[3dem] volta phase plate recovery time

Danev, Radostin danev at biochem.mpg.de
Sat Mar 25 11:40:31 PDT 2017

Hi everyone,

My original tests for the PNAS paper in 2014 were performed on an F20. There, we observed a correlation between the vacuum level (using or not the anticontamination device) and the recovery speed and concluded that the effect is due to the interaction of the beam-modified surface of the amorphous carbon with the residual gasses or the atomic species and radicals created by the ion pump.  On the F20 the recovery took a few days. The vacuum in a Titan Krios is much better than in an F20 and my subjective experience is that the spots take much longer to recover there. I’ve never had the chance to test the recovery speed on our Krios because the phase plate is used a lot and we want to spend the limited time we have on the  Krios for actual data acquisition.
After 2 1/2 years of use our Krios phase plate finally reached a point where we had to change it. There were too many dust-like contaminants on the surface which limited the usable areas to less than one third of the original areas. Those contaminants get deposited either during venting of the column for service or if one forgets to retract the phase plate when loading/unloading samples. Also, the non-contaminated areas were showing too much astigmatism variation from spot to spot. This could have been because of the "scars" that Matthias described.



From: 3dem [mailto:3dem-bounces at ncmir.ucsd.edu] On Behalf Of Craig Yoshioka
Sent: Friday, March 24, 2017 19:28
To: Anchi Cheng <acheng at nysbc.org>
Cc: 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] volta phase plate recovery time

Hi Anchi,

By the time we get through all the spots on all our films it usually has been over 2 months… I’m not 100% sure if all the old spots are gone… but I have not seen them, nor have I noticed their effects on the images after doing the full cycle.  When I have worried about it before in the past, I’ve just offset all the positions by using the motorized aperture controls to shift the whole phase plate.

Rado can correct me if I’m wrong, but I think secondary spots have the most deleterious effect if fairly close where they affect a large amount of low-resolution scattering.  I think if they are far enough out you would probably not notice their effect, and it probably would not be a showstopper anyways with random particle orientations and averaging.

On Mar 24, 2017, at 11:20 AM, Anchi Cheng <acheng at nysbc.org<mailto:acheng at nysbc.org>> wrote:

Hi, Wim,

Thanks for replying.  No, these are regular-spaced spots that show up after
using the patch position.  Similar to Figure 2 in Rado’s 2015 PNAS paper.
The spacing corresponds also the distance between the defined distance
between patches.  Incidentally, this phase plate is the cleanest I have ever
seen.  It was hard to find a feature on it to align.

We do have some burn spots disappeared after 1.5 month.  There were the
ones that was irradiated less.

I am hoping I get a number from you or others with phase plates longer than
we have how long you wait before using the same phase plate patch position



On Mar 24, 2017, at 4:15 AM, Wim Hagen <wim.hagen at embl.de<mailto:wim.hagen at embl.de>> wrote:

Hi Anchi,

Maybe it is contamination? I see some spots in some areas on our brand new phase plate, the contrast of the spots is reversed w.r.g. to a Volta patch. Here are some images with many bad spots and one 'quick and dirty fresh' Volta patch, 'above and below' plane:




On Thu, Mar 23, 2017 at 18:33, Anchi Cheng <acheng at nysbc.org<mailto:acheng at nysbc.org>> wrote:
Hi, all,

I am wondering what people’s experience in the length of time
they wait before they reuse a patch position on FEI volta phase plate.

We can still see rows of the different contrast (burn spot, we call it) at low mag
and very high defocus (-100 mm) after a month and a half.

If I return to a patch in 2 weeks, the phase shift development is faster.  In addition,
there is no guarantee that I am back at the exact position.


Simons Microscopy Microscopy Center
New York Structural Biology Center
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