Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Pavel Afonine]

Hi,


> Unfortunately not all structure
> factor programs will give you that F000.
>

phenix.f000 will give you F(0,0,0) value based on atomic model alone or
atomic model plus bulk-solvent.

Pavel



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Re: [ccp4bb] Electron scattering factors for SHELXL

[Pavel Afonine]

Hi,


> Or, alternatively, if anyone has used a different program to refine small
> molecule structures determined by ED, we would be happy to hear about that
> program too.
>

phenix.refine has an option to use electron scattering factors. I can
provide further assistance off-list or on phenix mailing list, if needed.

Pavel



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[ccp4bb] Electron scattering factors for SHELXL

[Whitley, Matthew J]

Greetings all,


We have solved a small molecule structure using electron diffraction and would 
like to refine the structure with SHELXL.  Coming from a macromolecular 
background, this is our first experience with SHELXL, and we are not exactly 
sure how to proceed.  The first thing to do seems to be to provide SHELXL the 
appropriate electron scattering factors for 200 keV electrons.  Can someone 
suggest the best way to do this?  Or, alternatively, if anyone has used a 
different program to refine small molecule structures determined by ED, we 
would be happy to hear about that program too.


Thanks in advance for your advice.

Matthew


---
Matthew J. Whitley, Ph.D.
Research Instructor
Department of Pharmacology & Chemical Biology
University of Pittsburgh School of Medicine



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Re: [ccp4bb] Change dimer assembly in ASU

[Randy Read]

Dear Ezequiel,

There is nothing special about which particular symmetry copies a molecular 
replacement program chooses, so there is no good reason to stick to those 
symmetry copies.  On the other hand, there are very good reasons to present a 
molecule that is as close as possible to what is biologically relevant, so you 
should definitely change the choices of symmetry copies to make a proper 
heterodimer in your PDB entry.  The easiest way I know to do that is with the 
option in coot: Extensions->Modelling->Symm Shift Reference Chain Here (after 
centering on an atom in a symmetry copy that you want to make the master copy).

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

> On 4 Mar 2019, at 17:27, Eze Chivi  wrote:
> 
> Dear CCP4bb community:
> My crystal is a heterodimeric complex. I solved the structure using MR with a 
> related structure (containig the dimer), using a highly automated pipeline. 
> However, the MR solution is not the dimer of biological relevance. The 
> experimentally validated dimer is formed between a protomer in the ASU and 
> one from the adjacent symmetry-related pair of molecules. Is it correct to 
> use a modelling program to assemble the "biologically correct" dimer and then 
> proceed to refinement? Or... is it need to keep the MR solution and inform in 
> the PDB header how the relevant dimer is formed? Many Thanks
>  
> Ezequiel
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 



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[ccp4bb] Open Position: Lead Research Specialist in Electron Microscopy

[Puneet juneja]

Dear all,

We have open position for a Lead research specialist at Integrated Electron
Microscopy Core at Emory University, Atlanta.
Experience working with Scanning and Transmission Electron Microscopes is
highly desired. Experience handling Biological samples and with Microtomes
will be advantageous.

Please follow the link for more description.

https://staff-emory.icims.com/jobs/23025/job

Thank you

Best, Puneet

Puneet Juneja, PhD
Core Director
Robert P. Apkarian Integrated Electron Microscopy Core
O. Wayne Rollins Research Center
Emory University School of Medicine
Ph:404-727-8960



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Re: [ccp4bb] (EXTERNAL) Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Edward A. Berry]

Also check if the mean value of the map over the ASU is zero. If so, the map 
was probably calculated without the 0,0,0 term of the Fourier series, so zero 
does not represent zero density but rather the mean density.

On 03/04/2019 12:43 PM, Ian Tickle wrote:


Hi Sen

If you multiply the electron density in a voxel by the voxel volume you should 
get an estimate of the number of electrons contained in that voxel, and then 
you can add up the numbers of electrons in all the voxels occupied by an atom 
to get the total number of electrons in that atom, which is basically the same 
as what you are saying.

However note that the electron density is a point sample: it's not the average 
density in the voxel, so the above calculation won't be quite accurate, 
depending on the 'smoothness' of the density.  This is like the error in an 
integral by use of Simpson's rule.  To be sure of accounting for all the 
density you need to sample it finely, say not more that Dmin/4.

There are two more issues here: first the atomic positions are never error-free 
which reduces the contribution to the density by the factor D in the expression 
2mFo-DFc (or mFo for centric phases) for the map coefficients.  So if the 
errors were sufficiently large D would tend to zero and you would get no 
density at all!  The density that you see is really only that part of the true 
density for which there is evidence in the experimental data.

