Largest cryo-neg stain differences?

Philip Koeck Philip.Koeck at
Thu Sep 19 01:05:42 PDT 2002

I can't offer a good example but some thoughts.
I'd be grateful for some feed-back from other list members.

If one can assume that:

all cavities of a protein are accessible to stain,

and the main effect of negative stain specimen preparation is a flattening
of the specimen on the film without changing dimensions in other directions,

then surface rendered reconstructions should look about the same for
negative stain and cryo as long as the specimen wasn't tilted for
image recording, since images are projections of the structure anyway.
(The projection will look the same whether the specimen is flattened or

The biggest difference might come from a wrong estimation of amplitude
contrast during CTF correction (discussed for instance in the EMAN
manuals and related publications).

I'm not accounting for any changes in conformational details due to drying.

Philip Koeck
Svdertvrns Hvgskola and
Karolinska Institutet
Dept. of Bioscience at Novum
S-14157 Huddinge
phone: +46-8-6089186
fax: +46-8-6089290


----- Original Message -----
From: "Ed Gogol" <gogole at>
To: <3dem at SDSC.EDU>
Sent: Wednesday, September 18, 2002 8:53 PM
Subject: Largest cryo-neg stain differences?

> I'd like to compare a structural difference we've recently seen between 3D
> reconstructions from neg stain and cryEM data with those previously noted.
> I can't think of very substantial differences in those structures of which
> I am aware, but I'm sure the recipients of this list have some good
> examples, so I ask you to send me any of which you know (a reference may
> helpful, also).
> Thanks,
> Ed Gogol
> Ed Gogol, Associate Professor
> School of Biological Sciences
> University of Missouri-Kansas City
> 5007 Rockhill Rd., Kansas City, MO 64110
> Ph : (816) 235-2584
> FAX : (816) 235-1503

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