Nathan Cowieson:
I have found that ion exchange is a good way to concentrate protein. If
there is no reason that you can't pass the whole 450 mls through the
column then you should do that.
Another way is to load dilute protein onto small hydroxylapatite column.
Provided that the buffer does
I have found that ion exchange is a good way to concentrate protein.
If there is no reason that you can't pass the whole 450 mls through
the column then you should do that. Another way to do this would be to
add ion exchange resin straight into the 450 mls, stir for a bit, let
it settle, po
Concentration of large volumes is a common bane of many biochemistry/protein
production labs. Diaflow can be quite expensive and regular concentrators
tend to take forever. Thus, my preferred solution is not to use
concentrators at all.
1. AS cuts do not really *require* high protein concentration
Dear All,
we have GCSF protein produced in inclusion bodies. we solubilise it refold
it and then concentrate it using proflux system. still the concentration
of the protein we get is less and volume is more for us to load in Ion
exchange chromatography. is there any simple technique that can be
Hello All,
Since I have long been such a big Mac stereo 3D proponent in the past,
it is especially important that I go on the record with an updated
perspective.
Based on all of the accumulated evidence to date, a verdict can now be
rendered: we have lost the case. For stereo 3D visualization
Has anyone tried XQuartz for this: http://xquartz.macosforge.org/trac/wiki
On Jun 26, 2008, at 2:24 PM, Ben Eisenbraun wrote:
A follow up note:
I was at Apple's WWDC a couple weeks ago, and during one of the lunch
time sessions for scientists, several people brought up the fact that
stereo
A follow up note:
I was at Apple's WWDC a couple weeks ago, and during one of the lunch
time sessions for scientists, several people brought up the fact that
stereo 3d was still broken on Leopard, and asked for it to be fixed.
The Apple engineer present hemmed and hawed a bit, and finally said t
I think it is only X11 apps. I am able to use 3D stereo using MacPyMOL on
my Mac tower runing 10.5.2.
Cheers,
Scott
> Is this true for native aqua gui programs, or just the X11 ones?
>
>
>
> On Thu, June 26, 2008 1:50 pm, eortlund wrote:
>> Hi Everyone,
>>
>> I am writing everyone just to
On Thu, Jun 26, 2008 at 02:00:45PM -0700, William Scott wrote:
> Is this true for native aqua gui programs, or just the X11 ones?
According to Warren Delano, the PyMOL developer, it's affects native
apps as well:
http://tinyurl.com/6ohzfc
I emailed him for clarification and he replied:
"as soo
Just to add on that: I converted to OSX in 2001 when it first appeared.
Before I was Irix/Linux and -alas- the relatively happy owner of a
SONY VAIO with Windows XP.
For 8 years I remained impressed. But, 10.5 has been a massive
disappointment after being spoiled for so long,
with stable wor
Is this true for native aqua gui programs, or just the X11 ones?
On Thu, June 26, 2008 1:50 pm, eortlund wrote:
> Hi Everyone,
>
> I am writing everyone just to remind all those who are thinking of
> upgrading to 10.5 that currently quad-buffered stereo will not work
> for coot, pymol etc... sin
Hi Everyone,
I am writing everyone just to remind all those who are thinking of
upgrading to 10.5 that currently quad-buffered stereo will not work
for coot, pymol etc... since Apple has not done a good job with the
video drivers in Leopard. So if you would like to use 3D stereo
viewing
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Le 26 juin 08 à 18:49, Ethan Merritt a écrit :
On Thursday 26 June 2008 09:36:16 am Serge Cohen wrote:
Please some one tells me if I'm wrong ... but I though that indeed
one
is NOT supposed to measure anomalous difference from reflections h
and
Hi Fred,
I would say that the helix stability will generally be affected by its
context within the protein, unless it is (unlikely?) separated from the core
of the protein and it has intrinsic stability (some peptide sequences do).
Also, in a particular context, you may have mutations that unfold
Hi Citizens:
I've taken the liberty of summarizing/anonymizing/interpreting a bit
with the varied and colo[u]rful responses. They fell into three
general categories. Thanks to all who responded and offered sage
advice...
1. The unanimous consensus was that headhunters aren't useful for
> Also only centric phases are restricted.
Yes. *Related* would have been be the proper term
for symmetry related reflections. In detail:
The phases of symmetry related reflection still
are *related* by
phi(hR)=phi(h)-2pihT (no restrictions on phi(h))
For centrics
phi(h)=pihT or pi(hT+1)
th
On Thursday 26 June 2008 11:35:31 am Bernhard Rupp wrote:
> Let's try this again, with definitions, and pls scream if I am wrong:
>
> a) Any reflection pair hR = h forms a symmetry related pair.
???
Maybe you meanh' = hR
>R is any one of G point group operators of the SG.
Hi Bernhard
This is OK, all it's saying is that if you generate by PG symmetry two
new reflection h' = hR' and h" = (-h)R" then the Bijvoet pair h' & h" is
symmetry-related to the Friedel pair h & -h.
