Diffraction Data Deposition -> Data Woes in general

From: Sheriff, Steven

All:

 

The recent discussion on the CCP4BB about Diffraction Data Deposition made me think at that at least certain people might be interested in an article in Thursday, Dec. 1, New York Times business section entitled "A Genome Deluge" in the print version:

 

http://www.nytimes.com/2011/12/01/business/dna-sequencing-caught-in-deluge-of-data.html?_r=1&scp=1&sq=Genome%20Deluge&st=Search

 

It makes the woes of crystallography data seem tame by comparison.

 

Steven

Script problem

From: Simon Kolstoe


Hi there,

I've got a text file with multiple conformations of a ligand that has been docked to a protein using autodock, which I am trying to split into separate pdb files in order to visualise in pymol/coot etc.

Previously I've used the script pasted below, but it is now falling over just after it creates the pdb file with the error:

expr: syntax error
csplit: }: bad repetition count
./split_results.com: line 11: syntax error near unexpected token `('
./split_results.com: line 11: `foreach f ($outputname.[0-9][0-9][0-9])'

Can any of you wizzy programmers give me a hand with getting this to work again? (it's on a mac just in the normal terminal)

Thanks,

Simon

The script:

#!
grep '^DOCKED' output.dlg | cut -c9- > my_docking.pdbqt
cut -c-66 my_docking.pdbqt > my_docking.pdb
# csh to split pdb files from autodock output.
# edit outputname.
#
set outputname=output
set a=`grep ENDMDL my_docking.pdb | wc -l`
set b=`expr $a - 2`
csplit -k -s -n 3 -f $outputname. my_docking.pdb '/^ENDMDL/+1' '{'$b'}'
foreach f ($outputname.[0-9][0-9][0-9])
mv $f $f.pdb
end

----------
From: Ian Tickle

Simon

This appears to be a csh or tcsh script: if so the first line must be
"#!/bin/csh" or "#!/bin/tcsh", otherwise it takes it to be a sh
script.

Cheers

-- Ian

----------
From: Paul Emsley


This doesn't answer your question.

But I'd just do it in Coot:

(define (split-multi-alt-confs)
 (using-active-atom
 (let ((alt-confs (residue-alt-confs aa-imol aa-chain-id aa-res-no aa-ins-code)))
   (for-each (lambda (alt-conf)
       (let* ((ss (string-append "//*/*/*: ," alt-conf ""))
              (imol-new (new-molecule-by-atom-selection aa-imol ss))
              (new-name (string-append (strip-extension (molecule-name aa-imol))
                       "-alt-conf-" alt-conf)))
         (set-molecule-name imol-new new-name)))
         (residue-alt-confs aa-imol aa-chain-id aa-res-no aa-ins-code)))))


Centre on your interesting ligand with multiple alt-confs and then use scripting -> scheme

(split-multi-alt-confs)

If you want to write out the various pdb files, you can add in a
(write-pdb-file imol-new (string-append (molecule-name imol-new) ".pdb"))
before the set-molecule-name... line.

Paul.

Linux stereo set-up

From: Michael Hothorn
Date: 1 December 2011 15:33

Dear all,

sorry for the off topic question (that has been asked many times before, but the hardware keeps changing): I want to buy a linux workstation with Nvidia 3D vision and an Alienware OptX AW2310 23-inch 3D TFT monitor. This set-up suggested by the CCP4 wiki for TFT stereo. Has anyone a similar set-up running under linux and can suggest a matching graphics card? It would be perfect if it could handle twinview with a second, non 3D/stereo TFT monitor. Does the Nvidia Quadro 4000 do this, and is the Nvidia driver running stable under linux?

Thanks
Michael

----------
From: Andrew Purkiss

Dear Michael,

We have exactly that set up running here. A dual screen linux machine
with one Alienware OptV AW2310 screen running in stereo using the NVIDIA
Quadro 4000 card and the second screen in 'normal' mode. As far as I can
remember, the only restriction is that the second screen can only
display the same resolution as the first. Just remember that you need
the optional stereo out connector as well (make sure it is the Quadro
4000 model). This uses an additional slot, separate from the graphic
card, on the back of the machine. The current NVIDIA driver works fine
and the quality of the stereo is very good.

Additionally, if you are going to have a lot of machines with this
setup, then you may want to consider the 3D Vision Pro, which uses radio
transmission to talk to the glasses and allows pairing of glasses to
individual computers. The standard 3D Vision systems uses Infra-Red and
the glasses can get confused with if two people are using stereo next to
each other. The 3D Vision Pro is considerably more expensive though.

Hope this helps,

Andrew

--
Andrew Purkiss
Cancer Research UK.

----------
From: David Schuller

I presume the Quadro 4000 should work, it is listed on the supported products page:
http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html

We have a Quadro FX 3800 card with the optional stereo bracket (900-50762-0000-000).
http://www.bhphotovideo.com/c/product/652465-REG/PNY_Technologies_900_50762_0000_000_Stereo_Bracket_for_Quadro.html

The 3800 puts out less heat:
4000  142 W
3800  108 W

And yes, we have run our setup with a second, non-stereo,  monitor.

My hope is that soon stereo-capable monitors using DisplayPort v1.2 and with the IR emitter built-in to the monitor will make it to retail, but I haven't seen anything like that for sale yet.

--

How to distinguish between Na+ and Mg2+?

From: Florian Sauer


Dear CCP4BBers,

I'm refining the structure of a Ca-binding protein with several EF-hands against 2.2A data.
There is clear density for an ion in several EF-hands coordinated by Asp/Glu, Ser, one backbone O and one water (coordination number 5 and 6). Ca2+ can be excluded as there are no anomalous difference peaks at these sites when I calculate a map from data collected at 2A wavelength.
I suppose that either Na+ or Mg2+ are bound.
I'd like to ask whether there is a clear way to distinguish between both ions in a model from data at this resolution.

Thank you in advance for your suggestions,

Florian

P.S. The distances between ion and protein are:

Asp/Glu carboxyl O: 2.04-2.75A
Ser OH: 1.98-2.6A
Backbone O: 2.4-2.65A

----------
From: Robbie Joosten

Hi Florian,

There are quite a few tools that do this check for you. To name a few: WASP
(old but good, build the ion as water), WHAT_CHECK
(http://swift.cmbi.ru.nl/servers/html/index.html), Check My Metal and
probably quite a few others. All of them use the bond valence sum, but they
all have a different implementation so the results may differ. That said, it
is usually reasonably easy to tell Na+ and Mg2+ apart.
At the risk of stating the obvious: think of what you added in the
crystallization, buffer counter ions are easily overlooked.

Cheers,
Robbie

Vote for Bill !

From: Bernhard Rupp (Hofkristallrat a.D.)


