[ccp4bb] Re>> Anomalous SAXS

[BN Chaudhuri]

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 Thu, May 10, 2012 at 4:30 AM, CCP4BB automatic digest system
<

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.

[ccp4bb] please unsubscribe me from the BB. Thanks!

[Brit Winnen]

  Ihr WEB.DE Postfach immer dabei: die kostenlose WEB.DE Mail App für iPhone und Android.   https://produkte.web.de/freemail_mobile_startseite/

Re: [ccp4bb] Anomalous SAXS

[Boaz Shaanan]

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 literature on the method 
and results on many metal proteins (I'm familiar with the EXAFS results on 
haemoglobin which caused quite a stir at the time).

 Cheers,

 Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710






From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Theresa Hsu 
[theresah...@live.com]
Sent: Wednesday, May 09, 2012 9:02 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Anomalous SAXS

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.

[ccp4bb] Final call for MAMCM abstracts

[David R. Cooper]

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 numbers to the 
caterers.  A few spots are still open in the Lipidic Cubic Phase (LCP) 
Crystallization Workshop, but the Structure Determination Workshop is now full.

Details of the meeting can be found athttp://www.mid-atlantic.org  .

Regards,
The MAMCM committee
David Cooper, Peter Horanyi and Michael Purdy

Re: [ccp4bb] saxs on xtals

[anna anna]

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 differences.

Jacob Keller,
we loaded ferritin with Fe and Co and oxidized them obtaining
CoxFe(3-x)O4/Fe2O3.
About the brillant spots, by eye  I attributed them to eventual ammonium
sulfate xtals (2M in xtallization conditions) but it could be something
else, compare to apo-ferritin will help.

James Holton,
I didn't think about it! Actually it's the same as nuclear spin in NMR: the
orientation is random until an external magnetic field is applied. It would
be very very interesting to collect diffraction under this condition, do
you know an equipped beamline?

Allister Crow,
thanks for encouragement! I knew that someone had already studied it...
your paper is very usefull. Myabe my case is different because I have Fe3O4
and an external magnetic field could induce order, I hope I can do this
kind of experiment.

John Hellywell,
I'll certainly measure at higer resolution.
Ferritin should be fully loaded since there are about 3500 metal atoms per
protein shell.

I'll keep you updated on my future results!

Re: [ccp4bb] Powder Rings in Single Crystals

[Garib N Murshudov]

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 different 
directions, noisy data etc). And there is another complication that bonds are 
involved in intensity curves via sinc function that is not completely local. I 
think there were attempts (by Hamburg group) with some success. What happened 
to their publication, I do not know.
You are right that in molecular replacement they are implicit. However if bonds 
are directed more or less in the same direction then assumption behind Wilson 
distribution breaks down and it may affect molecular replacement (not as severe 
as pseudo translation, nevertheless serious enough). Fortunately most molecular 
replacement programs are forgiving for such departures from assumptions.


regards
Garib



On 9 May 2012, at 20:28, Jacob Keller wrote:

> 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 
> molecule by finding the direction at which the ~3.2-3.5 Ang bin signal was 
> greatest. But I guess this is probably implicit in molecular replacement 
> anyway...
> 
> JPK
> 
> On Wed, May 9, 2012 at 2:08 PM, Nat Echols  wrote:
> On Wed, May 9, 2012 at 11:58 AM, Garib N Murshudov
>  wrote:
> > 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 of
> > Phosphor bonds). They are visible with normalised data better.
> 
> It has been pointed out to me that my example cut off the data at too
> low a resolution to see the peak for covalent bonds.  Here is a
> different version that shows a distinctive peak around 1.15A.
> 
> -Nat
> 
> 
> 
> -- 
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: j-kell...@northwestern.edu
> ***

Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] pdb and cif file generation from smiles string

[Paul Emsley]

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 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
to calculate them on my mac.

Pavel

On Wed, May 9, 2012 at 9:08 AM, Shya Biswas mailto:shyabis...@gmail.com>> 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 this
kind of job.
thanks in advance,
shya

Re: [ccp4bb] Powder Rings in Single Crystals

[Jacob Keller]

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 molecule by finding the direction at which the ~3.2-3.5 Ang
bin signal was greatest. But I guess this is probably implicit in molecular
replacement anyway...

JPK

On Wed, May 9, 2012 at 2:08 PM, Nat Echols wrote:

> On Wed, May 9, 2012 at 11:58 AM, Garib N Murshudov
>  wrote:
> > 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 of
> > Phosphor bonds). They are visible with normalised data better.
>
> It has been pointed out to me that my example cut off the data at too
> low a resolution to see the peak for covalent bonds.  Here is a
> different version that shows a distinctive peak around 1.15A.
>
> -Nat
>



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] pdb and cif file generation from smiles string

[Shya Biswas]

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 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 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
>>
>
>

Re: [ccp4bb] Powder Rings in Single Crystals

[Garib N Murshudov]

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 of Phosphor 
bonds). They are visible with normalised data better.
I think there was a paper by Morris and Bricogne in Acta Cryst about these 
things.

