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--></style><title>RE: [3DEM] A question about ice thickness of
cryo-EM</title></head><body>
<div>Hi Guobin,</div>
<div><br></div>
<div>The ice thickness is a product of the environmental
conditions (humidity, temperature), the composition of the sample, the
blotting duration, pressure and paper and also the characteristics of
the grid. I don't think the grid hole size or periodicity alone
dictates your ice thickness. With the Quantifoil 7/2 we can get
vitreous ice that ranges from ~25-800nm. And, as Yifan
mentioned, we can also get ice too thick to image through.</div>
<div><br></div>
<div>Cheers,</div>
<div>Paul</div>
<div><br></div>
<blockquote type="cite" cite><font face="Times New Roman" size="+1">Hi
Yifan,</font></blockquote>
<blockquote type="cite" cite><font face="Times New Roman"
size="+1"> </font></blockquote>
<blockquote type="cite" cite><font face="Times New Roman"
size="+1">Thanks for your response. You brought a really good
suggestion. I love to try it. However due to our very limited access
to the scope and due to the fact that we don't have a CCD camera, I
prefer to get a direct answer to the question from our 3DEM community.
I guess some people do have experience on this
issue.</font></blockquote>
<blockquote type="cite" cite><font face="Times New Roman" size="+1">By
the way, as indicated in my previous message, the purpose for me to
estimate the maximum of ice thickness is for my image analysis, which
implied that the ice thickness is still appropriate for imaging. On
the other hand, my experience suggested that ice thickness varies on
different type of grids, for example, on 7/2 quantifoil holy grids, I
usually get thinner ice than that on 3.5/1 quantifoil holy grids. But
I have never tried to figure out how significant the difference of ice
thickness could be.</font></blockquote>
<blockquote type="cite" cite><font face="Times New Roman"
size="+1">I'm still waiting for more response and an answer. Thanks
for attention and help!</font></blockquote>
<blockquote type="cite" cite><font face="Times New Roman"
size="+1"> </font></blockquote>
<blockquote type="cite" cite><font face="Times New Roman"
size="+1">Regards,</font></blockquote>
<blockquote type="cite" cite><font face="Times New Roman"
size="+1">Guobin</font></blockquote>
<blockquote type="cite" cite><font face="Times New Roman"
size="+1"> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1"> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">-----Original Message-----<br>
From: Yifan Cheng [mailto:Yifan_Cheng@hms.harvard.edu]<br>
Sent: Tuesday, February 15, 2005 6:39 PM<br>
To: Hu, Guobin ; 3dem@ucsd.edu<br>
Subject: Re: [3DEM] A question about ice thickness of
cryo-EM</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1"> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">Hi</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1"> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">Well,
the ice can be very very very thick no matter what grids you
use.</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">Did
you ever get cryo grids which is too thick to be seen
through?</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1"> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">What
you can do to measure the ice thickness is to burn a small hole
in</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">the
middle of the ice. Then tilt you holder to a high tilt say 60
degree</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">and
measure the size of the hole. This can tell you how thick is
your</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">ice.
Then you can calibrate it with your CCD camera by measure
the</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">counts
over an empty hole and over ice. Next time just by comparing
the</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">CCD
counts over ice and empty hole will give you some fairly
good</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">estimation about your ice thickness. Good
luck</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1"> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">Yifan</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1"> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1"> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1"> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">Hu,
Guobin wrote:</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1"> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">>
Hi colleagues,</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">></font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">></font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">>
For our image analysis, we need to estimate the maximum ice thickness
in</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">>
our cryo-EM specimen on 3.5/1 quantifoil grids. We may be able
to</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">>
estimate that based on the thickness of carbon foil. As indicated by
the</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">>
quantifoil product catalogue, the standard thickness of carbon foil
is</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">>
12 nm. While observations of our cryo-EM micrographs have suggested
that</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">>
the thickness of carbon foil is definitely much larger than 12 nm.
Does</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">>
anybody have an idea of what the maximum thickness of ice could be
on</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">>
quantifoil grids (3.5/1)?</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">></font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">>
Thanks for help!</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">></font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">>
Guobin Hu</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">></font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">></font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">></font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1"> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">--</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1"> </font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">************************************************************</font
></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">Yifan
Cheng, Ph.D.</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">Department of Cell Biology, Harvard Medical
School</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">240
Longwood Avenue, Boston, MA 02115, USA</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">Phone:
1-617-432-4095 (office), 432-4097 (wet lab),</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1"
> <span
></span> 432-4708 (EM lab), 432-4107 (computer
lab);</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">Fax: 1-617-432-1144
(department)</font></blockquote>
<blockquote type="cite" cite><font face="Courier New" size="-1">email:
Yifan_Cheng@hms.harvard.edu</font></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1">************************************************************</font
></blockquote>
<blockquote type="cite" cite><font face="Courier New"
size="-1"> </font></blockquote>
<blockquote type="cite" cite>
<div><br></div>
<div><br></div>
<x-sigsep><pre>--
</pre></x-sigsep>
<div><font face="Courier New" size="+1" color="#000000">Paul
Chipman<br>
Electron Microscopy Facility Manager<br>
Dept. of Biology, Purdue University<br>
Lilly Hall, Rm. B216<br>
Phone: 765-494-1487<br>
Fax:765-496-1189</font></div>
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