Hi Fellows,

here is your chance to vote for a crystallographer in the People's Choice
education program contest:

http://us2.campaign-archive2.com/?u=3e43dd9d1724b97d2bc286881&id=485f01c36b&
e=76452e4682



----------
From: Frances C. Bernstein


Herbert foundd that one is allowed to vote once per day
so that would be a good way to boost his count.  Note
that Bill is currently in second place and only a few
hundred votes behind so getting him to the top should
be doable.

                   Frances

Mystery density

From: Martin Montgomery

Posting on behalf of Katia Baranova (see below).  Any suggestions gratefully received!

Hello,

we have a puzzling density and hope someone has an idea of what it may be.

The pictures of it are here:

http://www.mrc-mbu.cam.ac.uk/sites/default/files/images/mystery/top.png
http://www.mrc-mbu.cam.ac.uk/sites/default/files/images/mystery/front.png
http://www.mrc-mbu.cam.ac.uk/sites/default/files/images/mystery/side.png

The space group is I422, resolution 1.6A

The trial contained Tris, DTT, EDTA, sodium, potassium, phosphate, and chloride.

The centre of our unknown feature is about 3.8A from the Arg and it is also on the four fold symmetry axis.

It is + 28 sigma in the center and  about + 9.5 sigma in each of the "tentacles".

Thank you very much!

Katia.

On 30 Nov 2011, at 17:30, Katia Baranova wrote:

Hello,

Well, it doesn't work.
Can you forward it please?

thanks a lot,

K

----------
From: Mark J van Raaij


although it is hard to see in 3 2D views, some of the tentacles appear connected to the protein, could they result from some of the long Lys or Arg side-chains not following the 4-fold symmetry? i.e. alternative conformations?
The density on the 4-fold may be ions, solvent, some metal ion? "Noise appears to collect on symmetry axes" (for want of a better way to put it), so the sigma-levels there are not very reliable. Sometimes one sees quite strong negative peaks on symmetry axes that can not be explained, so I would expect spurious positive peaks to also occur. Of course we normally just put a water in it if it can make reasonable hydrogen bonds.

Mark J van Raaij

----------
From: Carlos Kikuti

It's bang on the Y axis.... I'd just ignore it (treat it as just noise) and work on the rest of the model. There seems to be some trouble in other parts of it. (Had a similar case but at 3.5 A data).  I wonder what is the gap between Rfree and Rwork.

And I'm curious for what more experienced people will say about it.

Carlos


----------
From: Adrian Goldman


We had a similar case in our Eib structure (2xzr), with large peaks on a 3-fold.  We initially thought it was noise, but Andrei Lupas convinced us to look more carefully, and it turned out to be chloride ion.

You could do an wavelength scan at a beamline looking for anomalous signal at the longest wavelength you can get to.  If it's just noise, it shouldn't be particularly visible.  If it is chloride or phosphate, you should at least have a peak there.

Adrian

----------
From: Eleanor Dodson

Well - first thing to do is an DANO map and see if it is a metal ion. The relative height of the DANO peaks for S and anything else can give you some clues.

Eleanor

----------
From: Roger Rowlett

I think a metal ion is unlikely given that the nearest ligand(s) are Arg residues. I would lay money on an anion. The central feature looks very much like a bicarbonate ion, and is very similar to the bicarbonate ion bound in a generic anion binding site near 2 Arg residues on a NCS 2-fold axis in beta-carbonic anhydrase. The rest might be waters. If this sits on a crystallographic symmetry axis, things can look a little funky, but you do seem to have a triangular planar feature in a special position. For a similar binding interaction with bicarbonate, see PDB 3E3I, 3E3F, and Rowlett, et al. (2010) Biochemistry 49, 3640-3647, "Evidence for a Bicarbonate 'Escort' Site in H. influenzae beta-Carbonic Anhydrase."

Cheers
,

----------
From: Ed Pozharski

The center bit looks very much like phosphate - see what happens if one
is placed there

It may be educational to look at the maps in P1, just to see how much
trouble is caused by "noise accumulation on the symmetry axis"

--
Edwin Pozharski, PhD, Assistant Professor

Description of a newly solved structure

From: sadaf iqbal
Date: 1 December 2011 04:49

Hello everyone,

I have submitted one cysteine protease structure in PDB and now i have to describe the structure completely for my PhD thesis. I know some web servers who are good to provide knowledge about protein but i would like to ask expert persons of this field as i am quite new in describing a structure. Which softwares/web servers you prefer when you are going to describe one complete native structure? I am a chemist basically.

Thanks in advance

 

Sadaf Iqbal
PhD Scholar

----------
From: Sean Seaver


Hi Sadaf,

I would start with BRENDA ( http://www.brenda-enzymes.org/ ) for an overview on the protease.  The web servers and databases that you should consider will be highly dependent on the details of your particular structure.  I put together a list of some programs/servers/databases that you may want to consider ( http://bit.ly/d2I11n ).  I hope it helps.

Take Care,

Sean Seaver

P212121
http://store.p212121.com/

----------
From: Katherine Sippel

For drawing a 2D fold topology I'd suggest TopDraw (http://www.ccp4.ac.uk/html/topdraw.html). To see if you structure looks like other structures I'd look at the DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Dali is pretty good for digging out results/discussion fodder because it gives you another structure(s) to compare. PISA would be my suggestion for roughly identifying any oligimerization though it's best to back those claims up with experimental data. If you've got ligands bound Gerard Kleywegt and the PDBe staff have put together a lovely means of searching and representing motifs which is also useful for comparative purposes (http://www.ebi.ac.uk/pdbe-site/pdbemotif/). There are a panoply of good figure generating softwares available but my personal preference is Pymol for it's flexibility, comprehensive wiki, and supportive users groups (http://www.pymol.org/).

If your just looking for a description of what to put into a results and discussion section for a new structure you might try browsing through the Acta Cryst D archives for some good examples.

Hope this helps,

Katherine

----------
From: Nadir T. Mrabet

I would also suggest using MolProbity to assess structure quality.

Best,

Nadir

Phaser problem "child killed: segmentation violation in phaser"

From: Sita Ram Meena
Date: 29 November 2011 10:11


 Hi CCP4 community.

While running the Phaser in the CCP4 GUI, It was terminated and giving the error message.

#CCP4I TERMINATION STATUS 0 "child killed: segmentation violation"      
                                            
#CCP4I VERSION CCP4Interface 2.0.6

CCP4 Version ccp4-6.1.13


Thanks in advance.