These bumps have some consequences - B values calculated using Wilson plot 
usually jump up and dow around these bumps.


Garib


On 9 May 2012, at 19:44, Nat Echols wrote:

> On Wed, May 9, 2012 at 11:35 AM, Edward A. Berry  wrote:
>> Still I would expect to see peaks in a wilson plot around bond-length
>> resolution, similar to the peaks due to secondary structure at lower
>> resolution.
> 
> I was curious about this myself, so I looked at the Wilson plot for an
> atomic-resolution structure (attached).  There is at best a small hump
> around 1.5A; I suspect uncertainties in atomic positions (i.e. the
> B-factor) reduce the effect.  This was consistent in several other
> atom-resolution datasets (of different proteins).  I'm curious what
> the bump around 2.25A is.
> 
> -Nat
> 

Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] pdb and cif file generation from smiles string

[Pavel Afonine]

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 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
>

Re: [ccp4bb] Powder Rings in Single Crystals

[Tim Gruene]

-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 I would expect to see peaks in a wilson plot around
>> bond-length resolution, similar to the peaks due to secondary
>> structure at lower resolution.
> 
> I was curious about this myself, so I looked at the Wilson plot for
> an atomic-resolution structure (attached).  There is at best a
> small hump around 1.5A; I suspect uncertainties in atomic positions
> (i.e. the B-factor) reduce the effect.  This was consistent in
> several other atom-resolution datasets (of different proteins).
> I'm curious what the bump around 2.25A is.
> 
> -Nat

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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bAfYYAPMdjvJpO8Q1lEV+Tg=
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Re: [ccp4bb] Powder Rings in Single Crystals

[Edward A. Berry]

> 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 unit cell.
But the scattering rom each unit cell will be systematically out
of phase, so the resultant vector will go round and round the
argand diagram without adding up to anything measureable
(Fig 4.15 in Drenth 1st edition), unless the Laue conditions
are met, and this leads to diffraction spots.

Now if the crystal is not perfect, each unit cell won't be the
same in hi-res details, cancelation will be imperfect, and this may
be related to the "diffuse scatter" which can result from certain
types of disorder.

Still I would expect to see peaks in a wilson plot around bond-length
resolution, similar to the peaks due to secondary structure at lower
resolution.

ed

Tim Gruene wrote:

-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
which you don't observe interference.

Tim

On 05/09/12 16:16, Jacob Keller wrote:

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 various covalent bond lengths in proteins
(1.2-1.5 Ang), but have never heard of such. My thinking is that
the protein itself is essentially a powder sample within the unit
cell consisting of many small, randomly-oriented molecules (amino
acids) with their covalent bonds. Do the rings in fact exist, and
if not, why not? Maybe the electron density is not as "atomic," or
discrete, as the nuclei are? I wonder whether generally data
collected to beyond ~1 Ang have an intensity "bump" at those
covalent bond lengths, as I believe is seen in nucleic
acid-containing structures at the base-stacking distance (at the
right orientation)?

Jacob



- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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ZV+cZCyQgGLusrnufngyZ5A=
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Re: [ccp4bb] Powder Rings in Single Crystals

[Mark Wilson]

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 ~ 1 Å interatomic distances?  In my opinion, the answer is "no" unless 
translational periodicity is violated.  When translational periodicity is 
violated (as it is to some extent in all real crystals), then the 
non-Bragg (diffuse) scatter can contain many features, as it is the 
Fourier transform of the variance-covariance function for all disorder in 
the unit cell.  If I misunderstood Jacob's original question, my 
apologies.
Best regards,
Mark

Mark A. Wilson
Associate Professor
Department of Biochemistry/Redox Biology Center
University of Nebraska
N118 Beadle Center
1901 Vine Street
Lincoln, NE 68588
(402) 472-3626
mwilso...@unl.edu



Jacob Keller  
Sent by: CCP4 bulletin board 
05/09/2012 12:22 PM
Please respond to
Jacob Keller 


To
CCP4BB@JISCMAIL.AC.UK
cc

Subject
Re: [ccp4bb] Powder Rings in Single Crystals







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 the crystal/mother liquor combo is so high/broad that you can't see 
them anymore. I wonder whether when people soak in various heavy atom 
clusters, they see powder rings for the HA-HA distances in the unbound 
clusters?

