Dear CCP4 Developers,
What is the correct reference for JLigand to include in a publication ?
Thanks best regards,
Pedro Matias
Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
Hi all,
I have two datasets, both CO SAD data, one collected at CO anomalous
wavelength at synchroton and the other at home source. I wish to combine
these two data-sets and use for SAD phasing. Can anyone suggest how this
can be done?
Regards,
ARKO
--
*ARKA CHAKRABORTY*
*CAS in
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Dear Arko,
could you not try MAD with the two different data sets?
Otherwise you can check the strength of the anomalous signal for both
sets separately (I am sure pointless prints the anomalous CC over
resolution shell) and after merging them.
If
Hello Every one,
I am trying to purify a human protein in a
bacterial expression system of around 82 kDa (with a 5 kDa His tag, so
fusion protein is 87 kDa) which was cloned in pRSET-A vector. The Problem
is I am not able to get rid of the infamous contamination proteins
Hi -
Here at the NKI, we had formed a committee to look at ELN solution two
years ago.
We had interviewed three vendors, and run two tests with twenty users.
A brief description of the outcome:
1. None of the twenty test-users was satisfied with any of the two
solutions - and each was
Have you tried reverse purification over the Ni-NTA column? That is the typical
next step in purification after His-tag cleavage. Or did you mean to say that
the impurities elute off with your cleaved protein during the reverse
purification? If this is the case, you could try adding a reducing
On Wed, 2012-01-18 at 18:26 +0530, PULSARSTRIAN wrote:
The Problem is I am not able to get rid of the infamous contamination
proteins of arnA gene (72 kDa) and glmS gene (67 kDa).
This is only a problem if you plan to have imac purification as your
only step. If the goal is crystallization,
May be this one helps
The current study presents the design, engineering, and characterization of two
E. coli BL21(DE3) derivatives, NiCo21(DE3) and NiCo22(DE3), which express the
endogenous proteins SlyD, Can, ArnA, and (optionally) AceE fused at their C
terminus to a chitin binding
Another option is to try NEB NiCo21(DE3) cells.
http://www.neb.com/nebecomm/products/productC2529.asp
I have no relation to NEB beyond being a customer.
They've mutated GlmS to eliminate binding to IMAC resins and have
added chitin affinity tags to SlyD, ArnA and Can to allow simple post-
How to merge two or more runs depends on the software you used to
process the images. If you used MOSFLM/CCP4, then you would use the
programs REBATCH (perhaps REINDEX) and SORTMTZ to combine the unmerged
mtz files (the ones that come out of MOSFLM) before feeding them to
SCALA. My program
On Jan 18, 2012, at 6:17 AM, Anastassis Perrakis wrote:
Here at the NKI, we had formed a committee to look at ELN solution two years
ago.
We had interviewed three vendors, and run two tests with twenty users.
A brief description of the outcome:
1. None of the twenty test-users was
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Comments on the comments ;-):
On 01/18/2012 05:54 PM, James Holton wrote:
[...]
An important thing that is not done automatically, however, is to check
if your space group has more than one indexing solution. Basically, if
merohedral twinning is
By the way, I wouldn't use MAD to describe the mergeing of non-isomorphous
datasets. Strictly speaking, MAD is at least an attempt to measure both
anomalous (f) and dispersive (f') differences, and I don't think it is
appropriate to use the term MAD when you know the dispersive signal is
Isn't it true that we cannot even agree on what MAD stands for?
Is the following right?
M = Multiple-wavelength. I think everyone agrees to this, although I
believe I've seen the occasional (and sometime non-sensical) variant
A = Anomalous (I think everyone agrees, although this term should
On Jan 18, 2012, at 10:20 AM, Tim Gruene wrote:
Comments on the comments ;-):
Ditto
[...]
By the way, I wouldn't use MAD to describe the mergeing of
non-isomorphous datasets.
I agree, neither would I.
Just to be on the save side and avoid confusion by less experienced
readers of the
That is excellent! You refer obviously to the multiple anomalous
discussions on the bb? (Maybe d = disagreement?)
JPK
On Wed, Jan 18, 2012 at 11:42 AM, D Bonsor dbon...@ihv.umaryland.edu wrote:
Isn't it true that we cannot even agree on what MAD stands for?
Is the following right?
M =
Hi,
Regardless of what the consensus on naming for the technique, I'd
suggest you combine these datasets during phasing (I'm aware of MLPHARE,
SHARP, PHASIT supporting multiple anomalous datasets during phasing;
others probably do as well). Combining at the merging step
Make sure the imidazole is removed before you apply the TEV digested sample
back to the Ni column for the reverse Ni step.
Sounds like the expression level of your protein is low. You many consider
to improve the expression. Those contamination proteins disappear from Ni
elution when the
Can I be dogmatic about this ?
Multiwavelength anomalous diffraction from Hendrickson (1991) Science
Vol. 254 no. 5028 pp. 51-58
Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
Multi-wavelength
Can I be dogmatic about this ?
I wish you could, but I don't think so, because even though those
sources call it that, others don't. I agree with your thinking, but
usage is usage.
a SAD experiment is a single wavelength experiment where you are using the
anomalous/dispersive signals for
Can I be dogmatic about this ?
I wish you could, but I don't think so, because even though those
sources call it that, others don't. I agree with your thinking, but
usage is usage.
And 10,000 lemmings can't be wrong?
This begs the question* whether you want the lemmings to understand
you. One theory of language, gotten more or less from Strunk and
White's Elements of Style, is that the most important feature of
language is its transparency to the underlying thoughts. Bad language
breaks the transparency,
But if we were to follow that convention we would have been stuck with
Multi-wavelength Resonant Diffraction Experimental Results, or, quite simply,
MuRDER.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob
Keller
Sent: Wednesday, January
On Wednesday, 18 January 2012, Soisson, Stephen M wrote:
But if we were to follow that convention we would have been stuck with
Multi-wavelength Resonant Diffraction Experimental Results, or, quite simply,
MuRDER.
You could switch that to Multiple Energy Resonant Diffraction Experiment
but I
Hi every one
I have made a Cif file for the restraints of my ligand with Jligand, which is
attached to my protein via a lysine-aldehyde Schiff base formation.
The problem is that whenever I run the refmac with the Cif file with torsions
and link description, it changes the distance of the
Hopefully by the time your paper accepted it will be out. Here is the reference:
JLigand: a graphical tool for CCP4 template restraint library
Lebedev AA, Young P, Isupov MN, Moroz OV, Vagin AA and Murshudov GN (2012)
Acta Cryst D68, in press (submitted, in consideration or whatever)
I hope
Dear Sam
double bond is only used to find bon lengths and other parameters. Refmac
uses bond length.
As I see you would like to make a link between two residues. There is a
tutorial written by Andrey Lebedev that addresses exactly this type of
problems. Please have a look this site:
We are involved in R D of recombinant filgrastim and the standard sample
label mentions it as 30MiOU/ml i.e 300 mcg/ml. How can we determine the
IU/ml as we know our protein is 300 mcg/ml. can anyone please guide me on
the corelation.
regards,
megha
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