Sita Ram

----------
From: Randy Read

This was resolved offline.  It turns out that there's an obscure bug in Phaser triggered if you search for the same model twice as an alternative for itself (e.g. "SEARCH ENSEMBLE ensemble1 OR ENSEMBLE ensemble1 NUM 1").  When the input was fixed ("SEARCH ENSEMBLE ensemble1 NUM 1"), Phaser didn't crash any more, but unfortunately, it didn't solve the structure either.

The bug is fixed now for future versions of Phaser.

Best wishes,

Randy Read

sugar and coot

From: Jan van Agthoven
Date: 22 November 2011 00:16


Hi everyone!
Does anyone know if there is a way of auto-refining a sugar in Coot?
Jan

----------
From: Dirk


Hi,

I'm not sure if that is what you are looking for, but if you want to use the "real space refine zone" function in coot with sugars that is possible.
For a monosaccharide you will need a cif dictionary with the restraint definitions - in some cases present in the refmac monomer database, but be careful not all cif files there are correct. If none is present or if your monomer is disrupted during refinement you can look at the small molecule databases (Hic-Up etc) or calculate one with PRODRG  (http://davapc1.bioch.dundee.ac.uk/prodrg/). Load it with "File" "Import CIF dictionary and real space refinement should work.
If you try to refine a polysaccharide it's a bit more difficult since coot will ignore any glycosidic bond restraints - if two sugars are close by and one has well defined density and the other one not it might even place them on top of each other.
I like to use the anchor tool on the bonding atoms in those cases.
The other option for a polysaccharide is to use PRODRG to generate a single "monomer" out of your polysaccharide.

In any case at the end you have to inspect the geometry manually since the restraint definitions are often incomplete.

Greetings

Dirk

----------
From: Joel Tyndall

You can also try Jligand to generate your cif file

J

 

----------
From: Paul Emsley


Such a tool (if I understand correctly what you want) does not yet exist. However, I believe that things are not in as poor a state as one might infer from other posts.

Using the pre-release, you can

1) ideally position a NAG onto ASN
2) use multi-residue torsion to position a NAG by rotation of ASN chi angles
3) use the Ligand builder to build new carbohydrate monomers (it is my experience that PRODRG respects the wedge bonds - but I have heard that this is not always the case)

Using latest stable or later you can

4) multi-residue refinement (or sphere refine), which does a link analysis based on the coordinates of the residue selection (note that bonding atoms have to be within 3A to be considered a real glycosidic linkage)
5) add addition pseudo plane restraints to encourage ideal chair (in my experience, at low resolution or with poor density, carbohydrates tend to wander off and twist up without these)

The JLigand-Coot interface has stalled a bit, but I hope should be available for the Study Weekend.

The Refmac-Coot link-up using LINKR is under discussion with Garib and Eugene.

I would recommend against making a synthetic disaccharide carbohydrate with PRODRG.

Regards,

Paul.

----------
From: Heping Zheng


The issue I would raise here is not just for coot, but also for PDB format
itself. Last time I asked on ACA2011, Dr. Berman said polysacchride
residues in PDB is still not yet uniformly represented.

The issue I have is to polysacchride chains refinement in general, but
here more specific about branch chain of polysacchride chains. For
example, if you think about the case of N-glycosylation
Asn-NAG-beta1,4-NAG-beta1,4-Man-(alpha1,3-Man)-alpha1,6-Man ...

Now you have a branch chain, Now if I assume the following resseq
ASN A135
NAG A500
NAG A501
MAN A502
MAN A503
MAN A504

In my coot, version 0.6 revision 2540, You will be able to refine
A500-A503 as a whole since they are consecutive in resseq. But when I need
to refine NAG A500 together with ASN A135 locally, simply specify the
range is not enough, I need to specify a small radius to get it work, even
though the covalent link is defined in LINKR record. The same applies when
I want to refine just A502-A504 alpha1,6 glycosidic bond without refine
A503.

I am just wondering what is the state of the art for branch chain handling
in coot or another interactive refinement program.

best regards,
Heping Zheng

----------
From: Paul Emsley


Stuck email... try again...
 indeed. Quite so.  As I said (or more accurately, implied) LINKR recognition is
an on-going issue (i.e. it doesn't work yet). Yes. Well, I don't know much about about other programs, but in coot you can
use refine-residues or Sphere Refinement.
Even in 0.6.

Paul.

Postdoctoral position in Baltimore, MD

Date: 27 December 2011 20:04



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Our laboratory focuses on the molecular basis of function of proteins involved in the anti-HIV-1 immune responses, human immune defense in general, and cancer prevention (http://www.ihv.org/research/bio_recognition). Successful candidate will utilize the established high-throughput structural biology platform and biochemical/biophysical techniques to study novel targets on HIV-1 Env that are exposed during viral attachement/entry and are exclusively responsible for Fc mediated effector function (ADCC). Studies will focus on structural characterization and epitope definition of ADCC-mediating anti-HIV-1 Env mAbs, as well as the structure-based studies guiding development of protein-based therapeutics and novel vaccines.
The position requires a Ph.D. in biochemistry, molecular biology, or a closely related discipline with practical experience in molecular biology and protein science techniques including surface plasmon resonance, isothermal titration calorimetry and X-ray crystallography. Candidates need to be highly motivated individuals who enjoy working as part of a young, dynamic, collaborative and multidisciplinary team. Excellent oral and written communication skills and good presentation skills are essential.
Interested parties should submit electronically a CV, a statement of research interests and previous experience, and contact information of three references to mpazgier@ihv.umaryland.edu Review of completed applications will begin immediately.

Displaying CH---N weak hydrogen bonds

From: REX PALMER
Date: 1 December 2011 11:21

I am looking for a program that will display weak CH---N bonds.

The programs I know about only display classical hydrogen bonds such as OH---N etc.

Any suggestions please?

 

Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com

----------
From: Bruno KLAHOLZ

 

Dear Rex,

 

if you display hydrogens in Pymol you should be able to draw distances between any atoms

(select the 2 atoms of interest with Ctrl + middle mouse, and type "distance" into the command line).

However, one should obviously keep in mind the geometry of the free electron pairs to which H-bonds can be donated.

See for example Fig. 1 in

C-H...O hydrogen bonds in the nuclear receptor RARgamma--a potential tool for drug selectivity.  Structure. 2002 Sep;10(9):1197-204.

 

HTH,

 

Bruno

 

 

image compression

From: Frank von Delft
Date: 30 November 2011 19:48

(Old thread, just cleaning up, sorry...)


I thought James' algorithm didn't do anything to the spots, just to the stuff in between.

So one obvious way to handle this is for the data processing programs to be looking between the integrated spots as well, whether they're missing anything;  they could then flag it up if they are, prompting the experimenter to haul out the originals.

I mean, data processing programs are looking between spots already, aren't th... oh. Right.  Sorry, silly me.  Well, maybe they should.  Considering that's the reason we're pushing terabytes around cyberspace, according to this thread.  Personally I'd already be happy with an indication of how many spots I'm not integrating.

phx.