JPK

On Wed, May 9, 2012 at 11:51 AM, Philip Kiser  wrote:
Hey Jacob,

There was a paper by Robert M. Blessing et al (Acta Cryst D 1996) that
at least partially attributed the diffuse ring that one sees around
3-4 A to something similar to what you are describing (scattering
between amide oxygen and nitrogen  for example).

Philip

-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

[ccp4bb] Anomalous SAXS

[Theresa Hsu]

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.

[ccp4bb] International Workshop on New Developments of Methods and Software for Protein Crystallography, August 24-27, 2012 Xi’An, China

[苏晓东]

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 Northwestern Polytechnical University

This workshop is intended to reflect and summarize some important advances of 
protein crystallography in methodology and automation procedures, such as new 
ideas and implementations for protein crystallography with emphases on 
low-resolution phasing and futuristic methods for crystal, nano-crystal or 
non-crystal structure determination; Automatic, user-friendly pipeline 
developments; Future data acquisition and storage for structural biology, 
particularly at modern synchrotron sources. The workshop will also include 
topics in new methods in protein crystallizations, nano-liter robots, automatic 
data collection at third generation synchrotrons, new light sources such as FEL 
(Free-Electron Laser), new detectors, new ways of data collection and 
processing. 

The workshop is also good for scientists in the early stage of their career, it 
will provide platforms for young scientists and students to learn the recent 
advances and to exchange new ideas and results.  There will be poster and 
selected oral presentation sessions during the workshop, and abstract or 
full-paper book will be printed and published.  Travel sponsorship for students 
and postdocs will be provided by IUCr and the workshop.



Best regards!

Xiao-Dong Su, Professor

Chairman, Commission on Biological Macromolecules (CBM), International Union of 
Crystallography (IUCr);
Secretary-general, Chinese Crystallographic Society(CCrS);

College of Life Sciences, Peking University
100871 Beijing, China
Phone:  +86-10-62759743 
FAX: +86-10-62765669
E-mail: x...@pku.edu.cn

Re: [ccp4bb] pdb and cif file generation from smiles string

[Garib N Murshudov]

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, 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
> 
> ..
> Jürgen Bosch
> Johns Hopkins University
> Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> Johns Hopkins Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Office: +1-410-614-4742
> Lab:  +1-410-614-4894
> Fax:  +1-410-955-2926
> http://web.mac.com/bosch_lab/
> 
> 
> 
> 
> 

Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] Powder Rings in Single Crystals

[Jacob Keller]

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 the crystal/mother liquor combo is so high/broad that you can't see them
anymore. I wonder whether when people soak in various heavy atom clusters,
they see powder rings for the HA-HA distances in the unbound clusters?

JPK

On Wed, May 9, 2012 at 11:51 AM, Philip Kiser  wrote:

> Hey Jacob,
>
> There was a paper by Robert M. Blessing et al (Acta Cryst D 1996) that
> at least partially attributed the diffuse ring that one sees around
> 3-4 A to something similar to what you are describing (scattering
> between amide oxygen and nitrogen  for example).
>
> Philip
>
> --
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] pdb and cif file generation from smiles string

[Shya Biswas]

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
>
>
> ..
> Jürgen Bosch
> Johns Hopkins University
> Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> Johns Hopkins Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Office: +1-410-614-4742
> Lab:  +1-410-614-4894
> Fax:  +1-410-955-2926
> http://web.mac.com/bosch_lab/
>
>
>
>
>
<>

Re: [ccp4bb] pdb and cif file generation from smiles string

[Shya Biswas]

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,
Shya

On Wed, May 9, 2012 at 12:55 PM, Paul Emsley wrote:

> 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 this kind of job.
>>
>
> I believe that this is supposed to work:
>
> cprodrg XYZIN mol.smi XYZOUT mol.pdb LIBOUT mol.cif << !
> MINI PREP
> END
> !
>
> (it went boom when I tried it though - but perhaps you  can compile it
> better - or otherwise make it work.  I should add, for balance, that I use
> MDL molfiles with cprodrg and they work considerably more robustly).
>
> Paul.
>

Re: [ccp4bb] pdb and cif file generation from smiles string

[Paul Emsley]

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 this kind of job.


I believe that this is supposed to work:

cprodrg XYZIN mol.smi XYZOUT mol.pdb LIBOUT mol.cif << !
MINI PREP
END
!

(it went boom when I tried it though - but perhaps you  can compile it 
better - or otherwise make it work.  I should add, for balance, that I 
use MDL molfiles with cprodrg and they work considerably more robustly).


Paul.

