Single Particle Analysis - Science topic

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l Perhaps this protocol list can give us more information to help solve the problem.

Most of the free software that can do this is optimized for Unix. Why not install a free Unix version on your system? I combine the e2boxer tool of eman2 for particle picking, CTFfind or gCTF for CTF correction (can be installed within Relion gui) and Relion for sorting and averaging. If you have a direct detector you can run MotionCor2 to align the movie frames. Hope this helps.

A time-average mean squared is over time and an ensemble-average is over several trajectories. Have a look at ergodicity. You can throw a dice a thousand times and take the mean or you can throw a thousand dices at once an take the mean. This describes a random process for which the time average of one sequence of events is the same as the ensemble average because every dice represents a state in phasespace . In macroscopic systems, the timescales over which a system can truly explore the entirety of its own phase space can be sufficiently large that the thermodynamic equilibrium state exhibits some form of ergodicity breaking. The spontaneous magnetisation in ferromagnetic systems, whereby below the Curie temperature the system preferentially adopts a non-zero magnetisation even though the ergodic hypothesis would imply that no net magnetisation should exist by virtue of the system exploring all states whose time-averaged magnetisation should be zero is a classic example.

The responses so far have been basically correct. DLS does measure a relaxation time for the decay of the autocorrelation function of the scattered light, from which a diffusion coefficient inversely proportional to particle size can be extracted. If you have a monodisperse size distribution, ie all particles of the same size then a size measurement by tem should give a size similar to that measured by DLS. If you have a distribution of particle sizes then things become interesting. Your size distribution measured by counting particles and distributing them into a range of size bins, give a number average size. DLS weights the distribution differently, by size to the power 6, essentially giving a z-average distribution. Larger particles are therefore given more weight, making the "average" size look larger. Hence your results. The other point is that part of the weighting arises as from the intensity of the light scattered by your particles. For your size of particles it looks as though you are approaching the limit of size where you cann assume that your results are independent of the angle at which scattering is measured. Modern DLS instruments don't normally allow for variation in scattering angle so you probably will not be able to see that your diffusion coefficient is angular dependent, but it has to be borne in mind as a source of difference. I suggest you try finding a copy of Dynamic Light Scattering edited by Wyn Brown.