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
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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 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
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 the
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
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 meitian.w...@psi.ch wrote:
Postdoctoral Fello*Next Generation Detector for Protein Crystallography*
Your tasks
Built on the success of PILATUS
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
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
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
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=437043loc=ec_rcs
If you look around you will find what you need on that web page.
Jürgen
On May 9, 2012,
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 t...@shelx.uni-ac.gwdg.de wrote:
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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
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
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,
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,
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
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, Bosch,
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
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.
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
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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
ber...@upstate.edu
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 shyabis...@gmail.com wrote:
Hi all,
I am having trouble
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
does not give correct files needed to insert special symbol @ after N+
Shya
On Wed, May 9, 2012 at 2:57 PM, Pavel Afonine pafon...@gmail.com 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
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
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
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
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
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
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
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