Re: [ccp4bb] Powder Rings in Single Crystals

[John R Helliwell]

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, are for the ordered atoms and
whose scattering is all scooped up into the Bragg spots.
The ferritin iron core I imagine as being possibly powder pattern
generating as nanoparticles were mentioned; indeed as it turns out
from Anna's diffraction image they are narrow-ish but still diffuse
rings, whose width will allow an estimate of the nanoparticles
diameter. The intensities of these diffuse rings should also allow an
estimate of the number of the iron atoms in the core. And thereby the
number of nanoparticles can be estimated..
All very interesting!
John

On Wed, May 9, 2012 at 3:16 PM, Jacob Keller
 wrote:
> 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 various covalent bond
> lengths in proteins (1.2-1.5 Ang), but have never heard of such. My thinking
> is that the protein itself is essentially a powder sample within the unit
> cell consisting of many small, randomly-oriented molecules (amino acids)
> with their covalent bonds. Do the rings in fact exist, and if not, why not?
> Maybe the electron density is not as "atomic," or discrete, as the nuclei
> are? I wonder whether generally data collected to beyond ~1 Ang have an
> intensity "bump" at those covalent bond lengths, as I believe is seen in
> nucleic acid-containing structures at the base-stacking distance (at the
> right orientation)?
>
> Jacob
>
> --
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: j-kell...@northwestern.edu
> ***



-- 
Professor John R Helliwell DSc

Re: [ccp4bb] pdb and cif file generation from smiles string

[Antony Oliver]

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
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ

email: antony.oli...@sussex.ac.uk
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512


From: Shya Biswas mailto:shyabis...@gmail.com>>
Reply-To: Shya Biswas mailto:shyabis...@gmail.com>>
Date: Wed, 9 May 2012 12:08:39 -0400
To: mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] pdb and cif file generation from smiles string

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

Re: [ccp4bb] Powder Rings in Single Crystals

[Tim Gruene]

-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 18:35, Jacob Keller wrote:
> 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:
> 
> 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 which you don't observe interference.
> 
> Tim
> 
> On 05/09/12 16:16, Jacob Keller wrote:
 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 various covalent bond
 lengths in proteins (1.2-1.5 Ang), but have never heard of
 such. My thinking is that the protein itself is essentially a
 powder sample within the unit cell consisting of many small,
 randomly-oriented molecules (amino acids) with their covalent
 bonds. Do the rings in fact exist, and if not, why not? Maybe
 the electron density is not as "atomic," or discrete, as the
 nuclei are? I wonder whether generally data collected to
 beyond ~1 Ang have an intensity "bump" at those covalent bond
 lengths, as I believe is seen in nucleic acid-containing
 structures at the base-stacking distance (at the right
 orientation)?
 
 Jacob
 
> 
>> 
> 
> 
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFPqp7RUxlJ7aRr7hoRAtTyAKD92CJ7+MEWyfrhov9De2AoZsDiwwCeJwg3
FiAas+UvQaXpoRCsQ8cNGdI=
=bguN
-END PGP SIGNATURE-

Re: [ccp4bb] Powder Rings in Single Crystals

[Jacob Keller]

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 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
> which you don't observe interference.
>
> Tim
>
> On 05/09/12 16:16, Jacob Keller wrote:
> > 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 various covalent bond lengths in proteins
> > (1.2-1.5 Ang), but have never heard of such. My thinking is that
> > the protein itself is essentially a powder sample within the unit
> > cell consisting of many small, randomly-oriented molecules (amino
> > acids) with their covalent bonds. Do the rings in fact exist, and
> > if not, why not? Maybe the electron density is not as "atomic," or
> > discrete, as the nuclei are? I wonder whether generally data
> > collected to beyond ~1 Ang have an intensity "bump" at those
> > covalent bond lengths, as I believe is seen in nucleic
> > acid-containing structures at the base-stacking distance (at the
> > right orientation)?
> >
> > Jacob
> >
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>
> iD8DBQFPqpVlUxlJ7aRr7hoRAhZqAJ9M49u+cYsX+AhzRlYKOCTX8YCsbQCgzFBi
> ZV+cZCyQgGLusrnufngyZ5A=
> =cuQy
> -END PGP SIGNATURE-
>



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] pdb and cif file generation from smiles string

[Bosch, Juergen]

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, at 12:16 PM, Garib N Murshudov wrote:

Is that what you are looking for?

libcheck cn generate it (JLigand should be able). grade should also generate 
from smiles.

Garib




On 9 May 2012, at 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 this kind of job.
thanks in advance,
shya

Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk




<1.cif><1.pdb>

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/

Re: [ccp4bb] pdb and cif file generation from smiles string

[Garib N Murshudov]

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 the following smiles string:O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45Prodrg 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

Dr Garib N MurshudovGroup Leader, MRC Laboratory of Molecular BiologyHills Road Cambridge CB2 0QH UKEmail: garib@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] pdb and cif file generation from smiles string

[Bosch, Juergen]

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 Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/




<>

[ccp4bb] pdb and cif file generation from smiles string

[Shya Biswas]

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

Re: [ccp4bb] Powder Rings in Single Crystals

[Tim Gruene]

-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
which you don't observe interference.