Second, what exactly do you mean by "add all voxel densities around an atom"?  
The electron density could easily extend 2 Ang. from an atomic centre, depending on the 
atom's finite size (represented by the form factor), its thermal motion (B factor) and 
series termination effects (resolution).  So if you don't go out far enough you will fail 
to account for some fraction of the electron count.  The problem is of course you can't 
go so far as to overlap bonded atoms which will be well within 2 Ang. distance.  The 
standard method of dealing with this is to represent 'soft' atoms (where the distance 
between atoms may be less than the sum of their radii) as Voronoi polyhedra (like the 
packing of soap bubbles!).  Is that how you handled it?

Cheers

-- Ian


On Mon, 4 Mar 2019 at 15:47, Yao, Sen mailto:yaosen1...@gmail.com>> wrote:

Hi all,

I have been using the electron density maps available on the PDBe website 
to run some analysis. And I run into this question that I hope that I can get 
some help from the community.

In the ccp4 format, the electron density is represented as a 3-d array map, 
with each number corresponds to the density value of a voxel in real space. If 
I add all voxel densities around an atom together and divided it by the number 
of electrons of that atom, in theory it should give me a ratio with the unit 
Å-3 (angstrom to the power of -3), and this ratio should be inversely related 
to the voxel volume. (Correct me if I am wrong here.) However, after I got this 
ratio for each atom, aggregated it into chains and calculated a median, and 
then compared the chain median to the voxel volume over all PDB structures with 
electron density available, they show a slope of ~1/3 instead of expected 1 
(see attached link). That is, almost all the values in the electron density 
maps are only about 1/3 of represented electrons.

https://drive.google.com/file/d/1K_3uxZfUPuTdH1DtKJgKHLRUA5NHTVPB/view?usp=sharing 



So my question is, is there a conversion or scaling factor that PDBe uses 
to generate the ccp4 files? If so, is that information stored in the ccp4 files 
or anywhere else? And if not, why do I observe this 1/3 ratio pretty 
consistently across the whole PDB?

I would really appreciate any insights on this matter. Thank you!

Sincerely,
Sen

--

Sen Yao, PhD

Center for Environmental and Systems Biochemistry
Markey Cancer Center
University of Kentucky, Lexington KY

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Gerard Bricogne]

Dear Sen,

 I may be unaware of special features of these maps, but if they
are computed in conventional ways, they lack an F000 term. Therefore
the average value of the 2mFo-DFc map is zero, just as if it was a
difference map. This may explain why you do not find all the electrons
you would be expecting. To get this right, you would need to add that
F000 term to the set of Fourier coefficients going into the
calculation of the map. You can get a pretty satisfactory F000 value
by taking it from the Fourier transform of the model density, and
applying the appropriate scale factor. Unfortunately not all structure
factor programs will give you that F000. Instead, then, you can add
the numbers of electrons for all the atoms of your model in the unit
cell, put it on "map scale", divide it by the number of voxels in that
unit cell, and add it to all the map values in all the voxels you
examine.

 In any case, the use of a zero-mean map would be the cause of
your 1/3 factor. 

 Apologies to the PDBe if they have already thought of that and
are including the F000 (or average number of electrons per voxel) into
the calculation of their maps - I didn't see any sign that this was
being done.


 With best wishes,

  Gerard.

--
On Mon, Mar 04, 2019 at 10:36:11AM -0500, Yao, Sen wrote:
> Hi all,
> 
> I have been using the electron density maps available on the PDBe website
> to run some analysis. And I run into this question that I hope that I can
> get some help from the community.
> 
> In the ccp4 format, the electron density is represented as a 3-d array map,
> with each number corresponds to the density value of a voxel in real space.
> If I add all voxel densities around an atom together and divided it by the
> number of electrons of that atom, in theory it should give me a ratio with
> the unit Å-3 (angstrom to the power of -3), and this ratio should be
> inversely related to the voxel volume. (Correct me if I am wrong here.)
> However, after I got this ratio for each atom, aggregated it into chains
> and calculated a median, and then compared the chain median to the voxel
> volume over all PDB structures with electron density available, they show a
> slope of ~1/3 instead of expected 1 (see attached link). That is, almost
> all the values in the electron density maps are only about 1/3 of
> represented electrons.
> 
> https://drive.google.com/file/d/1K_3uxZfUPuTdH1DtKJgKHLRUA5NHTVPB/view?usp=sharing
> 
> 
> So my question is, is there a conversion or scaling factor that PDBe uses
> to generate the ccp4 files? If so, is that information stored in the ccp4
> files or anywhere else? And if not, why do I observe this 1/3 ratio pretty
> consistently across the whole PDB?
> 
> I would really appreciate any insights on this matter. Thank you!
> 
> Sincerely,
> Sen
> 
> -- 
> 
> Sen Yao, PhD
> Center for Environmental and Systems Biochemistry
> Markey Cancer Center
> University of Kentucky, Lexington KY
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 

 ===
 * *
 * Gerard Bricogne g...@globalphasing.com  *
 * *
 * Global Phasing Ltd. *
 * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
 * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
 * *
 ===



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Re: [ccp4bb] Racemic crystallography and structure solving problem

[Prasun Kumar]

Thank You Pierre!


