using EMAN’s cenalignint program prior to alignent and classification in SIMPLE. Note: SIMPLE does not search for translational parameters in “cluster”, but it does in “origami”. ; commandval = --no_center (only if unchecked, keep clear if checked)
SIMPLE Cluster parameters
____ “ring2” ; default value = (boxsize / 2) – 2 ; help = last ring for alignment (in pixels) ; commandval = --ring2 ; max = boxsize / 2
____ “number of classes” ; default value = (number of particles / minimum PPC) ; REQ ; help = Number of 2D classes to generate ; commandval = --ncls ; 
____ “minimum PPC” ; default value = 10 ; help = minimum number of particles per class ; commandval = --minp ; max = number fo particles
____ “num Eigenvectors” ; default value = 30 ; help = number of eigenvectors to use for clustering ; commandval = --nvars 
____ “mask radius” ; default value = (boxsize / 2) – 2 ; help = radius of external mask (in pixels) ; commandval = --mask ; min = 1 ; max = (boxsize / 2)
SIMPLE Origami parameters
____ “low-pass” ; default value = 20 ; help = low-pass limit for origami reconstruction (in Angstroms) ; commandval = --lp
____ “high-pass” ; default value = 100 ; help = high-pass limit for origami reconstruction (in Angstroms). If you work with really large compelxes (lots of inelastic scattering), you may want to change this value ; commandval = --hp
____ “starting states” ; default value = 2 ; help = starting number of conformational states to classify (note: if you have 1 conformational state, you may still wish to use 2 in order to suck up bad particles) ; commandval = --froms
____ “ending states” ; default value = 2 ; help = ending number of conformational states to classify (note: if you have 1 conformational state, you may still wish to use 2 in order to suck up bad particles) ; commandval = --froms
____ “maximum refinement rounds” ; default value = 10 ; help = maximum number of rounds for refinement ; commandval = --maxits
____ “molecular weight” ; default value = NA ; REQUIRED (raise error if empty) ; help = molecular weight (in KDa) ; commandval = --mw
____ “included fraction” ; default value = 0.8 ; help = fraction of particles to include; commandval = --frac ; max = 1
____ “auto-masking low-pass” ; default value = 40 ; help = auto-masking parameter; low-pass filter value of the mask ; commandval = --amsklp
____ “edge” ; default value = 3 ; help = size of softening of the molecular envelope (in pixels) ; commandval = --edge 
____ “translational search ; default value = 3 ; help = origin shift (in pixels) ; commandval = --trs ; max = (boxsize / 2)