Dear all,
I would like to know what program/software you usually use to plot the 2D
interactions between ligand and protein. As far as I know, LigPlot is powerful
but need some skills. Also a web-based program from PDB server is easy to use
but not very powerful.
What is your recommendation? T
Hey Narayanan
Not sure about about your spelling or capitalization but I am assuming the O is
a mistake. The, MiU is mega international units.
mcg is microgram ( when Greek symbol can't be typed).
You will need to know the assay that measures activity for G-CSF (filgrastrim).
Then the standa
Have you tried dialyzing the "purified" protein after elution into a no
imidazole buffer while doing TEV cleavage, and then reloading on to a His
column to remove the tag and TEV? I've found in my experience that this often
recaptures a lot of the background proteins.
If you're getting a 70kDa
With the starting remark that Wayne is "larger than life" in my mind, we could
call SAD the "Teeter Method"? I think it has a very nice ring to it and perhaps
Wayne would approve.
I learned something new today. Until now I thought that of course it is called
"dispersion". That is because in t
Dear Petr and other contributors to this thread,
I think it is never easy to call a method by that of "its inventor", as
there are usually many more than one inventor of the total know-how that
gets incorporated into the finished product that people end up using. Names
such as those of James
I never weigh in, so I don't know if I'll get in trouble here...
How would we distinguish MAD (to now be called "The Hendrickson
Method") from SAD ("The Hendrickson Method" - remeber crambin?
Nature, 1981)?
On Thu, Jan 19, 2012 at 3:59 PM, Anastassis Perrakis wrote:
> A, yes, inventor's names. A
On Jan 19, 2012, at 10:05 PM, Dale Tronrud wrote:
> ...
> If someone wrote in their paper "the Rossmann method was used to
> solve this structure" what method would come to mind?
>
The American method of course! Place the crystal in the beam, allow the
autoindexing routine to find the crystal
How many names do you propose to use to describe SIRAS?
If someone wrote in their paper "the Rossmann method was used to
solve this structure" what method would come to mind?
Dale Tronrud
On 1/19/2012 12:51 PM, Petr Leiman wrote:
It would be so much more convenient to call these techniqu
A, yes, inventor's names. Anyone reading who is less than 40 and knows what MTZ
stands for?
;-)
My favorite technique remains SADDAM - a side product of Gerard's War On Error,
that never did catch-up with the masses - experimentally or as an acronym.
A.
On 19 Jan 2012, at 21:51, Petr Leiman w
It would be so much more convenient to call these techniques (MAD, SAD, etc.)
by their inventor's name. This would simplify things immensely simultaneously
eliminating CCP4BB MADisagreements.
Although in our days of copyrights wars, the journals and perhaps conferences
where these methods were
Hi all,
Thanks a lot for the valuable suggestions.I have tried detwinning it but
the detwinning program in CCP4 takes care of only merohedral data( if I am
not wrong) and the other program( I guess Cell-now in Apex 2 by Bruker?)
which takes care of non-merohedral twinning is not accessible to i
On Thursday, 19 January 2012, Ian Tickle wrote:
> So what does this have to do with the MAD acronym? I think it stemmed
> from a visit by Wayne Hendrickson to Birkbeck in London some time
> around 1990: he was invited by Tom Blundell to give a lecture on his
> MAD experiments. At that time Wayne
This is a forwarded message. For inquires please contact Bill Weis (
bill.w...@stanford.edu).
Dear Colleagues:
We are delighted to announce that the* 6th International Conference on
Structural Analysis of Supramolecular Assemblies by Hybrid Methods *will be
held from *March 14-18, 2012 in Lake
... or just call it 'MAD', and you're bound to be correct !!
Everything is in the eye of the beholder, after all.
Marcus.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark J
van Raaij
Sent: 19 January 2012 17:59
To: CCP4BB@JISCMAIL.AC.UK
So, with the combined votes of Hendrickson, Blundell, Tickle and Google, can we
safely call it "Multi-wavelength Anomalous Diffraction" from now on and call
all other names wrong?
Mark
On 19 Jan 2012, at 18:50, Ian Tickle wrote:
> Perhaps I could chime in with a bit of history as I understand
Perhaps I could chime in with a bit of history as I understand it.
The term 'dispersion' in optics, as everyone who knows their history
is aware of, refers to the classic experiment by Sir Isaac Newton at
Trinity College here in Cambridge where he observed white light being
split up ('dispersed')
Hello,
I am trying to accurately quantify disulfide bond formation. I would like
to use a mass spec method involving two thiol reactive labels: one with
ethyl attached reacted before disulfide reduction and the other with methyl
attached reacted after disulfide reduction. I can label my own samp
Oh dear.
You definitely cannot de-twin a dataset by mergeing it with a
non-twinned dataset! And if the twin fraction of your synchrotron set
is much greater than 0.3 then it is unlikely that you will be able to
use the anomalous differences to solve the phase problem.
If I were you, I woul
As a self-declared "MAD Scientist" I suppose I should chime in.