On 08/11/2011 12:17, Herbert J. Bernstein wrote:

Um, but isn't Crystallograpy based on a series of
one-way computational processes:
      photons ->  images
      images ->  {struture factors, symmetry}
  {structure factors, symmetry, chemistry} ->  solution
  {structure factors, symmetry, chemistry, solution}
       ->  refined solution

At each stage we tolerate a certain amount of noise
in "going backwards".  Certainly it is desirable to
have the "original data" to be able to go forwards,
but until the arrival of pixel array detectors, we
were very far from having the true original data,
and even pixel array detectors don't capture every
single photon.

I am not recommending lossy compressed images as
a perfect replacement for lossless compressed images,
any more than I would recommend structure factors
are a replacement for images.  It would be nice
if we all had large budgets, huge storage capacity
and high network speeds and if somebody would repeal
the speed of light and other physical constraints, so that
engineering compromises were never necessary, but as
James has noted, accepting such engineering compromises
has been of great value to our colleagues who work
with the massive image streams of the entertainment
industry.  Without lossy compression, we would not
have the _higher_ image quality we now enjoy in the
less-than-perfectly-faithful HDTV world that has replaced
the highly faithful, but lower capacity, NTSC/PAL world.

Please, in this, let us not allow the perfect to be
the enemy of the good.  James is proposing something
good.

Regards,
   Herbert
=====================================================
               Herbert J. Bernstein
     Professor of Mathematics and Computer Science
On Tue, 8 Nov 2011, Harry Powell wrote:

Hi

I am not a fan
of one-way computational processes with unique data.

Thoughts anyone?

Cheerio,

Graeme

I agree.

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH

http://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011

----------
From: John R Helliwell


Dear Frank,
Re "pushing terabytes around cyberspace".

Well, actually, the synchrotron facilities hosting the datasets
locally that were measured there is a major step forward for
diffraction data preservation, especially for MX but also true for
SAXS, XAFS etc, as is being pushed forward by Alun Ashton and
colleagues at DLS. The European SR and neutron Facilities 'PaN' data
archiving initiative relates also firmly to this.

For the major hurdle of chemical crystallography datasets, with the
majority measured on local X-ray sources, I think it is looking
promising that local University data depositories will host these. At
least, the discussions with specialists here at University of
Manchester are underway and it looks promising.

The compression approach also sounds promising too, as indicated in
detail, including with a wide range of
tests, by James Holton.

Greetings,
John

--
Professor John R Helliwell DSc

how to add Cadmium ion to structure and do the refinement

From: Lu Yu
Date: 28 November 2011 20:16


Hi ALL,

This is the first structure I am working with.
As the title said, I was stuck in the middle of model building using coot, and I found a big positive peak for Cadmium ion. The coot program doesn't *know* the cadmium ion when I add a Cd atom there (under the "place atom at pointer" menu--> "Other" ), and the refinement program doesn't *know* how to refine this (failed when I refine the whole structure, and it may need appropriate values as restraints, but I don't know how to add these values ).

So I am wondering any one can give me any suggestion about, how to add cadmium ion in the position and do the refinement.

Thanks in advance,

Lu

----------
From: Roger Rowlett

Lu,

To add a metal ion to a structure, you can use "place atom at pointer" or "Get Monomer...". I usually use the latter. For instructions see http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Building+and+Validation#Adding_ligands_to_a_protein. For cadmium, I think you can enter "CD" for the monomer name (all caps). The documentation for Refmac has a complete list of recognized monomers and their 2-3 letter names.

To refine the metal in Refmac with restrained ligand distances, see http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Refinement#Restraining_metal_ligand_distances_during_refinement_in_REFMAC. Refmac will create a .cif file with the proper restraints when you try to run it the first time (and fails). Include the library (.cif) file when you re-run the job and all will be well.

BTW, if this is a Cd(II) ion, you should really edit columns 76-80 (I think that's right--you'll see the elements listed in the last 4 columns of each line of the pdb file) of the PDB file to read "CD+2" and not "CD  ", although in practice this may not make that much difference. But is is more accurate in terms of X-ray scattering if you indicate the ionic charge.

----------
From: Jim Pflugrath


If you edit the PDB file "by hand", then you should have no problems.  Some folks might cringe at this, but this does work:

1. Like Roger Rowlett said, "place atom at pointer".  You can place a chloride there.  Be sure to add to your molecule and not a new molecule.
2. Save the coordinates to a PDB file.
3. Edit the newly saved PDB file with the Chloride designation with an editor (emacs is great) and change the Chloride to a Cadmium.  What does a Cadmium look like in a PDB file? I don't have a clue, but I would search for "cadmium" at rcsb.org and save a PDB file with a cadmium in it.  Then you can see what a cadmium looks like in the example PDB file and mimic that in your file.

Jim
----------
From: Zhijie Li

Hi Lu,

 

Cadmium(II) seems to be in the standard monomer library in both Coot and CCP4. Thus you do not need to make it by yourself. I guess your problem was due to that you have put a "Cd" instead of "CD" when adding it in Coot. Refmac is case sensitive when identifying the compounds or atoms. All ions need to be in upper case to match their .cif files.

 

Please check the "share\coot\lib\data\monomers\c" and "ccp4-6.2.0\lib\data\monomers\c" folder. You should have a "CD.cif" there. This file is the monomer definition for Cd(II) ions. Please take a look in the file, especially this part:

 

loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 CD            CD     CD   CD        2.000      0.000    0.000    0.000

 

The 2.000 in the last line corresponds to the "_chem_comp_atom.partial_charge" entry. The 2.000 indicates that this is for a Cd(II) ion. If your Cadmium is Cd(II) then you are OK. No more worries.

 

If you think your Cadmium is Cd(III), then you need to change the partial_charge value to 3.000, and change all the "CD"s in this file to "CD3", then save it as another file, "CD3.cif" (make sure "CD3" is a unique name in the whole library), and use it for your refinement. Also in this case you need to put "CD3"s in your PDB file instead of "CD".

 

This is a simple case so you can edit by hand. Please take a look in the "FE.cif" and "FE2.cif" in the "f" folder to see how such cases should be handled. Also please note that the FE1.cif and FE3.cif are not for iron at all. This is an example showing that we should always have a look in the cif files to make sure the descriptions are correct for our ligand. If not we need to find the right one or make our own.

 

Zhijie

----------
From: Zhijie Li

Corrections of my previous email:

 

According to wikipedia:

"Although cadmium usually has an oxidation state of +2, it also exists in the +1 state."

So there is probably no Cd(III) for us to worry about.

----------
From: Eleanor Dodson


Hasanyone answered this?