Tim

On 05/09/12 16:16, Jacob Keller wrote:
> 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 various covalent bond lengths in proteins
> (1.2-1.5 Ang), but have never heard of such. My thinking is that
> the protein itself is essentially a powder sample within the unit
> cell consisting of many small, randomly-oriented molecules (amino
> acids) with their covalent bonds. Do the rings in fact exist, and
> if not, why not? Maybe the electron density is not as "atomic," or
> discrete, as the nuclei are? I wonder whether generally data
> collected to beyond ~1 Ang have an intensity "bump" at those
> covalent bond lengths, as I believe is seen in nucleic
> acid-containing structures at the base-stacking distance (at the
> right orientation)?
> 
> Jacob
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFPqpVlUxlJ7aRr7hoRAhZqAJ9M49u+cYsX+AhzRlYKOCTX8YCsbQCgzFBi
ZV+cZCyQgGLusrnufngyZ5A=
=cuQy
-END PGP SIGNATURE-

Re: [ccp4bb] Postdoc postion at SLS

[Petr Leiman]

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:meitian.w...@psi.ch>> wrote:
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. The proposed 
project is to exploit PILATUS and EIGER detectors in protein crystallography 
applications:

  *   Systematic data acquisition and processing optimization using PILATUS 
2M/6M detectors
  *   Development of fast data acquisition and processing methods with EIGER 1M 
detector in protein micro-crystallography
  *   Commissioning of the EIGER 16M detector at a protein crystallography 
beamline

Your profile
You hold a PhD degree in (bio-)chemistry or physics, and have several years of 
experience in protein crystallography. Working knowledge for data processing 
programs, and various phasing and refinement software is a must. Experience in 
computer programming would be a significant advantage. If you are a good team 
player with fine communication skills and sense of responsibility, this 
position will offer a great opportunity for you to develop your research career 
in an exciting and highly multidisciplinary environement.

For further information please contact Dr Meitian Wang, phone +41 56 310 41 
75, or Dr. Clemens Schulze-Briese, 
clemens.schulzebri...@dectris.com

Please submit your application online (including list of publications and 
addresses of referees) for the position as Postdoctoral Fellow (index no. 
6112-00).

Paul Scherrer Institut, Human Resources, Elke Baumann, 5232 Villigen PSI, 
Switzerland


http://www.psi.ch/pa/offenestellen/0329-2


__
Meitian Wang
Swiss Light Source at Paul Scherrer Institut
CH-5232 Villigen PSI - http://www.psi.ch/sls/
Phone: +41 56 310 4175
Fax:  +41 56 310 5292




--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Postdoc postion at SLS

[Jacob Keller]

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, PSI and Dectris Ltd.
> are developing the next generation single-photon counting detector (EIGER)
> featuring smaller pixel size, higher frame rate and dynamic range. The
> proposed project is to exploit PILATUS and EIGER detectors in protein
> crystallography applications:
>
>- Systematic data acquisition and processing optimization using
>PILATUS 2M/6M detectors
>- Development of fast data acquisition and processing methods with
>EIGER 1M detector in protein micro-crystallography
>- Commissioning of the EIGER 16M detector at a protein crystallography
>beamline
>
> Your profile
> You hold a PhD degree in (bio-)chemistry or physics, and have several
> years of experience in protein crystallography. Working knowledge for data
> processing programs, and various phasing and refinement software is a must.
> Experience in computer programming would be a significant advantage. If you
> are a good team player with fine communication skills and sense of
> responsibility, this position will offer a great opportunity for you to
> develop your research career in an exciting and highly multidisciplinary
> environement.
>
> For further information please contact Dr Meitian Wang, phone +41 56 310
> 41 75, or Dr. Clemens Schulze-Briese, clemens.schulzebri...@dectris.com
>
> Please submit your application online (including list of publications and
> addresses of referees) for the position as Postdoctoral Fellow (index no.
> 6112-00).
>
> Paul Scherrer Institut, Human Resources, Elke Baumann, 5232 Villigen PSI,
> Switzerland
>
>
> http://www.psi.ch/pa/offenestellen/0329-2
>
>
> __
> Meitian Wang
> Swiss Light Source at Paul Scherrer Institut
> CH-5232 Villigen PSI - http://www.psi.ch/sls/
> Phone: +41 56 310 4175
> Fax:  +41 56 310 5292
>
>


