[3dem] Particle number in a class to produce an average

[daixh]

·¢¼þÈË£º daixh
·¢ËÍʱ¼ä£º 2008-06-13 12:52:18
ÊÕ¼þÈË£º Steven Ludtke
Ö÷Ì⣺ Re: Re: [3dem] Particle number in a class to produce an average

Yeah, I am doing the reconstruction with EMAN1.8. The particles are about 460pixs with 1.06A/pix, boxed out with 512*512 boxes. The data are acquired on the JEM3100F, and the quality is pretty good. 
18054 particles applied with D5 symmetry are reconstructed, and the result is measured to be ~8A by the FSC=0.5 criteria. However, the structure itself seems to be far away from 8A resolution.(If it is turely 8A, we should more or less be able to see some 2nd structure elements, right?) I checked the particle numbers in each class. It seems that partial orientation preference exists and classes near the "side wiew" and "top view" have particles up to ~100, while many intermediate classes have <10 particles(~5-10) (However, these class averages are not eliminated by most stringent parameter settings in "refine" program of EMAN).  So, is this most probablely the reason? 
And to what extend can we trust the FSC curve? ...
Thanks for your patience.




Dai Xinghong
Laboratory of BioEM
School of Life Science
Sun Yat-sen University
Guangzhou, China. 510275
daixh at mail2.sysu.edu.cn
http://bioem.sysu.edu.cn
Tel:+86 20 84112286
Fax:+86 20 84110108

2008-06-13



·¢¼þÈË£º Steven Ludtke
·¢ËÍʱ¼ä£º 2008-06-13 10:52:20
ÊÕ¼þÈË£º daixh
³­ËÍ£º 
Ö÷Ì⣺ Re: [3dem] Particle number in a class to produce an average

There is no 'typical number' it depends VERY strongly on particle size, box size, MTF, 
CTF, and, frankly, the software.  A general rule of thumb for cryo data might be ~10-20
particles per class at a minimum if you are doing an EMAN or IMAGIC style reconstruction.
However, the number of classes will vary...

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