== Particle Box Size ==
 * For single particle analysis '''the particle box-size must be 1.5-2x the size of the largest axis of your particle'''. For subtomogram averaging, padding is largely handled internally, but the box should still have at least a 10-20% margin on the edge. This reduces the impact of edge effects on the reconstruction, and improves the smoothness of the FFT of the map, so Fourier interpolation is more accurate. If you are stuck with data which was boxed with an insufficient size, the --extrapad option in e2ctf_auto.py will help mitigate the problem, but will still not produce results as good as data that was properly boxed with sufficient padding.
 * The size should also be selected from the list below. There are several important reasons for this, including proper CTF correction, good centering, and speed. 
 * If you are using the --shrink option, the result should be a number from the list. ie - with shrink=3, you should use one of the numbers below multiplied by 3 as your original box size.
 * The appropriate sampling for images for single particle reconstruction is ~2/3 Nyquist. That is, take the best resolution you hope to achieve, and divide by 3. This is close to the optimal A/pix value for your project. If your sampling is worse than this (A/pix larger), then you are not using a high enough magnification on the microscope. If your data is significantly oversampled (smaller A/pix than needed), e2ctf_auto will automatically generate downsampled versions of your data for more efficient processing.

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''For those who don't like to read (a detailed discussion is below), here is the list of good box sizes:'' :

'''24, 32, 36, 40, 44, 48, 52, 56, 60, 64, 72, 84, 96, 100, 104, 112, 120, 128, 132, 140, 168, 180, 192, 196, 208, 216, 220, 224, 240, 256, 260, 288, 300, 320, 352, 360, 384, 416, 440, 448, 480, 512, 540, 560, 576, 588, 600, 630, 640, 648, 672, 686, 700, 720, 750, 756, 768, 784, 800, 810, 840, 864, 882, 896, 900, 960, 972, 980, 1000, 1008, 1024'''

for traditional single particle analysis. If you were to pick a size not on this list, moving up to the next number on the list would make your refinement FASTER, sometimes MUCH faster. For example, refinements would take almost 2x longer with a box size of 134 as compared to 136

These sizes are less well tested, but also probably good:
1050, 1080, 1120, 1134, 1152, 1176, 1200, 1250, 1260, 1280, 1296, 1344, 1350, 1372, 1400, 1440, 1458, 1470, 1500, 1512, 1536, 1568, 1600, 1620, 1680, 1728, 1750, 1764, 1792, 1800, 1890, 1920, 1944, 1960, 2000, 2016, 2048, 2058, 2100, 2160, 2240, 2250, 2268, 2304, 2352, 2400, 2430, 2450, 2500, 2520, 2560, 2592, 2646, 2688, 2700, 2744, 2800, 2880, 2916, 2940, 3000, 3024, 3072, 3136, 3150, 3200, 3240, 3360, 3402, 3430, 3456, 3500, 3528, 3584, 3600, 3750, 3780, 3840, 3888, 3920, 4000, 4032, 4050, 4096
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Various algorithms in EMAN2 will depend non-linearly on the box size of the particle. Sometimes (such as the case with FFTs), this behavior will appear bizzare. For example refinements with a box size of 128 will run almost 2x faster than a box size of 122.

For several important reasons including accurate CTF correction and proper centering, box sizes in EMAN must be 1.5-2x larger than the longest axis of your particle. Sometimes for large viruses, this is reduced to 1.25x due to the very large box sizes involved, but the chance of artifacts at the edge of the box will be increased.

The following plot is a section of the timing tests used to produce the above list (note that the above list was updated using a new calculation, the table below is no longer strictly accurate). This is the time required for a typical set of operations used in 3-D refinement at each size:

{{attachment:rel_time.jpg}}

The complete timing table is also available:

{{attachment:time_vs_size.txt}}