I will have a look and let you know.


Regards

Prasun


From: LEGRAND Pierre 
Sent: 04 March 2019 16:33:56
To: Prasun Kumar; CCP4BB@JISCMAIL.AC.UK
Subject: RE:[ccp4bb] Racemic crystallography and structure solving problem

Hi Prasum,

In such case, with xia2 you could try to add the option: small_molecule=true.
This will enable the consideration of centrosymmetric spacegourps.
Or you can try in pointless the options:
CHIRALITY  NONCHIRAL or CENTROSYMMETRIC

Your spacegroup could be P-1 (#2).
Good luck,
Pierre


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Prasun Kumar 
[prasun.ku...@bristol.ac.uk]
Envoyé : lundi 4 mars 2019 16:33
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Racemic crystallography and structure solving problem

Hi All:

I have performed racemic crystallography and got crystals that diffracted. The 
automatic processing softwares, XIA2 DIALS, (available in Diamond, UK) gives 
the space group as P1 and cell dimension
42.78   52.16   54.49   114.11  92.16   92.31.

Challanges start from here:

1) How much I should be assured of the space group as I expect my peptides to 
get crystallized in the same group, but by default we get the same space group.
2) Is there any seperate method for processing the raw images in my case.

I used the merged .mtz file for phasing. However, I always get the warning that 
eLLG score is low and it is difficult to fit a single copy of the ensemble. 
CC1/2 and I/SigI are in acceptable range. Completeness is also more than 95%.

My peptides, 30 residues long, form an oligomer. However, I do not have 
reliable model of oligomers to start with. I have taken a single helix of 
length 24, 12 and 6 residues to phase, but no luck so far.
Any guidelines will be really helpful.

I am happy to provide any other relevant information, if one wants.

Thanx in advance
Prasun



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[ccp4bb] Change dimer assembly in ASU

[Eze Chivi]

Dear CCP4bb community:
My crystal is a heterodimeric complex. I solved the structure using MR with a 
related structure (containig the dimer), using a highly automated pipeline. 
However, the MR solution is not the dimer of biological relevance. The 
experimentally validated dimer is formed between a protomer in the ASU and one 
from the adjacent symmetry-related pair of molecules. Is it correct to use a 
modelling program to assemble the "biologically correct" dimer and then proceed 
to refinement? Or... is it need to keep the MR solution and inform in the PDB 
header how the relevant dimer is formed? Many Thanks

Ezequiel



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[ccp4bb] Postdoctoral Position at UCL/Birkbeck, London

[Cheung, Alan]

Dear All

Institute of Structural and Molecular Biology
University College London and Birkbeck College
Postdoctoral Researcher in Structural Biology

A Wellcome Trust funded 3-year postdoc position is available in our lab to work 
on the molecular mechanisms of chromatin modification and transcription using 
biochemical, biophysical and structural biology methods.

Our lab is located in Birkbeck College as part of the joint UCL/Birkbeck 
Institute of Structural and Molecular Biology (ISMB).  The ISMB is a vibrant 
and international research community in the centre of London, and has in-house 
access to state-of-the-art structural biology and biophysics facilities.

Apply here: https://goo.gl/UBwvWK
Informal enquires can be sent to 
alan.che...@ucl.ac.uk

Our lab website: https://cheunglab.net
Our local community: http://people.cryst.bbk.ac.uk/~ubcg16z/empage.html
Our institute: http://www.ismb.lon.ac.uk/

Best wishes,
Alan




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Re: [ccp4bb] Racemic crystallography and structure solving problem

[LEGRAND Pierre]

Hi Prasum,

In such case, with xia2 you could try to add the option: small_molecule=true.
This will enable the consideration of centrosymmetric spacegourps.
Or you can try in pointless the options:
CHIRALITY  NONCHIRAL or CENTROSYMMETRIC

Your spacegroup could be P-1 (#2).
Good luck,
Pierre


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Prasun Kumar 
[prasun.ku...@bristol.ac.uk]
Envoyé : lundi 4 mars 2019 16:33
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Racemic crystallography and structure solving problem

Hi All:

I have performed racemic crystallography and got crystals that diffracted. The 
automatic processing softwares, XIA2 DIALS, (available in Diamond, UK) gives 
the space group as P1 and cell dimension
42.78   52.16   54.49   114.11  92.16   92.31.

Challanges start from here:

1) How much I should be assured of the space group as I expect my peptides to 
get crystallized in the same group, but by default we get the same space group.
2) Is there any seperate method for processing the raw images in my case.

