Hi Conan,
> Specifically, the reviewers question whether ripples may affect on the
> electron density around heavy metal center which has a Mo-S-As
> connection. From which angle or in which way this problem should be
> addressed most convincingly ?
The maximum entropy estimate of the map shou
Hi Peter,
If the crystals are brownish, then it may be crystals of Hexamine cobalt (III)
chloride.
If you have the final dialysis buffer of the protein, setting up a
crystallization trial with just the buffer may help you distinguish between
salt and protein.
Hope this helps,
Wataru
On 2011/
Wanted to get an opinion. I set up a screen a while ago and got these very
small cubic looking crystals 2-3 days later amidst a lot of precipitant. The
condition was Natrix E1 (0.04M LiCl, 0.02M MgCl2, 0.04M Sodium Cacodylate
pH5.5, 30% MPD, 0.02M Hexammine Cobalt (III) chloride). This protein's
Lucky you that Tassos is not awake yet :-) 3 MB attachment...
Anyhow the microcrystalline one is the most interesting of those 4 I'd try to
change the protein:precipitant ratio and wold introduce maybe a pH screen. What
are those conditions ?
Jürgen
On Jul 6, 2011, at 6:35 PM, joybeiyang wrote:
Hi all
I am thinking to delete flexible loop for crystallization of my protein. But i
am not sure how to decide which area i should delete. This protein have around
20% sequence identity with other solved structure. Can anybody suggest me how
to proceed for that. Is there any established strate
Dear CCP4 bulletin board:
I am doing some research on home SAXS systems (i.e., the BioSAXS from
Rigaku, among others) and was interested in finding out what the community's
experience has been with these systems in performing SAXS experiments at
home. I'll post a summary of all the responses to th
Hi all,
As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org)
carried out a substantial make-over of its website last summer, including the
launch of several new features (such as PDBprints - http://pdbe.org/pdbprints
- and a biologist-friendly structure browser - http://p
Postdoctoral Position Available
Laboratory of Professor Robert M. Stroud, Ph.D. (
http://www.msg.ucsf.edu/stroud/index.htm)
Department of Biochemistry and Biophysics
University of California San Francisco, USA
SUMMARY DESCRIPTION: Structural biology of HIV-host interaction
The Stroud Laboratory s
It'll depend on your data, but you'd probably be better off using the
inflection (rather than peak) and remote datasets for dispersive
difference maps. This signal is usually fairly weak to begin with, and
not using the infection datasets weakens it further.
Pete
FWIW - my understanding is
Dear Zbyszek
Wouldn't ripples be the results of calculating maps with truncated
Fourier summations (unavoidably), and, consequently, be more obvious
around a sharp feature such as an heavy atom metal center?
The mathematic basis can be found here:
http://en.wikipedia.org/wiki/Gibbs_phenomenon
Wi
There are tools out there that calculate such a map.
REVISE is one - I guess i is in the list of CCP4 programs.
i often do both maps independently and look at them for common peaks
The trouble is that dispersive differences are often less reliable than
the anomalous ones..
Eleanor
07/06/20
On Wednesday, July 06, 2011 10:36:20 am Jacob Keller wrote:
> > That would be an approximation of the map it seems you actually want,
> > which would use the F_A amplitude terms from MAD analysis together
> > with your current model phases rather than the MAD phase estimates.
> > You could, for exa
> That would be an approximation of the map it seems you actually want,
> which would use the F_A amplitude terms from MAD analysis together
> with your current model phases rather than the MAD phase estimates.
> You could, for example, use CAD to merge the FA column output by
> hkl2map with the ph
On Wednesday, July 06, 2011 09:46:14 am Jacob Keller wrote:
> Dear Crystallographers,
>
> it seems to me that for clearly identifying/characterising anomalous
> scatterers for a solved structure, one could make a map using two
> datasets: one at the f" peak, one low energy remote.
That would be
The question about Fourier transformation ripples has a straightforward
answer in a fairly typical situation:
A) data are collected to the resolution limit of diffraction,
B) phases are uniform in quality across the resolution range, which is
equivalent to R-free being uniform with respect to resol
Dear all,
The following paper describes 'element specific maps', calculated by collecting
data immediately above and below an absorption edge.
http://journals.iucr.org/d/issues/2005/05/00/he5321/index.html
I have used this technique, and it works very well. If anyone is interested I
have a s
Dear Crystallographers,
it seems to me that for clearly identifying/characterising anomalous
scatterers for a solved structure, one could make a map using two
datasets: one at the f" peak, one low energy remote. One would then
use the signal both from the Bijvoet differences in the peak dataset
pl
From: Giovanna Scapin [mailto:scaping10...@yahoo.com]
Sent: Wednesday, July 06, 2011 11:08 AM
To: Scapin, Giovanna
Subject: Fw: Three Nobel Laureates and other famous scientists in a Symposium
in Florence (Sept. 23rd 2011) devoted to the chemistry for Life and He
I would be very careful about any bond to As. I would imagine such
bonds would be very susceptible to radiolysis with typical radiation used
in the diffraction data collection. Have you performed some
diffraction experiments of various time lengths (or flux) and seen what
happens around this
I note that all three of those atoms should have anomalous scattering
and should show up as peaks in anomalous Fourier maps if you collected
data carefully enough at multiple wavelengths. The As K edge is 1.04 A,
which is easily within reach of most MAD synchrotron beamlines. The Mo
peaks are out o
On 07/04/2011 04:24 PM, ruheng wrote:
>
> Dear all,
>
> Recently we are working on an archaebacteria protein which was expressed and
> purified from E.coli by conventional procedures. After we solved the
> structure, we found that there is an extra density in one of the argninine as
> shown in
Tim Gruene writes:
> [summer break flame]
> I'm sure there are a lot more computer admins than crystallographers who
> prefer high-tech over fancyness - aka outlook usually marking my signed(!)
> emails as spam ;-)
>
> And, yes, I know that both thunderbird/enigmail and kmail combine both very
>
Dear All, Hi. I was asked in a manuscript revision to discuss about the
possible effects of Fourier transformation ripples on the crystallographic
results. Specifically, the reviewers question whether ripples may affect on the
electron density around heavy metal center which has a Mo-S-
[summer break flame]
I'm sure there are a lot more computer admins than crystallographers who
prefer high-tech over fancyness - aka outlook usually marking my signed(!)
emails as spam ;-)
And, yes, I know that both thunderbird/enigmail and kmail combine both very
elegantly, but with mutt I can sim
Hi Tim,
Sure, does this look better? Actually, the choice is mine (although the
default which I prefer, honestly, is HTML).
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bg
Leave it to the crystallographers to be the last on the Planet with
text-only email readers Just before the ccp4bb will migrate to
google+ :)
Flip
Op 7/6/2011 10:27, Tim Gruene schreef:
Dear Boaz (and others)
it immensly improves readability of your emails if you can ask your email clien
Dear Boaz (and others)
it immensly improves readability of your emails if you can ask your email client
to also include a plain text version of your email on top of the html-version
;-)
Cheers,
Tim
On Tue, Jul 05, 2011 at 05:55:28PM +, Boaz Shaanan wrote:
>
>
>
>
>
>
> Hi,
>
>
> The
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