-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

[ccp4bb] Postdoc postion at SLS

[Meitian Wang]

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. The proposed 
project is to exploit PILATUS and EIGER detectors in protein crystallography 
applications:
Systematic data acquisition and processing optimization using PILATUS 2M/6M 
detectors
Development of fast data acquisition and processing methods with EIGER 1M 
detector in protein micro-crystallography
Commissioning of the EIGER 16M detector at a protein crystallography beamline
Your profile
You hold a PhD degree in (bio-)chemistry or physics, and have several years of 
experience in protein crystallography. Working knowledge for data processing 
programs, and various phasing and refinement software is a must. Experience in 
computer programming would be a significant advantage. If you are a good team 
player with fine communication skills and sense of responsibility, this 
position will offer a great opportunity for you to develop your research career 
in an exciting and highly multidisciplinary environement.

For further information please contact Dr Meitian Wang, phone +41 56 310 41 75, 
or Dr. Clemens Schulze-Briese, clemens.schulzebri...@dectris.com

Please submit your application online (including list of publications and 
addresses of referees) for the position as Postdoctoral Fellow (index no. 
6112-00).

Paul Scherrer Institut, Human Resources, Elke Baumann, 5232 Villigen PSI, 
Switzerland


http://www.psi.ch/pa/offenestellen/0329-2


__
Meitian Wang
Swiss Light Source at Paul Scherrer Institut
CH-5232 Villigen PSI - http://www.psi.ch/sls/
Phone: +41 56 310 4175
Fax: +41 56 310 5292 

[ccp4bb] Powder Rings in Single Crystals

[Jacob Keller]

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 various
covalent bond lengths in proteins (1.2-1.5 Ang), but have never heard of
such. My thinking is that the protein itself is essentially a powder sample
within the unit cell consisting of many small, randomly-oriented molecules
(amino acids) with their covalent bonds. Do the rings in fact exist, and if
not, why not? Maybe the electron density is not as "atomic," or discrete,
as the nuclei are? I wonder whether generally data collected to beyond ~1
Ang have an intensity "bump" at those covalent bond lengths, as I believe
is seen in nucleic acid-containing structures at the base-stacking distance
(at the right orientation)?

Jacob

-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] saxs on xtals

[Jrh]

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 Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
 
 

On 8 May 2012, at 16:54, anna anna  wrote:

> Dear all,
> first of all I want to thank you for your attention and all your brilliant 
> suggestions that really cleared my head!!!
> Thanks to you (or because of you!!) now I have many ideas and very much to do.
> 
> Colin,
>  I was just re-considering my diffraction images. Who knows if they are 
> single xtals indeed! 
> Let's see if I understood your point. Assuming that they are single xtals, if 
> they are located at independent positions in the protein-cage it would be 
> like powder diffraction, with rings at diffraction angles corresponding to 
> magnetite lattice. If they are ordered they should give a diffraction 
> pattern. The corresponding lattice can differ from the protein lattice, do 
> you agree? If this is true, what would I see? Two superimposed diffraction 
> patterns? 
> Actually, I am not able to evaluate it... I attached one of the diffraction 
> images. It seems to me that there are two diffused rings at about 2.5 and 2.9 
> A.
> 
> Michael, I just read your reply. I think that the eventual periodicity of the 
> partcles can't be completely independent of the protein periodicity (I 
> attached a hypotethical scheme), as you suggest I will try P1.
> Once I tryed a naive version of what you suggest: I put a magnet over the 
> xtallization plate. All my collegues made fun of me... :) !!
> 
> I will check the literature that you all quoted (hard work!)
> 
> Thank you again, new suggestions will be really appreciated.
> 
> Cheers,
> anna
> 
> 
> 2012/5/8 R. M. Garavito 
> Dear Anna,
> 
> I know that you already have gotten replies from some top experts, but your 
> intriguing problem brought up some issues I have run across in the past.  
> 
> First, from you experience with single crystal diffraction, your results are 
> not that much different from those seen in virus structures where the nucleic 
> acid structure is averaged out.  As the nucleic acid doesn't (and mostly 
> can't) adopt the symmetry of the protein shell, the crystallization process 
> alone does the "averaging."   Just because that ferritin and magnetite have 
> cubic symmetry elements, if they don't line up, the magnetite structure can 
> be "averaged out" upon crystallization.  So, working at lower symmetry may 
> not help, unless there is some directional correlation of the magnetite 
> symmetry and position with the crystal axes.  But try P1 and see what happens.
> 
> A second comment is why not try neutron scattering (SANS or single crystal 
> neutron diffraction), particularly as you can match out the protein with D2O 
> and see just the magnetite.  While the same concerns apply for single crystal 
> neutron diffraction, you see more clearly regions of higher average density 
> inside the protein shell.  
> 
> And lastly, have you tried crystallizing your ferritin/nanoparticle complexes 
> in the presence of a magnetic field?  It would be a neat trick, and people 
> have tried such things in the past, such as for orienting biomolecules.  Some 
> even used old NMR magnets.  Would be wild, if it worked.
> 
> Good luck,
> 
> Michael
> 
> 
> R. Michael Garavito, Ph.D.
> Professor of Biochemistry & Molecular Biology
> 603 Wilson Rd., Rm. 513   
> Michigan State University  
> East Lansing, MI 48824-1319
> Office:  (517) 355-9724 Lab:  (517) 353-9125
> FAX:  (517) 353-9334Email:  rmgarav...@gmail.com
> 
> 
> 
> 
> 
> On May 7, 2012, at 12:30 PM, anna anna wrote:
> 
>> Dear all,
>> I'd like some suggestions/opinions about the sense of an experiment proposed 
>> by a collaborator expert in saxs.
>> In few words, he wants to collect SAXS data on a suspension of protein xtals 
>> to investigate "low resolution periodicity" of the xtal (more details 
>> below). 
>> The experiment requires a very huge number of xtals to obtain the circles 
>> typical of saxs and it is very time-consuming to me (I know nothing about 
>> saxs, I have only to prepare the sample). I proposed to measure a single 
>> rotating xtal (like in XRD) but he told they don't have a goniometer on saxs 
>> beamline.
>> Here is my concern: does it make sense to measure many xtals together? Don't 
>> we lose information with respect to single xtal? And, most of all, what can 
>> I see by saxs that I can't see by waxs??
>> Sorry for the almost off-topic question but I think that only someone who 

