Hello,
What is the best way to calculate and represent Fourier Difference Maps?
Eugenio De la Mora Lugo
Instituto de Biotecnologia
Universidad Nacional Autonoma de Mexico
Hi,
If you are plagued by 'generic' proteolysis, it is not likely that changing
buffers from TRIS to phosphate will help reduce the breakdown. You may want
to ask yourself several key questions regarding the breakdown:
1. is it proteolysis or abortive translation?
2. is it happeni
Hi,
This is going to be an off topic question concerning this community. I have a
protein 6XHis tagged. When retrieved from the Ni-NTA column with imidazole
found to be degraded, appears like a deep band with other bands (touching each
other below the main band) in SDS PAGE. The protein is a
Ah, there's the rub. No, my simple-minded approach was to calc. the MD
density, averaged over, e.g. 100,000 MD snapshots (~1 us of time), by
placing (5) Gaussians at each instantaneous atomic position, then adding
them all up. Each atom got it's correct Gaussian, along with a b-factor
of 1 A^2, but
Dear Ian,
I agree entirely about the k-curve approach. SHELX/S/C/D/E have
always used it to derive E-values.
Best wishes, George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-55
This indeed raises the question of whether the assumed Wilson
distribution is valid, and it's another point I was in fact going to
bring up. As presently constructed, Truncate fits a straight line to
the Wilson plot (based on Imeas) in order to determine the overall scale
& B, but to avoid the pro
Dave
It's hard to say without actually doing the calculations, it may well be
that I'm being too pessimistic about your prospects! One thing I'm not
clear about is how you actually calculated your map from the MD atomic
positions: did you take into account the resolution limits, data
completeness
In addition to Ian's circular argument, there is the problem that
the assumed distribution is only approximately valid, indeed in the
presence of (translational) NCS it could well be a poor approximation.
Refinement against suitably weighted measured intensities (which may of
course be slightly n
This goes back to the issue I was raising, namely that ^2 (from the
Truncate output mtz F column) is not the same as Imeas (in the IMEAN
column) so you won't get exactly the same results from the Wilson plot,
particularly at high res where the average I/sigma is low. Since the
plot actually demand
Dear Colleagues,
The ICSG 2008 International Conference On Structural Genomics is coming up
Sept 20-24 in Oxford, UK. We have a terrific program lined up and I hope
that you'll register now if you haven't already! I've copied the latest
announcement of the meeting below.
All the best,
Tom Terwil
try espript or its online equivalent. I've always found it very good.
http://espript.ibcp.fr/ESPript/ESPript/
best regards,
Paul..
###
Dr. Paul A. McEwan
Protein Crystallography Group
Office C58
Centre for Biomolecular Science
University of Nottingham
Notting
Positions are available for a postdoctoral fellow and graduate student
at the University of Maryland, Baltimore in the Department of
Pharmaceutical Sciences.
These positions involve the study of structural mechanisms of molecular
recognition by proteins. Projects in the lab include:
(i) structura
Dear All:
I have a quesiton regarding the data set of the mutant protein. The mutant
protein crystalizes in the same condition as natave protein. The native
protein's unit cell is a=31.92, b=65.96,c=83.37, P212121.
When I tried to process the data set of the mutant protein, I have the
tricilic c
Try stride..
http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py
--- On Fri, 22/8/08, Buz Barstow <[EMAIL PROTECTED]> wrote:
From: Buz Barstow <[EMAIL PROTECTED]>
Subject: [ccp4bb] Software for Drawing Protein Secondary Structure
To: CCP4BB@JISCMAIL.AC.UK
Date: Friday, 22 August, 2008, 2:57
Thanks, Ian, this is very helpful. Data are 50 - 2.4 A, 90% complete,
70% in 2.5 - 2.4 A shell. Rf/R = 0.235/0.194 (with the few key atoms
omitted; they lie on the 4-fold axis, by the way). = 60 A^2. P4212,
~12,000 atoms in the model. Do these stats impact your recommendations
at all, or raise new
Hello all,
I believe I have a P41 perfectly twinned as a P41 21 2. I'm using the
detwin_perfect.inp in CNS in every round of refinement to detwin the
original P41 data as I update the single molecule in my asymmetric
unit (so far).
[1] Should I be able to find the second molecule (from re
Dear All,
Does anyone know of a program that is capable of drawing the secondary
structure of a protein molecule?
I'd really like to be able to take a protein molecule, and draw the
secondary structure out along a line, indicating the positions of
secondary structural elements like sheets
rerun truncate with input amplitudes..
eleanor
James Pauff wrote:
If I've lost my SCALA MTZ, and have only the truncated.mtz for my dataset,
which program is the quickest means of obtaining a Wilson plot?
Thank you again,
Jim
--- On Wed, 8/20/08, Eleanor Dodson <[EMAIL PROTECTED]> wrote:
Rerun truncate on your data ans look at the graphs - they often give
clues if the distribution is distorted..
Eleanor
PS - maybe we are a nervous lot, but we always re=process synchroton
data again at home with time to think about it..
James Pauff wrote:
Hello all, thank you for the respons
Dear Hongmin,
The only way to get round the problem is to answer no when being asked
if you want to install Microsoft .NET Framework.
It is normally installed with windows.
Best Regards
Francois Remacle
CCP4
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Beh
Those who are using my teaching material might like to know
that I have recently updated it, but I have left the password
unchanged. However the biggest changes were in the environmental
chemistry course (in German) because the environment (or at
least our perception of it) is changing so fast. The
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