Possibilities
1) COOt by default may have written your CD to another coordinate file - usually called PointerAtoms.pdb

2) You got the atom into the pdb you want to refine but it is wrongly labelled.

You need
ATOM    471  N   ASP A  81      23.896   6.780   5.956  1.00 60.81..

the atom label moved to the left, and the residue to be called CD and the atom type (last entry on ATOM line) to be CD
ATOM    471 CD   CD  A  81      23.896   6.780   5.956  1.00 60.81..

The residue number must be different from any existing residue..

The REFMAC log will trell you what it disliked, but not very well marked..

----------
From: Lu Yu

Hi,
Thanks for your advice!
My problem has been solved, coot has cadmium ion (which I didn't know at first), and the reason that it didn't work at first is I put Cd instead of CD (should be *upper case*) under the "place atom at pointer" menu, so the refmac and coot don't recognize it. Now I learned new things!

Many thanks!

Lu

jumping ligand

From: Ed Pozharski
Date: 30 November 2011 18:40


Did anyone ever seen a ligand molecule (or water, maybe) moved into a
symmetry-related position upon refinement in refmac?  If that is a
feature (e.g. to make sure that non-protein stuff is coordinated to the
spot of the closest contact), how can I disable it?

Cheers,

Ed.

--
----------
From: Garib N Murshudov

Does it happens when you use automatic NCS restraints?

Garib N Murshudov

Superpositions: Deviation by Residue

From: Jacob Keller
Date: 28 November 2011 22:22

Dear Crystallographers,

is there a ccp4 program--or otherwise--which can compute ca-ca
distances of corresponding residues between two superposed structures?

Jacob



----------
From: Bosch, Juergen

I'd say you have to look into the USF toolbox e.g. Moleman2

You want to calculate rmsd's there's an option for that.

Jürgen

----------
From: Mario Sanches

Hi Jacob,

I used Moleman to do that once  (http://xray.bmc.uu.se/usf/moleman2_man.html)

The Distance LIst command is probably what you are looking for.

Mario Sanches

----------
From: Jacob Keller

Let me refine my question (sorry for my lack of clarity): is there a
program that will output the distances between the corresponding ca's
of a superposition on a residue-by-residue basis, and not just a
global RMSD value (doubtless these numbers are part of the
superposition algorithm itself)? I want to plot these values as a
function of residue number to show which parts of the structures
deviate more or less from each other.

Jacob

----------
From: Abhinav Kumar


CCP4's superpose does this.
It produces a table like this, but only for residues that are used in the alignment.
.-------------.------------.-------------.
|    Query    |  Dist.(A)  |   Target    |
|-------------+------------+-------------|
| + A:ARG  10 |            |H+ A:GLN 223 |
| + A:ARG  11 |            |H+ A:ASN 224 |
|H+ A:LYS  12 | <..6.19..> |H+ A:PRO 225 |
|H+ A:LYS  13 | <--4.03--> |H+ A:ASN 226 |
|H+ A:LYS  14 | <--3.73--> |H+ A:GLN 227 |
|H+ A:GLN  15 | <..4.05..> |H- A:LEU 228 |
|H+ A:LYS  16 | <..3.41..> |H- A:ILE 229 |
|H+ A:GLU  17 | <..1.75..> |H. A:SER 230 |
|H- A:ILE  18 | <++1.97++> |H- A:LEU 231 |


Thanks,
Abhinav

----------
From: Robert Immormino


Hi Jacob,
This sounds like what you get from ddmp (
http://www.csb.yale.edu/userguides/datamanip/ddmp/ddmp_descrip.html ).
Good Luck,
-bob

----------
From: Eric Pettersen

On Nov 28, 2011, at 4:03 PM, Jacob Keller wrote:

If you use the MatchMaker tool in UCSF Chimera to make the superposition, it has an option to show the corresponding sequence alignment.  The sequence alignment will have an "RMSD" header running across the top, which is a bar graph of the RMSD values.  You can the alignment's Headers->Save... menu item to save the numerical values to a file if you want.

If you already have the structures superimposed on your own, you can use Chimera's Match->Align tool to create a superposition-based sequence alignment, and do the same thing with its RMSD header.

Some links:

Chimera home page: http://www.cgl.ucsf.edu/chimera

alignment tool's RMSD header: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/multalignviewer.html#assessment

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu

----------
From: Edward A. Berry


The program:
http://sb20.lbl.gov/berry/for/pdbdist2b.for
does this.

If you run it by the wrapper pdbd2b:
echo 'Find distances greater than threshold between corresponding atoms in 2 PDB files'
echo 'Usage: pdbd2b file1 file2 startres# [thresh]'
pdbdist2b <<eof
$1
$2
$3 10000
$3
$4 3.0
eof

then the format is:
 pdbd2b file1  file2 startresiduenumber threshold
(set the threshold to -1 to print all distances)

then it is easy to redirect the output table to a textfile which can be
imported to scalc or excel for plotting.

It is kind of stupid: ignores chain letters, and once it finds
startresiduenumber in both files it proceeds without looking at numbers
or chains, so the atoms have to be in the same order in both files.
But if you have an insertion deletion you can just run twice, starting after the midmatch the second time.

 N   GLU A  13  N   GLU A  13      0.0105
 CA  GLU A  13  CA  GLU A  13      0.0092
 CB  GLU A  13  CB  GLU A  13      0.0186
 CG  GLU A  13  CG  GLU A  13      0.0369
 CD  GLU A  13  CD  GLU A  13      0.0490
 OE1 GLU A  13  OE1 GLU A  13      0.0623
 OE2 GLU A  13  OE2 GLU A  13      0.0494
 C   GLU A  13  C   GLU A  13      0.0231
 O   GLU A  13  O   GLU A  13      0.0648
 N   THR A  14  N   THR A  14      0.0156
 CA  THR A  14  CA  THR A  14      0.0112
 CB  THR A  14  CB  THR A  14      0.0160
 OG1 THR A  14  OG1 THR A  14      0.0164
 CG2 THR A  14  CG2 THR A  14      0.0273
 C   THR A  14  C   THR A  14      0.0157
-
written for g77 but seems to compile with gfortran
I need to look in Dave's calendar prog to remind me how to get
command lines parameters in fortran - then can dispense with the wrapper.

----------
From: Tim Gruene



Dear Jacob,

Coot prints this information to the terminal, so you can start coot and
'tee' its output into a file.

