Very interesting question,
you can probably look at the following, related paper -
Biophys J. 2012 Feb 22;102(4):927-33. Epub 2012 Feb 21.
Multi-wavelength anomalous diffraction using medium-angle X-ray
solution scattering (MADMAX).
Makowski L, Bardhan J, Gore D, Rodi DJ, Fischetti RF.
On Th
Ihr WEB.DE Postfach immer dabei: die kostenlose WEB.DE Mail App für iPhone und Android. https://produkte.web.de/freemail_mobile_startseite/
Hi Theresa,
A well known method to investigate the surroundings of metals in proteins
(metal-protein distances etc. ) is EXAFS (Extended X-ray Absorption Fine
Structure). It has been implemented in quite a few specialized synchrtoron beam
lines since the early 80s. I'm sure there's plenty of
The 42nd Mid-Atlantic Macromolecular Crystallographic Meeting is quickly
approaching, and Saturday, May 12th is the last day to submit an abstract for
consideration for an oral presentation. Poster abstracts can be accepted later,
but please register by May 21st so we can provide accurate numbe
Thanks to all again! Find below my answers/comments to all your replies.
Colin Nave,
I'll certainly collect higher resolution dataset to look for more
diagnostic rings.
Apo-ferritin xtallizes in the same conditions with the same cell (I know it
from literature), I'll measure it too, to look for di
Yes, in principle, on paper it is possible. Moreover in many cases by looking
at the various directional Wilson plots you may be able to see direction of
helices (just like in DNA/RNA). However in general case it is a little bit
tricky (mixture of different secondary structures directed in diffe
Your responses are tantalizing. In what way are the files not correct?
As Garib says, the N+ is not chiral (and hence @ should not be needed).
Paul.
On 09/05/12 20:13, Shya Biswas wrote:
does not give correct files needed to insert special symbol @ after N+
Shya
On Wed, May 9, 2012 at 2:57
It seems to me that spherical forms of Wilson plots could be used to
determine how many bonds of what nature were oriented in which direction,
and this may have been what Bricogne's micro molecular replacement
technique was capitalizing on? For example, one might be able to orient a
straight DNA mo
does not give correct files needed to insert special symbol @ after N+
Shya
On Wed, May 9, 2012 at 2:57 PM, Pavel Afonine wrote:
> Shya,
>
> Elbow command:
>
> phenix.elbow --smiles="O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45"
>
> will give you CIF and PDB files. I just tried, it took 5 minutes
As far as I know there are several bumps: around 3.5-4 (there are some at low
resolution related with molecular shapes also) - secondary structures, ~2.2
related with angles and around 1.2 related with covalent bonds. For DNA/RNA
there is one more bump around 1.6-1.7 ( I thought that is because
Shya,
Elbow command:
phenix.elbow --smiles="O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45"
will give you CIF and PDB files. I just tried, it took 5 minutes to
calculate them on my mac.
Pavel
On Wed, May 9, 2012 at 9:08 AM, Shya Biswas wrote:
> Hi all,
> I am having trouble generating a pdb and
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Nat,
isn't this partially discussed by Morris' and Bricogne's article about
"Sheldrick's 1.2A rule and beyond" (Acta Cryst D59, 2003)?
Tim
On 05/09/12 20:44, Nat Echols wrote:
> On Wed, May 9, 2012 at 11:35 AM, Edward A. Berry
> wrote:
>> Still
> A protein would only scatter but not diffract
or Diffract but not scatter? isn't diffraction a kind of scattering?
But yes, the atoms in the unit cell may seem random in that
distance range (in fact this is assumed in wilson scattering)
but in a perfect crystal they will be the same in each uni
Perhaps I misunderstood Jacob's original question, but it seems like two
different phenomena are being discussed here. My read of Jacob's original
question was, roughly, shouldn't we observe non-Bragg, powder-like
scattering from a well-ordered macromolecular crystal due to the abundance
of ~
Dear all
Is there any interesting aspects of metal proteins that can be used with
anomalous SAXS similar to MAD in MX? Can metal distance be measured with
time-resolved method (ligand binding and so on)? I knnow examples for materials
like nanoparticles but how about proteins?