Re: [ccp4bb] number of reflections

[Tim Gruene]

-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
> only around 40,000.  I am wondering why the number of reflections
> don't match up.  I notice that the resolution range in PHENIX does
> not match that in HKL2000.  I assumed the resolution range could be
> altered, but if it is using data from the indexing (output.sca
> file) I figured it would match. Can anybody explain why this is?
> It confuses me figuring out which number of reflections to use when
> writing tables.  I normally use the number from the indexing file.
> Is this something related to default parameters in PHENIX?
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFPqkH5UxlJ7aRr7hoRAn+vAKDuvs2+u8KQvJ/J9c+q5HlMI/fwkACdGgUa
kmYgAHPpmpC1RDK8ttL7oto=
=ziou
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[ccp4bb] data backup

[sonali dhindwal]

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 which include links to all 
the projects, input, output and log files.

Thanks in advance.
Regards

-- 
Sonali Dhindwal

“Live as if you were to die tomorrow. Learn as if you were to live forever.”

Re: [ccp4bb] viewing small mol cif & fcf files?

[Jrh]

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 the time in chem X. Nb I am also a maps 
person but getting better at the various above, my tutor being Dr Madeleine 
Helliwell.
John

Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
 
 

On 9 May 2012, at 10:00, Frank von Delft  wrote:

> Could you elaborate on-list?  Is that what small mol people do - not look at 
> density, but only at esds?
> 
> I have to tell someone which one of two compounds is the correct one, 
> question being whether a Cl group is switched with a methoxy.  Being a 
> protein man I was going to look at the maps - but the programs won't show 
> them.
> 
> Okay, Platon it is. Thanks!
> 
> phx
> 
> 
> 
> On 09/05/2012 09:22, John R Helliwell wrote:
>> 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 think.
>>> 
>>> Anybody know how to display this as electron density maps?  I tried coot and
>>> mg, they barfed though - not sure whether that's a file problem though.
>>> 
>>> Thanks for help!
>>> phx
>> 
>> 

Re: [ccp4bb] viewing small mol cif & fcf files?

[George Sheldrick]

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 
file. Assuming that you have a LIST 4 fcf file,
you need to run PLATON (as pointed out by John) to make the SHELXL .ins 
and .hkl files and then run SHELXL with the LIST 6 command inserted in 
the ins file, then you can input the resulting res and fcf files into 
Coot. Even better, you can ask whoever gave you the files for their ins 
and hkl files (they must have refined the structure with SHELXL because 
as far as I know, only SHELXL writes fcf files).


However in my experience Coot may not display the bonds correctly for a 
typical small molecule without a known residue name. There are several 
excellent small molecule GUIs that are much more suitable for displaying 
small molecules and their maps. We use sheXle which is particularly 
simple and intuitive but Olex2 is also popular. These two are free, in 
the case of shelXle also for commercial users. They also support various 
stereo modes. You can google them to get the downloading information.


Best wishes, George

On 05/09/2012 10:22 AM, John R Helliwell wrote:

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 think.