Tim

- --
- --

----------
From: Jacob Keller


Dear Crystallographers,
Thanks very much for all who responded to my request. Below is a
compiled list of the various ways to skin this crystallographic cat!
Jacob
-Moleman ca plot distance-CCP4's superpose-distance matrix analysis,
e.g. http://www.csb.yale.edu/userguides/datamanip/ddmp/ddmp_descrip.html,
or other programs-Lsqkab, with the "deltas" card-If you use the
you want. OR If you already have the structures superimposed on your
RMSD header.-Coot prints this information to the terminal, so you can
start coot and 'tee' its output into a file.-Various fortran/homebrew
programs available from individuals-LGA server:
http://proteinmodel.org/AS2TS/LGA/lga.html

----------
From: Eleanor Dodson


Dont you get that from SSM and lsqkab (you have to turn on - list atom distances or some such in the GUI)

Eleanor

----------
From: Gerard DVD Kleywegt


You mean to produce something like this? http://xray.bmc.uu.se/usf/pics/distplot_1chr.gif

That can be done with LSQMAN - http://xray.bmc.uu.se/usf/lsqman_man.html#S65

Of course, there are lots of other interesting metrics and plots to assess structural differences between two models - http://xray.bmc.uu.se/usf/lsqman_man.html#H17

One of my favourite ones is the CD plot, for comparing multiple models, which looks a bit like a gel: http://xray.bmc.uu.se/usf/pics/cdplot_1ldn.gif

For other options, see http://xray.bmc.uu.se/usf/lsqman_man.html#H19

--DVD

******************************************************************
                          Gerard J. Kleywegt

effective chemical lysis of E. coli under anaerobic conditions

From: Jim Spencer, Cellular and Molecular Medicine
Date: 29 November 2011 14:49


Dear All,

Apologies for the off-topic question.  I'm seeking suggestions on the best way to achieve an effective, but not over-harsh, chemical lysis of E coli expressing an oxygen-sensitive Fe-S protein.  We need to lyse anaerobically but do not have access to a sonicator that we can use in the glove box.  We have used a proprietary detergent mix in previous attempts but have not been overly impressed with the results- lots of protein (more than I would expect based on past experiences with related enzymes) remains in the pellet.  I've seen literature protocols based on Triton (up to 1.2%) but am worried (perhaps without basis) that this might interfere with downstream steps (reconstituting the Fe-S cluster and possibly crystallisation).  The protein is His-tagged.

Does anyone know a better way?

Thanks in advance.

Best wishes

Jim

----------------------
Dr. James Spencer,

----------
From: Artem Evdokimov

0.5% octyl-thioglucopyranoside + lysozyme + DNAse in 30 mM TRIS pH 8.0 - degassed/sparged and supplemented with whatever reducing agent you need. Stir in cold for 30-40 minutes at a ratio of 3ml of solution to 1g of cell pellet (wet).

 

Artem

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Disappearing crystals

Hi All,

I have just noticed a very strange thing and need some help in understanding it.  I recently found two crystals in a condition from a screen (0.05M Calcium chloride dihydrate, 0.1M M Bis-Tris pH6.5 and 30% PEG MME 550).  The small crystals appeared after a month and started to grow over the next 5 days after I first saw them (see pictures attached).  I just check the same drop today and now the crystals are gone.  So I was wondering what happened and if anyone experienced this before.  Any insight or advice on what to do would be greatly appreciated.

Thanks

Christine

From: David Schuller

Was the heating/cooling turned down over the Turkey day holiday?

----------
From: YoungJin 

Hi Christine,
I had similar experience. In my case, another crystal showed again with different size a few days later. Sometimes, it seems like it is a common event to others as well as I heard although my case only takes about a week to be crystallized.  I'd rather wait or just set up again or in a slightly different way.

Wish you well.

Young-Jin

----------
From: Enrico Stura 
When advice on crystallization is needed, it is important to give details of
the protein concentration, the buffer the protein is in as well as the method
used to grow the crystals.

Problem: The crystallization conditions are essentially low salt: 100mM buffer
and only 50mM CaCl2. So the buffer that the protein is in is very important !!
Fluctuation in the reservoir/drop environment will lead to crystals dissolving.

Solution: Balance the salt in the reservoir and in the protein:precipitant drop and make sure
the temperature is kept constant.

Since I do not have all the necessary information, the diagnosis and the solution proposed
are likely to be wrong!

Enrico.

----------
From: Jan Dohnalek 
We have seen such behaviour connected to temperature fluctuations.

Jan

--
Jan Dohnalek, Ph.D
----------
From: Fischmann, Thierry

Yes, and if they don't reappear it may be worth moving the trail to an incubator set at a slightly different temperature than "room temperature". You may have to try both lower or higher temperatures if you have no idea how the temperature may have changed (it's the temperature of the room when the crystals showed up that matters, obviously).

Alternatively you could set up "fresh" trails with same conditions but for a deliberate and controlled screening around what the room temperature typically is.

Good luck

Thierry

----------
From: Harman, Christine 
Hi,
Thank you so much for your replies.  A lot of you have mentioned fluctuations in temp as the major contributor.  And a few of you have asked for more details of my protein/buffer and set up.  To my knowledge, the tray has been kept at constant 20 C (in an incubator) with exception of course to when I remove the tray to view the drops.  It could be possible that my inspection of the tray might have contributed to an increase in temp, but only temporarily.  I am very careful about the time the drop sees intense light, but it is possible the temp could have changed enough to cause this problem.  Just to give a few more details.  My protein (a Fab fragment/peptide complex (hopefully) is in buffer containing 100mM Sodium Acetate pH 5.5 with 150mM NaCl at a protein concentration of ~4.3mg/mL.  After setting up my drop with reservoir solution I add NaCl to well to give ~75mM NaCl to match ionic strength of protein in drop which is diluted 1:1 with well solution.  I do hope this problem is temperature.  Although I am a little sad to not be able to freeze those crystals I did see, I still consider myself lucky to get such good result from a condition right from the screen so there will be some definite optimization set ups with this condition.  Could I safely say though that the crystals I observed are not salt..:)  I guess that is one good thing to take from this.  Any more suggestions on optimization would be very welcomed.

Thanks again to all you,

Christine

----------
From: Mathews, Irimpan I. 
Hi Christine,

Another minor point (mainly for hanging drops) not mentioned in the messages.

When you bring the crystallization tray from lower temperature to room temp. there is a possibility for condensation and slowly droplets near the protein drops gets absorbed into the protein drop.  If this happens, depending on the condition and character of the protein,  the crystals could crack or dissolve.

In your case, condensation might have happened during your last check and the crystal may have affected by this issue.  To avoid this problem: while taking the tray from the incubator place another tray on the top of your protein tray and keep them outside for few mts before checking with the microscope.

best wishes,
Mathews

----------
From: Artem Evdokimov 

In addition to others' excellent suggestions, I'd like to offer more option to consider:

Your crystallization set-up has some form of chemical non-equilibrium with respect to protein. It may just be my imagination but something is happening to the yellow precipitate in your drops, namely it's going away. Is it possible that you have a slow proteolysis (or something) happening to your protein, where one of the proteolytic products is crystallizing, however it's not the *final* proteolytic product so crystals are transient for as long as a 'steady state pool' of the appropriate form is above the solubility threshold (this implies equilibrium between soluble protein and crystals, which is not a huge stretch).