The notation in your previous e-mail was somewhat imprecise, e.g. if h =
hR that implies that
Bernhard Rupp wrote:
I quote from these pages:
"Bijvoet pairs are Bragg reflections which are true symmetry
equivalents to a Friedel pair. These true symmetry equivalents
have *equal amplitudes, even in the presence of anomalous scattering*."
This is poorly worded. I would change it to
There was a mistake in the letter that listed the Bijvoet pairs
for a monoclinic space group and that is confusing you. Let me
try.
The equivalent positions for a B setting monoclinic are
h,k,l; -h,k,-l.
The Friedel mates for the general position (h,k,l) are (-h,-k,-l).
This means tha
I quote from these pages:
"Bijvoet pairs are Bragg reflections which are true symmetry
equivalents to a Friedel pair. These true symmetry equivalents
have *equal amplitudes, even in the presence of anomalous scattering*."
Sounds more like centric or perhaps simply symmetry related to me.
A few
Hi, Bernhard,
Check out page 8
http://students.washington.edu/zanghell/TAs/BSTR521/notes/anomalous_scattering.pdf
I thought that Friedels are reflections related by pure inversion
symmetry, while Bijvoets are reflections related by non-inversion symmetry
of the reciprocal lattice. Thanks,
Let's try this again, with definitions, and pls scream if I am wrong:
a) Any reflection pair hR = h forms a symmetry related pair.
R is any one of G point group operators of the SG.
This is a set of reflections (S). Their amplitudes
are invariably the same. They do not even show up
as
Hi everyone,
Has anybody know some program to calculate the dipole moment of helices? Which
relevant parameters should I have to calculate to compare stability of helices?
I would like to compare the stability of different mutations on helices, but
don't know if it makes sense when you take the
On Thursday 26 June 2008 09:36:16 am Serge Cohen wrote:
> Please some one tells me if I'm wrong ... but I though that indeed one
> is NOT supposed to measure anomalous difference from reflections h and
> h' if those are related by one of the symmetry operator of the point
> group...
This statement
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Please some one tells me if I'm wrong ... but I though that indeed one
is NOT supposed to measure anomalous difference from reflections h and
h' if those are related by one of the symmetry operator of the point
group...
That is in monoclinic (
Our eCheminfo Autumn CoP meeting this year includes an extensive session of 1.5 days on PDB Ligands chaired by Marc Nicklaus (NIH) which should be of particular interest to the CCP community. Meeting announcement including CFP and Bursary Award preogram
below.
best regards
Barry Hardy
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I've always thought that a Bijvoet pair is any pair for which an
anomalous difference could be observed. This includes Friedel pairs
(h & h-bar), but it also includes pairs of the form h & h', where h'
is symmetry-related to h-bar. Thus Friedel pairs are a subset of all
possible Bijvoet pai
Friedel pairs
Bijvoet differences
Friedel pair is strictly F(hkl) and F(-h,-k,-l).
Bijvoet pair is F(h) and any mate that is symmetry-related to F(-h), e.g.,
F(hkl) and F(-h,k,-l) in monoclinic.
There are always anomalous differences, though they can be unmeasurably
small.
Bernie Santarsiero
On Thu, June 26, 2008 10:55 am, Bernh
Dear All,
I wonder about the conventions using Friedel vs Bijvoet pair.
a) there are no differences. As long as h = -h, it's a Friedel
or a Bijvoet pair. They are the same.
b) A Friedel pair is any reflection h = -h including hR = -h, i.e.
including centric reflections.
A Bijvoet pair
Hi Ruben,
I have never used TMAO myself but this paper might give you a better idea:
Jeruzalmi, D. & Steitz, T. Use of organic cosmotropic solutes to
crystallize flexible proteins: application to T7 RNA polymerase and its
complex with the inhibitor T7 lysozyme. J Mol Biol, 1997, 274, 748-56
T
One question is, why do you want to fix that and from what literature
are you expecting the values?
BeF3- is often a ground state analogue for GTP binding proteins for
example.. and the depending on the coordination state, the bond angle
and length might change a bit I would have thought.. for exa
Hi everyone,
I am refining a protein structure containing a Beryllium Fluoride (BeF3)
ligand. I am using Refmac5 in ccp4i.
The distances between the Be and the F atoms are slightly longer than what I
would expect (1.7A instead of ~1.5A).
Does anyone know how I can fix the distances and rest
Hi everyone,
I am refining a protein structure containing a Beryllium Fluoride (BeF3)
ligand. I am using Refmac5 in ccp4i.
The distances between the Be and the F atoms are slightly longer than what I
would expect (1.7A instead of ~1.5A).
Does anyone know how I can fix the distances and rest
Hi all!
Just want to ask whether some of you has experience with TMAO (or
similar conformation stabilizers) for setting up crystallization
screenings?
Which concentration range would you use? Would you add TMAO to the
protein tube and afterwards add the mixture to the plates?
Just wanted to know yo
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