Alex,
You should check out this webserver: http://services.mbi.ucla.edu/anisoscale/
If it cannot solve your problem, it will at least point you in the direction of
some answers.
Good luck,
Mike
- Original Message -
From: "Alex Barth"
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, April 5,
Hi Heping,
Thanks for the list. It is very helpful and interesting. Out of curiosity:
how did you generate this list? Is there a way to search none-linear motifs
in PDB? Or did you write a script for searching database?
BTW, the ALA in 1xm7 looks unreal. A three-way tri-sulfide? The electron
Ronnie --
The list that I have in a home database contains 89 instances of a CXC in
53 files when C-C forms a disulfide bond. The records returned are ordered
by the name of "X" residue from CXC motif for convenience.
There is indeed PRO in one case (2zxt), but it is not the major
observation in
Thanks for the explanation Ed, that makes sense.
- Original Message -
From: "Edward A. Berry"
To: mi...@chem.ucla.edu
Cc: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, April 5, 2011 12:22:21 PM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
W
When the c axis is perpendicular to the image, i.e. parallel to the xray beam,
the only information about spacing along the c axis comes from the distance
between the lunes. There should be a circle of spots around the direct beam
with l=0, the a clear space, then a ring with l=1, then a clear spa
dengzq1987,
I am also working on a data set that has this exact alignment/mosaicity problem
noted by others. If you make a movie of your dataset that displays your images
in series, or if you just click through them quickly in adxv or your program of
choice, you will see that very few of the sp
Ronnie,
There are several. The example I know is 1DBI - I have little doubt
that there are more out there...
If you are interested by the close proximity in sequence then you might
also like to know that there are examples of 'CC' motifs with disulfides
- look at 1KB0 - a PQQ-dependant alco
Postdoc position at University of Konstanz
Interested candidate please write to Prof Wolfram Welte,
wolfram.we...@uni-konstanz.de.
"A post doctoral position is available instantly at the University of
Konstanz in a collaborative EU project (FP7).
The position is limited to February 2012. A six m
In the first image (spot 2) the long unit cell is obvious from the closely
spaced
spots, but this kind of image can be handled easily by Denzo. The second one
(spot 1), although at first glance the spots seem well separated, is the
problem.
As Bert pointed out the mosaicity is high, so the lunes
From the two images, it appears there are two short cell axes and one long axis
- it also looks like trigonal or hexagonal, then the long axis should be c. Of
course lower symmetry with a nearly hexagonal-shaped cell can not be ruled out.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Mac
Dear dengzq1987,
while we are bragging about long cells and high resolution, our bacteriophage
T4 short tail fibre crystals of spacegroup P321 had cell axes of a=b=50.7 Å,
c=436 Å, but we got a very good 1.5 Å resolution dataset for it (pdb code 1OCY).
The crystals were long rods with hexagonal
On Tue, 2011-04-05 at 13:05 +0800, dengzq1987 wrote:
> I have a crystal that diffracts to about 4 A. in some direction the
> spots overlap. we can't use the data to index .we think it is because
> that there is a long unit cell axes. so is there any method to solve
> this problem?
With denzo, a
Pictures are helpful to narrow the range of recommendations. It would be even
more helpful to see the entire image, to know the orientation of the rotation
axis, detector distance used, frame width, and any other information on the
setup you can provide.
Nukri
Ruslan Sanishvili (Nukri), Ph.
XDS should be able to help you with this it's not terribly overlapping and 3D
profile fitting does wonders.
Jürgen
On Apr 5, 2011, at 9:10 AM, dengzq1987 wrote:
hello Jürgen_Bosch,
because i have collected the data,but can't index.in some direction,the spot is
separated .but the others are se
You may have a fairly long cell edge (or two if you are dealing with P3 or P6),
but you also seem to have high mosaicity (pic spot 1). Try the useful
strategies suggested here. It may also be worthwhile to shoot a few roomtemp
crystals to see if your cryo is at fault for your high mosaicity.
Be
my crystal is not plate.it is Hexagonal and very large.
2011-04-05
dengzq1987
发件人： Jacob Keller
发送时间： 2011-04-05 20:53:41
收件人： CCP4BB
抄送：
主题： Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
For plate crystals with the long axis normal to the plate surface
(anecdotal
Hampton Research actually sells bent loops. At least used to.
Raji
On Tue, Apr 5, 2011 at 8:52 AM, Jacob Keller wrote:
> For plate crystals with the long axis normal to the plate surface
> (anecdotally, this is usually the case), you can use bent loops. Bent
> loops can be made using tweezers
I have a question related to protein structure, but not crystallography per se.
Has anyone see a disulfide forming between the two cys of "CXC" in the middle
of
a loop, and create a sharp turn, where X is not a proline? I seems to me that
geometrically this would be possible but I am not sure h
For plate crystals with the long axis normal to the plate surface
(anecdotally, this is usually the case), you can use bent loops. Bent
loops can be made using tweezers by folding over the loop onto the
stem and crimping with the tweezers. When the loop relaxes a bit, it
will leave a ~90deg-bent lo
What do you consider long ? 200, 300 ? 600 A ? Before shooting try to run
strategy or xplan. Move the detector back to first reliably be able to
determine your cell. Then double your estimated mosaicity and see what strategy
suggests. If you don't get many overlaps (<5%) then try a closer distan
Ideally you should rotate your crystal around the long axis during data
collection. This is however easier said than done since often such
crystals grow a plates with the long axis perpendicular to the plane of
the plate.
As long as the long axis is more or less oriented perpendicular to the
Hi dengzq1987,
You don't say how many axes are long. I will assume one. In that case, here is
a compilation of what others have already recommended, with some additions:
1. Orient the crystal so that the long axis is along the rotation axis. It can
be done during mounting the crystal on the loo
Dear all,
i am new in the field and my crystals give anisotropic pattern.
I would really appreciate if someone who has experience with data collection
with anisotropy diffraction to recommend relative literature on data
strategy concerning anisotropy.
Cheers,
Alex
Hi Vandana,
in addition to the hints already mentioned some experimental setups
offer the posiblitiy to swing out the detector via a theta-angle option.
this might be useful when increasing the crystal-to-detector distance to
avoid overlaps.
Cheers,
Georg
Am 05.04.11 11:20, schrieb vandana
Hi Deng,
On Tue, 2011-04-05 at 07:31 +0200, Poul Nissen wrote:
> Deng,
> You need a good synchrotron source with a low point spread detector,
> but not least a careful consideration in crystal mounting so that your
> crystal rotates apprx around the long axis during data collection to
> optimise t
hello
if u are getting merged spot then try to increase detector distance it may
work . instead of this u try to reduce delta phi (gonimeter phi angle per
frame) default it is 1 degree u can try 0.5, 0.25 degree.
Dear BB,
Please forward to any potential PhD applicants.
Thanks
Ed
PhD studentship in Structural Molecular Biology in collaboration with
AstraZeneca.
Part of an integrated approach to discovering cell-permeable inhibitors of
alpha helix-mediated protein-protein
interactions.
See
http://www.
On 4/4/2011 2:15 PM, Jacob Keller wrote:
I like your IMGATM proposal, but wouldn't it also potentially break
some of the programs?
That depends on the program. Programs I write that read PDB files
silently ignore keywords that they don't recognize. A model with
IMGATM (or whatever keyword
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