Anybody know how to display this as electron density maps?  I tried coot and
mg, they barfed though - not sure whether that's a file problem though.

Thanks for help!
phx






--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

[ccp4bb] PhD studentship at University of Southampton and Diamond Light Source

[Gwyndaf Evans]

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".

Please see 
http://www.findaphd.com/search/ProjectDetails.aspx?PJID=38577&LID=1422 for more 
details of how to apply.


Catching Reaction Intermediates in the Multi-step PLP biosynthesis with 
Microfocus Synchrotron Techniques in situ

The Diamond Light Source and the University of Southampton offer a PhD in 
macromolecular crystallography. The work will establish new experimental 
techniques to analyse enzymatic reactions in protein crystals. The project 
pushes the boundaries of current experimental work, developing new methods for 
experimental data collection to give a live picture of catalysis. Training is 
unique through a combination of techniques in biochemistry, crystallography and 
computing skills for advanced data analysis.
Background. Investigating crystallographic complexes of proteins with small 
molecules is important to understand enzyme catalysis. Studies of this kind are 
also essential to understand drug binding to target proteins, such as enzymes. 
This proposal deals with the enzyme PLP synthase that catalyses more than a 
dozen steps in the biosynthesis of vitamin B6. PLP synthase is of interest for 
developing new intervention strategies for microbial or parasitic targets.
Methodology. Techniques employed range from standard biochemical methods to 
produce protein and macromolecular crystals to the most advanced methodology 
currently available to collect crystal data at a Synchrotron source. 
Biochemistry and protein crystal growth will be carried out at Southampton at 
the Institute for Life Sciences (www.southampton.ac.uk/ifls/) where the 
Macromolecular Crystallisation facilities of the Southampton Diffraction Centre 
are found (www.southampton.ac.uk/sdc). The work is shared with the Diamond 
Light Source to make optimum use of the advanced capabilities becoming 
routinely available on the beam-line I24 
(www.diamond.ac.uk/Home/Beamlines/MX/I24.html).
Workplace. The Life Sciences building provides a multidisciplinary, stimulating 
and supportive environment for post-graduate students. As part of your research 
programme you will gain subject-specific and generic skills through attendance 
of training courses and seminars. In parallel you will have regular supervision 
sessions and you will also be involved in some undergraduate student 
supervision as you progress. You will be encouraged to present your findings at 
internal and external meetings and to contribute to the writing of papers for 
publication. The Diamond Light Source is a synchrotron light source and a 
leading scientific facility of its type in the world. Located on the Harwell 
Science and Innovation Campus in South Oxfordshire, it is host to facilities 
supporting cutting edge research in all fields of science. Beamline I24 for 
macromolecular microcrystallography is the premier facility of its type in the 
world utilizing the very latest in cutting edge optics and detectors. You will 
have the opportunity to work closely with the beamline team and develop 
methodology that capitalizes on the very latest technology.
Application Deadline: May 24th 2012
Interview Date: May 31st 2012
Start Date: September 1st 2012 (earliest), December 1st 2012 (latest)
Requirements: Equivalent of a first or upper second-class degree in 
biochemistry, chemical sciences, natural sciences, physics or informatics.
Dr Ivo Tews, University of Southampton, ivo.t...@soton.ac.uk, 
http://www.southampton.ac.uk/biosci/about/staff/it1y09.page, p: 02380 59 4415
Dr Gwyndaf Evans, Diamond Light Source, gwyndaf.ev...@diamond.ac.uk, 
http://www.diamond.ac.uk/Home/Science/Expertise/GwyndafEvans.html, p: 01235 778 
164



Dr Gwyndaf Evans
Principal Beamline Scientist for I24 Microfocus MX
Macromolecular Crystallography Village Coordinator
Diamond Light Source
Harwell Science and Innovation Campus
Didcot OX11 0DE
United Kingdom

Tel: +44-1235-778164Fax: +44-1235-778448   Email: 
gwyndaf.ev...@diamond.ac.uk

Re: [ccp4bb] viewing small mol cif & fcf files?

[John R Helliwell]

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 think.
>
> Anybody know how to display this as electron density maps?  I tried coot and
> mg, they barfed though - not sure whether that's a file problem though.
>
> Thanks for help!
> phx



-- 
Professor John R Helliwell DSc

Re: [ccp4bb] viewing small mol cif & fcf files?

[Paul Emsley]

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 a file 
problem though.




Thanks to help from Eugene last year, you should be able to read the 
coordinates at least in Coot.  There is no gui for it though.


read_small_molecule_cif('pk-1234.cif')

I would have thought that you could read the fcf file too - but maybe 
that is in a format that I have not seen.


Paul.