If this is the case, I'd check your drops with MS after a few days to see if anything interesting is happening. Options include but are not limited to: proteolysis, oxidation, chemical reaction of protein, chemical reaction of buffers and/or additives, and so on :)

Artem

P.S. It could simply be that your protein is initially precipitated but then driven back into solution? It happens.

A.

----------
From: Enrico Stura 
Dear Christine,

I had guessed that you had more salt in the protein solution
than in the reservoir with a relatively  low protein concentration.

The protein is in:  and the reservoir is: We can suspect that no matter what temperature the equilibrium will move
towards dilution in the drop.

Basic suggestion:
Set up a range from 20-30% PEG MME 550
with at least 150mM NaCl in the reservoir.

Fine tuning:
Add high MW PEG (10K or 20K 1-5%) it should have a stabilizing effect
Try a range of salts apart from NaCl: The clasics are: Li2SO4, KSCN, MgCl2.
Try additive amounts od MPD 0.5-3%.
Try a small tight range of various pH.

Enrico.

----------
From: Patrick Shaw Stewart 

Christine, I have a couple more comments

First, if those crystals come back, I would certainly try microseeding into random screens.  You should be able to pick up new conditions that have a little more salt in them, and are therefore stable regarding the movement of water.  (If you can't get the crystals back, I would try microseeding with the precipitate that you have.)

Second, it's helpful to understand that the movement of water in and out of the drop is connected to heat flows, not temperature.  The heat flow drives the movement of moisture (in addition to the salt etc. of course).

Once you understand that you can easily get rid of e.g. condensation on the tape by putting e.g. a warm book on top of the plate in the cold room (or a book from the cold room under the plate at room temp).  Similarly, you can prevent dilution of your drops by thinking about heat flows.

Some say that it's essential to use Blundell and Johnson.  Others say only Bergfors on crystallization, Lord of the Rings or even Harry Potter can provide the necessary inspiration.

Good luck

Patrick

Ref for microseeding: Allan D’Arcy, Frederic Villarda, May Marsh. An automated microseed matrix-screening method for protein crystallization.  Acta Crystallographica section D 63 (2007), 550–554.

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identify a rotation centre: domain rotation

From: WENHE ZHONG
Date: 23 November 2011 14:45


Dear members,

I would like to have your ideas if there is any way to identify a rotation centre of domain in two different states using CCP4 or other program.

The situation is: the domain of the protein will rotate between two different states (depending on substrate binding) around 8 degree, and it is (nearly) clearly that the domain is rotated around a rotation centrel. So the question is how to identify this "rotation centre" in this 3D model? The ideal is to identify a region of residues in the domain which are most closed to the rotation centre.

The tool I am using right now is the "superpose" tool in CCP4 package. The output which I think mightbe uesful is:

CENTROID OF "WORKING" MOLECULE  :              157.812 152.396 -70.778
     CENTROID OF "WORKING" MOLECULE  :(fractional)  157.812 152.396 -70.778
     CENTROID OF "REFERENCE" MOLECULE:              157.251 151.877 -70.874
     CENTROID OF "REFERENCE" MOLECULE:(fractional)  157.251 151.877 -70.874
     Distance between CENTROIDS      :                0.770
     Direction cosines of vector between CENTROIDS:   0.729   0.674   0.124

I would say the "CENTROID" it mentioned above, such as (157.251 151.877 -70.874), is possibly near to the "rotation centre". I would like to have your opinion though. Thank you.

King regards,
Wenhe

----------
From: Eleanor Dodson


I guess the rotation centre is approximately the mid point between the two centroids..

But these look surprisingly similar? I would hsave expected after an 8 degree rotation there would be some greater difference..

Eleanor

----------
From: Edward A. Berry


Would this work?
Take the rot-trans operator from superpose or lsqman and express
the rotation matrix as polar coordinates of rotation axis (and angle about it).
Get the rotation axis as direction cosines, which will be a vector along
the rotation axis of the matrix. Now take the component of the
translation vector along that rotation axis, and subtract from the
translation vector, to get the component of the translation vector
which is orthogonal to rotation axis. Divide that by two and,
as a vector from the origin, it defines a point on the
rotation axis. Add any multiple of the rotation axis vector to
this and it gives another point on the rotation axis.
Test these points by operating on them with the orig
rot-trans operator, they should just move along the rotation axis
by the screw component of the rotation

----------
From: Edward A. Berry

No! the "divide by 2" part is for a 2-fold rotation- not 8*.
Sorry, and hope the O.P. didn't waste any time trying to implement this.

----------
From: Eric Pettersen

Perhaps this video would be helpful: http://www.cgl.ucsf.edu/chimera/videodoc/AlignDomains/index.html

The "axis point" shown in the reply log at the very end is what I think you want.

BTW, the video is a little out of date, in that if you get the very latest daily build the MatchMaker tool can match the smaller domains with having to delete part of the structure.

--Eric

Anomalous signal for chlorides

From: Yuri Pompeu
Date: 25 November 2011 23:31


Hello everyone,
I have a good data set to 1.17A that I solved by MR.
I come accross some sites that appear to be chlorides. I was
wondering if they could have some anomalous signal.
I also have a well ordered phosphate  and a couple of S from Met´s.
How do I go about probing the signal from these?
Thank you. Best,

----------
From: Boaz Shaanan

Hi,

You could calculate an anomalous difference map using your current phases and see whether you see any peaks around the atoms you suspect are Cl, S or P (although the latter should have a clear tetrahedral geometry, certainly at your resolution). It all depends of course on the wavelength at which you collected your data (check Ethan Merritt's site), but again at your resolution you may very well hit lucky.

  Cheers,

             Boaz


Boaz Shaanan, Ph.D.

----------
From: Yuri Pompeu


Hi Boaz,
Yes indeed, the phosphate group of the molecule looks quite beautiful at 1.17A and it has a really big peak 18sigma!
Is there a utility for calculating anomalous maps, or is it simply an option in the refinement program?

----------
From: Pavel Afonine


Hi Yuri,

phenix.refine, for example, always outputs Fourier map coefficients for anomalous difference map if input input data contain Fobs+ and Fobs- (or Iobs+ and Iobs-).

Pavel

----------
From: George Sheldrick


Dear Yuri,

The new program ANODE (J.Appl.Cryst. (2011) 44, 1285-7, Open Access) is designed for this and is very simple to use. It may be downloaded from the SHELX beta-test server (please email me if you require downloading intructions).

