[3dem] FFT question

[benoit.zuber at ana.unibe.ch]

Hi
In our case the problem was the anticontaminator cryoblades touching the holder. This was occuring only when the cold trap was cold. Fiddling with it, we could get it in a better position and the cutoff was gone (took us about 1 year to figure out :-D
Cheers
Benoit

De : 3dem <3dem-bounces at ncmir.ucsd.edu> au nom de Garry P Morgan <Garry.Morgan at Colorado.EDU>
Date : mardi, 2 janvier 2018 à 22:22
À : Wim Hagen <hagen at embl.de>
Cc : "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Objet : Re: [3dem] FFT question

Wim,
another piece of the puzzle…the same holder is in our F20 today (with a US4000 ccd) and the FFT, while not from a drift corrected K2 movie stack, looks pretty good to my eye (see attached).
so i think the v-groove on our F30 is adjusted to the other holder, and this is the most likely explanation for what we’re seeing.  thanks again to you and everyone for all the feedback.
cheers,
Garry


[cid:image001.jpg at 01D38886.D864B470]

On Dec 29, 2017, at 4:40 PM, Wim Hagen <hagen at embl.de> wrote:

> Hi Garry,
>
> If only one holder is bad, the scope seems to be ok, so no worry about acoustics, mechanical vibrations or EM-fields.
>
> Is the FFT cut-off direction parallel to the holder rod (stage-X direction)? That most probably indicates a mechanical stage/holder problem, like a bad stage adjustment for that holder, and/or heavy nitrogen bubbling in the dewar which shakes the holder in its “weak direction”.
>
> On a Tecnai compustage, the holder rod is supported by three points, one in the front, one in the middle and an adjustable one in the back (the so called V-groove). Supporting a rod on three points requires proper alignment of one point, hence the adjustable V-groove. Additional problems:
> - Holders are not straight.
> - Cryo-holders shrink and bend when cooled down (~140 um shrinkage).
> Try balancing a pencil on three fingers with each point equally supporting the pencil, now imagine a bend pencil..
>
> Officially, the stage V-groove can only be adjusted to one holder and if it is a cryo-holder, the adjustment needs to be done with a cold holder. Often things work with multiple (cryo-)holders, warm and cold, but to me this is sheer luck.
> In my Philips days I once build a Tecnai with three cryo-holders meeting spec with one stage adjustment, the trick was to get all cryo-holders from stock and have the mechanical shop measure all holders to find three that were "bend in the same direction”…. But this only works until one holder gets sent off for repair and comes back with a different shape:
>
> Has the badly behaving holder suffered damage or has it been repaired?
>
> How does it behave when warm (less weight on V-groove, no nitrogen bubbling)?
>
> - FFT cut-off along the rod on cold holder: since the other holder is ok, most probably mechanical stage adjustment (for this holder, so catch-22) and/or nitrogen bubbling.
> - FFT cut-off NOT along the rod on warm holder: since the other holder is ok, maybe some slight charging in the holder tip, clip-ring, and/or sample, from magnetism and/or dirt. Try plasma cleaning everything.
>
> Cheers,
>
> Wim Hagen
> EMBL Heidelberg
>
>
>> On 29. Dec 2017, at 20:23, Garry P Morgan <Garry.Morgan at Colorado.EDU> wrote:
>>
>> Hi,
>> we’re getting consistently clipped FFT’s on our TF30…the attached image is from a 50-frame, summed/aligned image of the carbon (of a cryo-grid). the drift numbers are reasonably low, there is no astigmatism.  just wondering if any of you can provide a possible explanation of this?  it definitely looks like drift or some sort of movement, right?  we have 2 Gatan 626 holders, and it seems to only be happening with one of the holders…has anyone encountered a problem like this associated with a holder?
>> thanks,
>> Garry
>>
>> <unknown.jpeg>
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