The acronym "MAD" has indeed appeared by several different names in the
literature. Here is the "Google vote":
"multiwavelength anomalous diffraction" - 16500 articles in Google
Scholar (including Yang et. al. (1990))
"multiwavel
On 1/19/12 5:32 AM, Tim Gruene wrote:
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Hi Megha,
your email could hardly be more cryptic to me, and maybe you increase
the chance of getting help by explaining
- - what is R& D
- - what is MiOU?
- - what is mcg? (milli-centi-gram?)
(I understand ml,
Hi all,
Thanks for providing multiple solutions to my problem. Prof . Tim Gruene
and Prof. James Holton provided some nice solutions. However since the data
are collected from different crystals, I am not sure whether I can do MAD
phasing. My aim is to merge the two data-sets to circumvent the p
It would help if we knew the crystallization conditions and the protein
solution components. Also, what are the map sigmas and e/A^3? It seems odd that
there isnt positive density on the Fo-Fc map across the entire blob seen on the
2Fo-Fc map, considering you do not have anything modeled in. My
I have actually done this by running a normal PAGE gel without
stacking gel and switching the electrodes, which seemed to work
swimmingly.
JPK
On Thu, Jan 19, 2012 at 9:25 AM, Katherine Sippel
wrote:
> Hi Rashmi,
>
> In my experience native (even blue native) on proteins around that pI is
> sket
Who says this is on a twofold? Also, it would be very helpful to know
what was in the crystallization condition.
JPK
On Thu, Jan 19, 2012 at 12:44 AM, stacy William wrote:
> Dear All,
> I am working on plant proteins and solved a structure, there is an extra
> density which i cannot fix . I am
Hi Rashmi,
In my experience native (even blue native) on proteins around that pI is
sketchy at best. The electrophoretic mobility once it gets past the
stacking gel goes to crap meaning long electrophoresis times and it needs
to be done on a chillable system or in a cold room. If this is a multime
my comment on expression of protein being low
and nonspecific binding.
Amount of protein of expressed protein less = less resin = less
nonspecific binding?
(one have to do experiments to
find right amount of resin to get least non-specific binding
still pull out most of your protein of interest is
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Le 19/01/12 14:03, anita p a écrit :
> Hi All,
> Has anyone run a native gel for proteins at pI>8 .
> I want to pour my own native gel. Do I run a discontinuous page or a
> continuous one?? Please help with regards to the buffer system to be
> used, and the dye to be used.
> With regards
> Rashmi
Hi All,
Has anyone run a native gel for proteins at pI>8 .
I want to pour my own native gel. Do I run a discontinuous page or a
continuous one?? Please help with regards to the buffer system to be used,
and the dye to be used.
With regards
Rashmi
Any crystal can be worked at as P1.
What you know is that your crystal is not p212121
It can be
P21212
P21221
P22121
P1121
P1211
P2111
P112
P121
P211
P1
And then there is twinning ...
Suggestions:
Use Pointless or Phenix.xtriage, feeding the unmerged p1 data to decide.
Use the Zanuda serv
If you believe it to be rea density and not an artefact, this could be a
wee PEG molecule, for instance...
Artem
On Jan 19, 2012 4:34 AM, "Tim Gruene" wrote:
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>
> Dear :),
>
> electron density near special positions often bears some artefacts
> be
Your mileage will vary: prset is an almost always quasi constituitive
vector due to leakage, with additional induction upon expression of T7 pol.
This is not always bad since some proteins do not fold well upon avalanche
inducton but do in fact fold when expressed at a trickle (even good old lac
pr
You can try zanuda from York's site.
www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
It may help. It may be that you have a twinned crystal. As far as I know best
available test for twinning is L-test (truncate produces this test). When you
go from P1 to P212121 if L-test shows increased twinning
Dear all,
I have a data, and it has R/Rfree problem.
The data could be processed as P212121 and P1.
The resolution was 2.9, and unit cell parameters were a=73.527, b=90.035,
c=237.980, α=β=μ=90 and a=73.709, b=90.099, c=238.172, α=89.939,
β=89.945, μ=89.993 for P212121 and P1, respectively.
avoid pRSET would be my recommendation - my impression from a couple of
examples is pRSET gives badly folded protein.
Can you easily subclone it in a better expression vector?
(personally, even if it were not so easy, I would reclone it in another
expression vector).
Mark J van Raaij
Laboratorio
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Dear :),
electron density near special positions often bears some artefacts
because it is apparently difficult to calculate, i.e. the blob maybe
just some noise enhanced by its proximity near that two-fold axis.
Cheers,
Tim
On 01/19/2012 07:44 AM, s
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Hi Megha,
your email could hardly be more cryptic to me, and maybe you increase
the chance of getting help by explaining
- - what is R & D
- - what is MiOU?
- - what is mcg? (milli-centi-gram?)
(I understand ml, but I do not remember having met any of
Stacy,
It looks like it's just some noise on your two-fold symmetry axis.
You could probably model some/most of it with a couple of water molecules.
Tony.
On 19 Jan 2012, at 06:44, stacy William wrote:
> Dear All,
> I am working on plant proteins and solved a structure, there is an extra
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