Dear Laurent,
1) Refmac mentions gaps explicitly in the LINK records, the PDB does it in a
REMARK record (by comparing the atom records to the sequence of your
crystallised construct). If you just remove the gap-LINKs before deposition
(without adding TER records) it should work.
2) First of all
Good morning CCP4 list
I am trying to deposit structures refined with refmac (latest version
5.8.0049, windows seven), and I have two issues raised at the validation
step :
1) there are chain breaks in my protein (for disordered loops). Refmac
adds a LINKR record for the description of the b
Thanks everyone for your valuable suggestions
On 4 February 2014 20:47, jai mohan wrote:
> Dear Shanti Pal Gangwar,
> You are trying to solve your crystal structure of what! whether its a
> peptide or protein or enzyme or nucleic acid? There are several reasons
> behind getting a high Rmerge, i
I will be curious to know about people's experiences with membrane
proteins and lysing yeast cells with the Microfluidizer and how that
compares with using a Retsch Miller, i.e. grinding in a liquid
nitrogen cooled stainless steel chamber and plunging in liquid
nitrogen in between grinding cycles.
Biophysical Highlights from 54 Years of Macromolecular Crystallography
Jane Richardson and David Richardson
http://www.sciencedirect.com/science/article/pii/S0006349514000332
—
Da-Neng Wang, Ph.D.
Professor
Structur
Hi Richard,
I am not sure if this is what you are looking for: second order nonlinear
optical imaging of chiral crystals (SONICC). It is not based on a
computational algorithm but the nonlinear optical property of chiral
crystals to double the wavelength when illuminated by intense light.
S
Or if the tip is hopelessly pitted you can get a new one (for a Branson 1/2
inch horn) at:
http://www.proequip.com/productlist.asp?pcid=31
(thanks to:
http://blogs.cornell.edu/collinslab/2010/04/12/time-for-a-new-tip/ )
Reza Khayat wrote:
A lot of "ageing" sonicators are not really ageing. Have
Govindjee and Fork's biography of Stacey French is available here:
http://www.nasonline.org/publications/biographical-memoirs/memoir-pdfs/french-c-stacy.pdf
or if your library subscribes to photosynthesis research,
http://link.springer.com/article/10.1007%2Fs11099-006-0041-6
Mark J van Raaij
I'm joining the pig-pile on the Emulsiflex. I like it because:
a. The folks at Avestin are very helpful (they're Canadian--just
naturally nice)
b. It'll break yeast as well as E coli
c. It seems pretty gentle to me (we pack it in ice, so there's
negligible sample heating)
A lot of "ageing" sonicators are not really ageing. Have you tried cleaning the
tip of the sonicator? If not, remove the tip from the sonicator and use a 800
Grit wet sandpaper to make it as shiny as it was when you first bought it. I do
this every three times I use the sonicator. A lot of crap
Dear colleagues,
On behalf of the organizing committee, I would like to welcome you at
the Dynamo International Symposium on
"Evolution, Biogenesis and Dynamics of Energy Transducing Membranes"
in Paris, April 9th-12th 2014.
The meeting cover a wide range of integra
3 to 1 ratio of bper and yper, 2-3 ml per gram of e. coli plus lysozyme and
bensonaze... I have not used a sonicator in years :) about 1% of proteins
dont like detergents, in which case there are other non mechanical options.
A.
On Feb 4, 2014 10:49 AM, "Phoebe A. Rice" wrote:
> Some time ago,
BeadBeater. http://biospec.com/. Gentle, aerosol-free way to break
15-350 mL of cell paste (2-150 g wet packed cells).
Cheers,
___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
te
I would also recommend the Emulsiflex line of cell disruptors from Avestin
- it has been my favorite and most easily used instrument of cell
destruction.
On Tue, Feb 4, 2014 at 9:17 AM, Mark J van Raaij wrote:
> LOL.
>
> In any case, a French press is also not french, according to Wikipedia it
>
Adapted from periplasmic fractionation protocol, but for cytoplasmic
proteins:
1. Incubate resuspended cells with lysozyme in normal buffer but with
20% sucrose.
2. Spin down sphaeroplasts (unbroken cells with no cell wall - ultra
fragile). This also removes periplasmic proteases.
3. Resus
LOL.
In any case, a French press is also not french, according to Wikipedia it was
invented by Charles Stacy French of the Carnegie Institution of Washington
(hence French press with capital F).
