Thanks for all of the helpful suggestions. In reply to some of the
comments, I did purify by eluting with imidazole from a Ni-NTA column.
The imidazole I used is 99% pure, although I'm not sure whether it is
reagent or molecular biology grade. I also do use DTT in my lysis and
elution buffers, s
The question was well crafted. It behooves on part of the respondent to
understand the question or clarify before answering.
On Fri, Aug 29, 2008 at 2:24 PM, Ian Tickle <[EMAIL PROTECTED]
> wrote:
>
> Agreed - but it wasn't entirely clear from the original question that
> this was the purpose of
A senior postdoctoral position is available at the Marine Biological
Laboratory in Woods Hole MA to continue our study on the crystal structures
of blood coagulation proteins, particularly Factor VIII (Structure.
2008;16:597-606). This is the protein missing in hemophilia. The candidate
should h
Since we learn a lot from this BB, here is a new view.. ;)
-- Forwarded message --
From: Rajan Pillai <[EMAIL PROTECTED]>
Date: Mon, Sep 8, 2008 at 6:46 PM
Subject: Re: [ccp4bb] Ratio of Number of Reflections to Number of
restrained Parameters
To: Partha Chakrabarti <[EMAIL PROTEC
Dear Experts,
At the risk of exposing excess ignorance, truncate makes me
very nervous because I don't quite get exactly what it is
doing with my data and what its assumptions are.
>From the documentation:
... the "truncate" procedure (ke
[flame war snipped]
It's usually considered bad manners to publicly post private
correspondence without permission, even if it may have some
entertainment value.
One should consider using plonk instead: http://en.wikipedia.org/wiki/Plonk
James
--
James Stroud
UCLA-DOE Institute for Genomi
Hi Phoebe,
I believe the usefulness and general correctness of the French & Wilson
protocol (as implemented in TRUNCATE) has been well-validated over the
years. There was some debate about 20 years ago on whether or not to use
it, but I think pretty much everyone has converged on using it for the
On Monday 08 September 2008 12:30:29 Phoebe Rice wrote:
> Dear Experts,
>
> At the risk of exposing excess ignorance, truncate makes me
> very nervous because I don't quite get exactly what it is
> doing with my data and what its assumptions are.
>
> From the documentation:
> ==
Does somebody have a .pdf of that French and Wilson paper?
Thanks in advance,
Jacob
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
It is A34: 517
http://journals.iucr.org/a/contents/backissues.html
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On Sep 8, 2008, at 1:19 PM, Jacob Keller wrote:
Does somebody have a .pdf of that French and Wilson paper?
Thanks in advance,
Jacob
***
Borhani, David wrote:
...
but I think pretty much everyone has converged on using it for the
past many years.
Many small molecule crystallographers seem to refine on intensity and so
avoid need this procedure. Towards the end of the recent thread "Wilson
plot from truncated.mtz" it had seeme
Okay, thanks very much!
Jacob
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: [EMAIL PROTECTED]
***
On Monday 08 September 2008 13:29:24 Jon Wright wrote:
> Borhani, David wrote:
> > ...
> > but I think pretty much everyone has converged on using it for the
> > past many years.
>
> Many small molecule crystallographers seem to refine on intensity and so
> avoid need this procedure.
I would ra
I would also recommend reading of the following paper:
D.S. Sivia & W.I.F. David (1994), Acta Cryst. A50, 703-714. A Bayesian
Approach to Extracting Structure-Factor Amplitudes from Powder
Diffraction Data.
Despite of the title, most of the analysis presented in this paper
applies equally
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Jon Wright
> Sent: 08 September 2008 21:29
> To: Borhani, David
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] truncate ignorance
>
> Borhani, David wrote:
> > ...
> > but I think pretty much eve
> I believe also that in an earlier posting Peter Zwart said he thought
> that CNS doesn't take account of the Wilson distribution when doing its
> version of the correction; if this is true (and I have no independent
> evidence that it is since I'm not a CNS user), then the above argument
> i
But there's a fundamental difference in approach, the authors here
assume the apparently simpler prior distribution P(I) = 0 for I < 0 &
P(I) = const for I >= 0. As users of Bayesian priors well know this is
an improper prior since it integrates to infinity instead of unity.
This means that, unlik
Having read the remainder of the paper more carefully I note that the
authors do go into an extensive discussion about Jeffreys (which they
don't recommend) and Wilson priors, which indeed overcome my objection
to the use of the improper prior. They conclude that the simpler
expression is adequate
How a seemingly innocent question can explode ...
I actually thought I understood this but little of what has been
discussed matches my "mental picture" of the truncate process.
Truncate can do multiple things, but the truncate part I believe really
just deals with converting I to F and the i
> However, when you
> need amplitudes, truncate is the way to go.
Better is to buy a detector that records amplitudes rather then intensities:
http://shelx.uni-ac.gwdg.de/SHELX/#FAQs%20smallmol
P
Dear Matt,
Based on the follow-up information that you posted, I would be willing to
bet that the color you observe is caused by various Ni complexes formed with
DTT/BME/etc. Dialysis won't necessarily remove these complexes (especially
if protein is part of the complex) and EDTA may not destroy t
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