Thank you.
Dear All, I would like to announce the following meeting:
International Workshop on New Developments of Methods and Software for Protein
Crystallography, August 24-27, 2012 Xi’An, China
Organizers: Commission on Biological Macromolecules, IUCr; Chinese
Crystallographic Society (CCrS) and Northw
Interesting: N+ does not seem to be chiral. Three out of four carbons attached
to it seem to be equivalent.
Garib
On 9 May 2012, at 18:13, Shya Biswas wrote:
> The following seems to work with phenix:
> O=C(C[N@+]23CN1CN(CN(C1)C2)C3)c45c45
> Shya
>
> On Wed, May 9, 2012 at 12:15 PM, Bo
Yes, I just looked up the paper--seems right on topic--a powder-type ring
at ~4.2 Ang, corresponding to Calpha-Calpha distances! But no 1.2-1.5 Ang
ring, from what I saw. Maybe it gets swamped out by other things. I am
thinking that the variety/distribution of bonds/distances of length 1-3 Ang
in t
The following seems to work with phenix:
O=C(C[N@+]23CN1CN(CN(C1)C2)C3)c45c45
Shya
On Wed, May 9, 2012 at 12:15 PM, Bosch, Juergen wrote:
> Is that your molecule ?
>
> On May 9, 2012, at 12:08 PM, Shya Biswas wrote:
>
> O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45
>
>
> ..
Hi Paul
The pdb file that you send me does not have the right geometry, have tried
phenix elbow, same problem not the right geometry however in consultation
with Nigel it looks like a special symbol had to be inserted in smiles, he
send me a file that looks like correct.
thanks to all who helped,
S
On 09/05/12 17:08, Shya Biswas wrote:
Hi all,
I am having trouble generating a pdb and cif file from the following
smiles string:
O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45
Prodrg fails to run when i draw the molecule in JME editor was
wondering if anyone knows a better program which does th
Dear Jacob,
Our, ie protein, crystals usual diffuse scattering ring involves a
typically 2.8 Angstrom solvent oxygen to oxygen distance.
There must be a 1Angstrom OH diffuse scattering ring but the weakness
of the hydrogen scattering mitigates against that.
The covalent links, to which you refer, a
Considering all the recent posts on this very forum regarding the excellent
Grade; I would suggest a quick visit here…
http://grade.globalphasing.org/cgi-bin/grade/server.cgi
Tony.
---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
S
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello Jacob,
I do not know the data, but the word 'fibre' sounds close to
'one-dimensional crystal', especially considering the screw axis you
have in DNA, at least within the resolution limits that the pictures
suggest.
Cheers,
Tim
On 05/09/12 18:3
Well, what about the original DNA fiber diffraction images--no
microcrystals there, as far as I know, but one can clearly see the stacking
distances and the phosphate backbone.
JPK
On Wed, May 9, 2012 at 11:03 AM, Tim Gruene wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Jaco
multiple ways of getting there:
I used Picto (OpenEye)
But you can also search PubChem with your smile string and find a perfect match
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=437043&loc=ec_rcs
If you look around you will find what you need on that web page.
Jürgen
On May 9, 2012,
Is that what you are looking for?libcheck cn generate it (JLigand should be able). grade should also generate from smiles.Garib
1.cif
Description: Binary data
1.pdb
Description: Binary data
On 9 May 2012, at 17:08, Shya Biswas wrote:Hi all,I am having trouble generating a pdb and cif file from t
Is that your molecule ?