In any case, I agree, Emulsiflex, Constant Systems One-shot, Microfluidizer
etc. is the way to go i
Hi Phoebe,
Another possibility is the Emulsiflex (from Avestin, in canada). Not a
cheap piece of equipment, but very sturdy and efficient to up to 200 mL of
extract (runs on house-air). Can deal with E coli (and even yeast if you
have the models with internal compressor). It comes in 3 sizes I thi
Emulsiflex C5
alternative freeze-thawing, the old way we used to do this spiking with some
Lysozyme
or grinding it in a LN2 cooled mortar, is very effective and pretty cost
effective, assuming you don’t pay for the LN2
Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomber
Hi Phoebe -
"Cost-effective" may not be the applicable word here, but the
Microfluidizer works very well:
http://www.microfluidicscorp.com/index.php?option=com_content&view=article&id=19&Itemid=76
This gadget runs on house compressed air (don't try to use a compressed
air tank - you'll empty
Some time ago, there was a nice discussion of cost-effective, wimpy
protein-friendly ways to break open E. coli. We're thinking about replacing an
aging sonicator. If people have a favorite gizmo, could they repeat that
advice?
thank you,
Phoebe Rice
+++
I had a student who unsubscribed because of too many emails.
I'll tell you what I told her: "Create a filter so the emails don't show up
in your inbox and make sure that you can easily find them."
She didn't do that but her loss.
Since you have gmail here's what you need:
https://support.google.co
[Advertisement on] http://www.janscientific.com/#!/gallery [Advertisement off]
Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W870
Dear Shanti Pal Gangwar,
You are trying to solve your crystal structure of what! whether its a peptide
or protein or enzyme or nucleic acid? There are several reasons behind getting
a high Rmerge, it not only depends on the data quality. What are all the
efforts! that you have applied to solved
Some years ago, I remember hearing about a microscope that used *visible* light
combined with some proprietary image processing algorithm to
distinguish between protein crystals, salt, and background. I can't remember
the company name or researchers involved.
Has anyone here heard of this?
Ri
…the slash at the end is obviously the secret sign for “google-translate into
a randomly picked language”
http://scripts.iucr.org/cgi-bin/citedin?dz5235
From: Rick Lewis [mailto:r.le...@ncl.ac.uk]
Sent: Dienstag, 4. Februar 2014 15:24
To: b...@hofkristallamt.org
Subject: Re: [ccp4bb
EDSTATS is part of CCP4
.which in fact I cite in 33% of all of its CrossRef references
http://scripts.iucr.org/cgi-bin/citedin?dz5235/
Touché.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank
von Delft
Sent: Dienstag, 4. Februar 2014 14:40
To: CCP4BB@JISC
And really we should not be using real space CC or real space R anymore
- not since Tickle 2012
(http://scripts.iucr.org/cgi-bin/paper?S0907444911035918)
EDSTATS is part of CCP4.
phx
On 04/02/2014 13:31, Bernhard Rupp wrote:
> interpretable electron density map is obtained to which most
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Hash: SHA1
Dear Shanti Pal Gangwar,
which strategy did you pursue after MR - did you start model building,
or did you start with refinement? In case of the latter you may have
erased what actually helps you get a better model. One easy way to
check is the geomet
> interpretable electron density map is obtained to which most of your
protein model can be fitted properly. The primary numeric indication for
that are your R-factors.
Minor comment: The measure for the fit of the *model (density) to the
electron density* is actually a local real space correl
Hello Shanti,
Typically, one can safely claim a solved structure once an interpretable
electron density map is obtained to which most of your protein model can be
fitted properly. The primary numeric indication for that are your R-factors.
The high values you have suggest that either something
Hi all,
I24 is the microfocus MX beamline at Diamond offering a fully tuneable and
versatile X-ray beam for some of the most challenging crystals in structural
biology. There is currently an opportunity to join I24 as a support scientist
at the start of an exciting period of significant upgrade
Well - that depends on many things.
Are you sure of the spacegroup? Those R factors sometimes indicate a
wrong selection of SG P212121 instead of P21212 for example..
Are you sure the data is not twinned?
Do the maps show features which are not in the model?
etc etc
Eleanor
On 4 February 2014
Hello,
To answer the question of Dilip, you can change starting sequence
numbers in ESPript by editing the MSA file as explained in the doc
http://espript.ibcp.fr/ESPript/ESPript/esp_userguide.php
We got in touch with him by mail to answser his question in more details.
We take this opportunity
Grant
This is typically done by calculating the inertia tensor
based on any coordinates you want to consider (usually CA,C,N)
[x.x x.y x.z]
[x.y y.y y.z]
[x.z y.z z.z]
Then "diagonalize" this using a standard eigen routing - many around,
sort the eigen vectors by eigen value and the longest scal
Dear All
I have solved one structure by MR. The data data quality was poor so the
Rmerge was high. The resolution of the data is 3.3 Angstrom.The refinement
statistics are also very poor Rw/Rf= 40/42 %. After many efforts we are not
able to get reasonable Rw/Rf.
My question is "can it be claimed
Dear all, may I draw your attention to the following conference announcement:
Join us at the 2014 Gordon Conference On
Ligand Recognition & Molecular Gating:
Structure and Dynamics of Ion Channels, G-protein Coupled Receptors, and Solute
Transporters
(Ventura, CA March 23-28)
The Gordon Researc
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