Dear all
Would anyone knows of source of cheap precast SDS-page gels?
Thank you.
An mtz file gives you a list of reflection related things . From this list
you can calculate an electron density map.
From this map you can extract density values, but you probably will want to
use some software to do this - counting numbers would become tedious!
Eleanor
On 28 August 2014
Dear CCP4
I wanted to ask has anyone tested 3D protein structure by cryo-electron
microscopy? what is the suitable concentration required for this procedure
Best Regards
Rana
Hi,
The research group of Dr. Reza Khayat at the City College of New York
(www.khayatlab.org) is seeking candidate postdoctoral fellows to study host
pathogen interaction using a combination of cryo-electron microscopy (cryo-
EM), X-ray crystallography, biophysics and biochemistry. The research
Define cheap. Several vendors offer SDS PAGE minigels for about $10 US a
pop. I get mine from Novex.
Roger Rowlett
On Aug 29, 2014 2:22 AM, Theresa Hsu theresah...@live.com wrote:
Dear all
Would anyone knows of source of cheap precast SDS-page gels?
Thank you.
Dear All,
I frequently use the Coot feature Fetch PDB and MAP using EDS... with
great success when peer reviewing literature reports. However, when I try
this for the recent KRAS structures deposited by Kevan Shokat and Jim Wells
(Nature 2013), the Coot generated maps are garbage, although the
Hi Nick,
Not sure what happened here, it seems like a bug in this EDS entry. You can try
PDB_REDO for maps. In recent versions of COOT (version 0.8*) the button for
getting maps and a model is just under that for EDS. There is a plugin for
older versions of COOT. They look okay, but the model
Yes, but the technique is still in its infancy stage.
DOI: 10.1016/j.sbi.2014.03.004
Cheers-
Brad
On Fri, Aug 29, 2014 at 6:34 AM, rana ibd
0285de88044a-dmarc-requ...@jiscmail.ac.uk wrote:
Dear CCP4
I wanted to ask has anyone tested 3D protein structure by cryo-electron
microscopy?
What happened to this service? I was reading about it in a book (crystallography made crystal clear) but can't find it anymore.Did the EU shut it down?Biotech Validation Suite for Protein Structures
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Hi Rana,
in contrast to Brads answer, and in case I understand you well, Cryo
EM is not in ts infancy stage (as long as you do not talk about Cryo
EM on crystals.
For cryo EM you need only several ul of a nM solution.
I can always suggest you the 3dem bb. There are of course still
Theresa,
Try Genscript. They have probably special now going on, so box of 10 SDS PAGE
costs $39.
I'm not associated with Genscript in any way and I don't use their SDS PAGE.
Vaheh Oganesyan
www.medimmune.com
-Original Message-
From: CCP4 bulletin board
Dear Rana,
Brad's post compelled me to reply to you. The Cryo EM field is well into its
pro stage.
If you can be specific about the MolWt, size and if it makes any complex, then
much precise and helpful answers to your question can be provided.
Best
Anindito Sen Ph.D
JeoL
On
Hi all-
I interpreted the original question, wrongly so, as an inquiry into using
cryoEM for 3D *crystallography, *which is very new, and not general 3D
structure determination, which of course has been utilized for the last few
decades. My apologies! Yes, there are plenty of success stories out
Could anyone remind me how to calculate anomalous difference Fourier maps
using model-calculated phases? I was doing it by
(1) calculating PHcalc from a pdb file using Sfall, then
(2) merging PHcalc with Dano of experimental SFs, then
(3) calculating a map with Dano and PHcalc using FFT
I think the answer is in this paper:
LOW-RESOLUTION ELECTRON-DENSITY AND ANOMALOUS-SCATTERING-DENSITY MAPS OF CHROMATIUM HIGH-POTENTIAL IRON PROTEIN
By: STRAHS, G; KRAUT, J
JOURNAL OF MOLECULAR BIOLOGY Volume: 35 Issue: 3 Pages: 503- Published:
1968
On Fri, 29 Aug 2014, Alexander
See also:
page 141 in The Bijvoet-Difference Fourier Synthesis,
Jeffrey Roach, METHODS IN ENZYMOLOGY, VOL. 374
Pavel
On Fri, Aug 29, 2014 at 12:17 PM, Ronald E Stenkamp
stenk...@u.washington.edu wrote:
I think the answer is in this paper: LOW-RESOLUTION ELECTRON-DENSITY AND
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Here is how I view this stuff. In general the diffraction pattern
does not obey Fridel's law, which means that the actual electron
density map is a set of complex numbers. The map that consists of
just the real part of these density values is
The request to calculate a map using DANO means the CCP4 implemtation of
the FFT program moves the input PHIC phase by 90 degrees as Zbysek says..
Eleanor
On 29 August 2014 20:23, Pavel Afonine pafon...@gmail.com wrote:
See also:
page 141 in The Bijvoet-Difference Fourier Synthesis,
You might consider using AnoDe (J. Appl. Cryst. 44 (2011) 1285-1287).
This program and its documentation are available via the SHELX homepage.
You will need a PDB file name.pdb of the native structure and a file
name_fa.hkl that contains the anomalous differences. You can use SHELXC
or XPREP
MTZ files are not maps. They can usually be converted into maps, but
that depends on the type of information they contain. Coot lets you load
an mtz and immediately view a map, but only because it internally picks
the coefficients that you probably want to use and then internally
executes an
The CCP4 FFT program does the 90-degree rotation automatically if you
use DANO= as the column assignment. The rotation is because anomalous
difference arise from scattering that is 90 degrees out of phase with
normal electrons.
-James Holton
MAD Scientist
On 8/29/2014 11:43 AM, Alexander
That is, the optimum noise filter is generally the same shape as the signal of
interest ...
Has this been proven, or it just common sense? And if the filter is the same
shape as the signal, why does one need the signal at all? I guess I don't know
precisely what you mean, but anyway, I like
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