[3dem] simulated micrograph for ctf determination?

[Joachim Frank]

Dear Alex & Jinghua:

simulations that generate projection, then apply the CTF, then add  
noise leave out an important part: structural noise, which has to be  
added BEFORE application of the CTF.  The consideration of this  
pre-CTF noise complicates the overall picture.  See Baxter et al., JSB  
2008.  Modeled data designed for testing classification algorithms  
have been deposited at the EBI.  It should be easy to put a script  
together following the recipe of the paper, and the SNRs we measured,  
using any image processing system (SPIDER, IMAGIC, EMAN, etc.)

--Joachim

Quoting Alexandre Cunha <cunha at caltech.edu>:

> We are also interested in something similar. We searched but didn't
> find programs that can take a known protein complex, for example from
> the PDB, and automatically generate random noisy projections similar to
> what could be a real single particle experiment. Ideally we would like
> to be able to control image properties (level and type of noise, CTF,
> etc.) so to parameterize and quantify our classification methods
> accordingly.
>
> Any recommendations are really appreciated.
>
> - Alex.
>
> Steven Ludtke wrote:
>> There are several programs which will do this. For my part, you can  
>>  use ctfit or applyctf  in EMAN1. However,
>> even with realistic pink noise added, these images still remain an   
>> imperfect simulation of real images. Different
>> programs use different strategies for the raw image processing   
>> (working with the whole micrograph, boxed out
>> particles, boxed out carbon film, etc.), so it's hard to come up   
>> with a single uniform test for them all...
>>
>> ----------------------------------------------------------------------------
>> Steven Ludtke, Ph.D.
>> Associate Professor, Dept. of Biochemistry and Mol. Biol.      Those who do
>> Co-Director National Center For Macromolecular Imaging            ARE
>> Baylor College of Medicine                                     The converse
>> sludtke at bcm.edu <mailto:sludtke at bcm.edu>  -or-    
>> stevel at alumni.caltech.edu <mailto:stevel at alumni.caltech.edu>         
>>        also applies
>> http://ncmi.bcm.edu/~stevel
>>
>> On Sep 10, 2009, at 4:55 PM, jinghua tang wrote:
>>
>>> To test various programs for determine the CTF, or simply the   
>>> defocus, does anyone have
>>> a way to generate a simulated micrograph in which different CTF   
>>> was applied?
>>>
>>> Thank you in advance for your kind helps!
>>>
>>> Jinghua
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>>
>>
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-- 
Joachim Frank, Ph.D.
Howard Hughes Medical Institute Investigator,
Professor, Department of Biochemistry and Molecular Biophysics,
and Department of Biology, Columbia University,
650 West 168th Street, P&S Black 2-221
New York, NY 10032
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