George

----------
From: Randy J. Read

Dear Yuri,

In addition to the other good options that have been presented, you can use the log-likelihood gradient maps in Phaser to find anomalous scatterers. We find this to be very sensitive, and it has the advantage of being iterative (i.e. when you find some anomalous scatterers, this improves your model and thus the sensitivity for finding additional sites).

When you're starting from a refined model, we think it is best to look for purely imaginary scatterers to add to the real scattering in your model. In the ccp4i GUI, choose the "SAD with molecular replacement partial structure" mode, provide the data (with F+ and F-), the wavelength, and the current model, then turn on LLG-map completion and select the "Complete with purely anomalous scatterer" option.

If you want to see the initial LLG map, set the number of completion cycles to 0 and turn on the option to output log-likelihood-gradient map coefficients. Open these in coot as a difference map, choosing the columns FLLG_AX and PHLLG_AX. If you let Phaser complete the sites, then the final LLG map should be nearly flat and you have to look at the PDB file containing the sites that it found.

Best wishes,

Randy Read

--
Randy J. Read

----------
From: Jacob Keller


Not that Phaser needs my approval, but I recently did exactly what
Randy recommended and it really found basically all of the S and Cl
sites, with data at resolution 2.2 Ang and wavelength 0.979 Ang, too.
I also played a bit with the sigma cutoff for adding new sites so that
the stronger sites (Se in my case) are found but the weaker ones not.
Also, don't forget to click the "output LLG map coefficients" option
to get the right columns in your mtz.

Jacob

--
*******************************************
Jacob Pearson Keller
*******************************************

----------
From: Eleanor Dodson


There are many ways of course to do this..
But if you are using the CCP4 GUI, refmac refinement it is a 2 step process.

CAD to add the DANO SIGDANO columns from the input data back into the refmac output

fft
 Select anomalous map

Use DANO SIGDANO PHIC FOM asinput

Switch on the peak search

Read that pdb into coot and check that the highest peaks are on anomalous scatterers - you usually find the S are visible too..

 If the data is reasonable I do it routinely to verify results - are the SO4s really sulfates etc etc..

Eleanor

Powder Diffraction

From: REX PALMER

Does anyone have an up-to-date account of protein structure anlysis from powders?

 

 

Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com

----------
From: Lucas

Since it was powder diffraction that made me fall in love with
crystallography as an undergrad (before switching to protein
crystallography as a grad student), I was obviously very excited when
I first heard about protein powder diffraction in a meeting some years
ago, in a lecture by Andy Fitch from the ESRF. I've exchanged some
mails with him and also Irene Margiolaki, who were very kind and sent
me lots of unpublished stuff and experimental hints (sample
preparation is probably the most difficult part in protein powder
diffraction). A good idea would be to contact them (it may be easy to
find their info in the ESRF website).

The GSAS groups was also working on this, and the major difference,
from what I remember, is that they were doing all the process (until
refinement) in the same way that was done with regular powder samples
(with a modified version of the GSAS program), while the group in ESRF
converted the powder data to MTZs and then used PX software.

By that time it seemed that they were the only groups doing it, but a
quick search in pubmed using "protein powder diffraction" shows some
recent articles from other groups, so it seems it's pretty much alive.
The following articles are from 2011:

X-ray diffraction from membrane protein nanocrystals.
http://www.ncbi.nlm.nih.gov/pubmed/21190672

Exploiting powder X-ray diffraction for direct structure determination
in structural biology: the P2X4 receptor trafficking motif YEQGL.
http://www.ncbi.nlm.nih.gov/pubmed/21382498

Lucas Bleicher

faculty position in China

Date: 19 December 2011 13:12



A faculty position is available in the structural biology laboratory in Zhejiang A&F University, China. The laboratory focuses on the study of key signal transduction proteins and their structure-function relationship, including RNAi technology. This position is for a scientist with Ph.D. training in molecular biology, structural biology or related sciences. Experiences in molecular sub-cloning, protein purification, protein interaction analysis are required. Experience in protein crystallography is preferred but not required. Candidate must be highly self-motivated, easy to adopt into a collaborative environment. Successful applicant will receive generous startup package including family relocation and housing benefits.

Applications should send their curriculum vitae, cover letter and a brief research statement in one PDF file and arrange to have two references sent to Dr. Yingwu Xu at yxu@zafu.edu.cn or yxu013@qq.com Phone: (086)-571-6374-1673.

Seventh International Workshop on X-ray Radiation Damage to Biological Crystalline Samples, Diamond Light Source, 14-16th March 2012: Registration now open.

Seventh International Workshop on X-ray Radiation Damage to Biological Crystalline Samples, Diamond Light Source 14-16th March  2012: Registration now open.

 

This series of workshops was originally concerned with the effects of radiation damage during investigation of protein structures by X-ray crystallography. Other techniques of structural biology are now being included to ensure greater information exchange. The workshop will therefore be of interest to all those using ionising radiation to examine biological structures at the molecular level.

It will consist of around 30 talks of 20 minutes each grouped under the topics below and ample time will be left for discussion. Confirmed speakers are indicated under each one.

1.       Basic understanding of radiation damage mechanisms.

Ian Carmichael, Kristina Djinovic Carugo, James Holton, Alke Meents

2.       Temperature-dependent (including RT) radiation damage.

Sasha Popov, Robert Thorne, Martin Weik

3.       Reducing and mitigating radiation damage

Elspeth Garman, Robin Owen

4.       Practical aspects of managing radiation damage.

Tom Burnley, Zbyszek Otwinowski, Tatiana Petrova, Enrique Rudino-Pinera

5.       Damage at new sources - XFEL

Henry Chapman, Lukas Lomb

6.       Radiation damage in complementary fields

Dominique Bourgeois, Liz Duke, Richard Henderson, Raimond Ravelli, Eddie Snell It will consist of around 30 talks of 20 minutes each covering:

 

Registration and Abstract submission are now open.  Registration and further information can be found at

 

http://www.diamond.ac.uk/Home/Events/RD7---2012.html

 

The cost of registration is £100 (£120 after February 20^th 2012).

 

At registration, delegates are invited to upload abstracts for submitted talks and poster presentations. Please use the abstract template available on the site ensuring you indicate whether you would prefer an oral or poster presentation. The closing date for submission of abstracts for Oral presentations will be Monday 6th February 2012. For all other Abstracts the closing date will be Monday 20th February 2012.  

 

The organisers are Robin Owen, Armin Wagner, Elspeth Garman, Martin Weik, John McGeehan, Sean McSweeney, Colin Nave, Raimond Ravelli, Gerd Rosenbaum, James Holton, and Soichi Wakatsuki.