[cid:FDC217A8-8891-4163-88FE-3886A27C2823@sph.ad.jhsph.edu]
On May 9, 2012, at 12:08 PM, Shya Biswas wrote:
O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistr
Hi all,
I am having trouble generating a pdb and cif file from the following smiles
string:
O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45
Prodrg fails to run when i draw the molecule in JME editor was wondering if
anyone knows a better program which does this kind of job.
thanks in advance,
shya
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Jacob,
A protein would only scatter but not diffract, the latter - in my
understanding - being the result of constructive interference from a
regular array of unit cells .
A powder pattern is the superposition of many small crystals amongst
whic
Jacob, do not worry. Data collection for a typical crystal takes only 0.75
seconds.
Petr
On May 9, 2012, at 5:18 PM, Jacob Keller wrote:
I saw something online about the EIGER 16M: 201 GB of data per second! Is that
number correct?
JPK
On Wed, May 9, 2012 at 9:58 AM, Meitian Wang
mailto:me
I saw something online about the EIGER 16M: 201 GB of data per second! Is
that number correct?
JPK
On Wed, May 9, 2012 at 9:58 AM, Meitian Wang wrote:
> Postdoctoral Fello*Next Generation Detector for Protein Crystallography*
> Your tasks
> Built on the success of PILATUS detector technology,
Postdoctoral Fello
Next Generation Detector for Protein Crystallography
Your tasks
Built on the success of PILATUS detector technology, PSI and Dectris Ltd. are
developing the next generation single-photon counting detector (EIGER)
featuring smaller pixel size, higher frame rate and dynamic range
Dear Crystallographers,
the "saxs on crystals" thread reminded me of a question I have had for a
while, and never having collected data better than ~1.6 Ang or so, cannot
answer myself from experience: I would think that there might be
powder-like diffraction rings at distances corresponding to th
Dear Anna,
Very interesting diffraction pattern.
Any chance of measuring to higher resolution?
Ie to try and capture the higher order rings, which presumably are there.
Also interesting that these rings seem quite weak ie the ferritin perhaps not
fully loaded?
Best wishes,
John
Prof John R Helli
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear ...,
are you by any chance comparing merged with unmerged data?
Tim
On 05/09/12 04:32, West,Dayne M wrote:
> When I index data, high resolution for example, I can get over
> 100,000 reflections. However, when I refine using PHENIX, it says
>
Dear All,
I want to take the backup of all my data which i have refined using CCP4. Can
you please guide if I copy all the ccp4 data folders and then transfer to some
other system and install ccp4, if will be possible to restore all the data on
ccp4 window the way i find it on my current system
Frank,
Maps are viewed for eg charge density studies, orientation of methyl groups (
when need checking ), but omit maps and maps generally in chemX are examined
usually as peak lists.
Nb the diffraction resolution is much more homogeneous than MX and atomic
resolution or better basically all th
Dear Frank,
Small-molecule fcf files are usually created (by SHELXL) using the LIST
4 instruction and do not contain the phase information needed to make a
map. To read the fcf into Coot you need LIST 6 format. You can check
this by looking at _shelx_refln_list_code near the start of the fcf
Dear All,
I'd like to draw your attention to an joint PhD studentship between Southampton
University (Dr. Ivo Tews) and Diamond Light Source (Dr. Gwyndaf Evans) on the
topic "Catching Reaction Intermediates in the Multi-step PLP biosynthesis with
Microfocus Synchrotron Techniques in situ".
Ple
Dear Frank,
PLATON.
[Or make the transition to bond distances and angles with esds,
instead of maps.]
Greetings,
John
On Wed, May 9, 2012 at 6:10 AM, Frank von Delft
wrote:
> Hi daft question: I was sent cif and fcf files for a small molecule crystal
> structure - solved with Bruker software, I
On 09/05/12 06:10, Frank von Delft wrote:
Hi daft question: I was sent cif and fcf files for a small molecule
crystal structure - solved with Bruker software, I think.
Anybody know how to display this as electron density maps? I tried
coot and mg, they barfed though - not sure whether that's
42 matches
Mail list logo