I used the merged .mtz file for phasing. However, I always get the warning that 
eLLG score is low and it is difficult to fit a single copy of the ensemble. 
CC1/2 and I/SigI are in acceptable range. Completeness is also more than 95%.

My peptides, 30 residues long, form an oligomer. However, I do not have 
reliable model of oligomers to start with. I have taken a single helix of 
length 24, 12 and 6 residues to phase, but no luck so far.
Any guidelines will be really helpful.

I am happy to provide any other relevant information, if one wants.

Thanx in advance
Prasun



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[ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Yao, Sen]

Hi all,

I have been using the electron density maps available on the PDBe website
to run some analysis. And I run into this question that I hope that I can
get some help from the community.

In the ccp4 format, the electron density is represented as a 3-d array map,
with each number corresponds to the density value of a voxel in real space.
If I add all voxel densities around an atom together and divided it by the
number of electrons of that atom, in theory it should give me a ratio with
the unit Å-3 (angstrom to the power of -3), and this ratio should be
inversely related to the voxel volume. (Correct me if I am wrong here.)
However, after I got this ratio for each atom, aggregated it into chains
and calculated a median, and then compared the chain median to the voxel
volume over all PDB structures with electron density available, they show a
slope of ~1/3 instead of expected 1 (see attached link). That is, almost
all the values in the electron density maps are only about 1/3 of
represented electrons.

https://drive.google.com/file/d/1K_3uxZfUPuTdH1DtKJgKHLRUA5NHTVPB/view?usp=sharing


So my question is, is there a conversion or scaling factor that PDBe uses
to generate the ccp4 files? If so, is that information stored in the ccp4
files or anywhere else? And if not, why do I observe this 1/3 ratio pretty
consistently across the whole PDB?

I would really appreciate any insights on this matter. Thank you!

Sincerely,
Sen

-- 

Sen Yao, PhD
Center for Environmental and Systems Biochemistry
Markey Cancer Center
University of Kentucky, Lexington KY



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[ccp4bb] Racemic crystallography and structure solving problem

[Prasun Kumar]

Hi All:

I have performed racemic crystallography and got crystals that diffracted. The 
automatic processing softwares, XIA2 DIALS, (available in Diamond, UK) gives 
the space group as P1 and cell dimension
42.78   52.16   54.49   114.11  92.16   92.31.  

Challanges start from here:

1) How much I should be assured of the space group as I expect my peptides to 
get crystallized in the same group, but by default we get the same space group.
2) Is there any seperate method for processing the raw images in my case.

I used the merged .mtz file for phasing. However, I always get the warning that 
eLLG score is low and it is difficult to fit a single copy of the ensemble. 
CC1/2 and I/SigI are in acceptable range. Completeness is also more than 95%.

My peptides, 30 residues long, form an oligomer. However, I do not have 
reliable model of oligomers to start with. I have taken a single helix of 
length 24, 12 and 6 residues to phase, but no luck so far. 
Any guidelines will be really helpful. 

I am happy to provide any other relevant information, if one wants.

Thanx in advance
Prasun



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[ccp4bb] PhD available

[Murray, James W]

Dear all, 

I have a PhD available, deadline 12th March, on the structural biology of 
nitrogenase oxygen protection. Please email me if you are interested. Normal 
UKRI funding rules apply.

https://www.imperial.ac.uk/life-sciences/postgraduate/research/phd-opportunities/

best wishes

James

Biological nitrogen fixation is catalysed by nitrogenase. Nitrogenase is a 
complex enzyme, with three subunits, binding several cofactors. The best 
studied nitrogenase has molybdenum in the active site, and is encoded by nif 
genes. The nif operon encodes other assembly factors and conserved proteins of 
unknown function. Two alternative nitrogenases, with vanadium or iron instead 
of molybdenum, encoded by vnf and anf clusters, are even less 
well-characterised. Nitrogenase is inactivated by oxygen, and this 
vulnerability, combined with the complicated assembly, makes heterologous 
expression of nitrogenase challenging. However, expression of nitrogenase in 
crop plants could revolutionise agriculture, by ending the need for polluting 
nitrogenous fertilizers.

We have recently biochemically and structurally characterised the Anf3 protein 
(Fig 1), which protects the iron-only nitrogenase from oxygen. Anf3 is 
associated with two other conserved genes anf12, which are of unknown function 
but also essential for iron-only nitrogenase. Our work on the oxygen-protective 
FeSII protein (PDB 5FRT), is a prerequisite to determining the mechanism of 
nitrogenase protection. In this project we will structurally and functionally 
characterise the remaining nif and alternative nitrogenase genes. This will 
require biochemistry and X-ray crystallography in the Murray group, and 
biophysical techniques such as EPR and spectroelectrochemistry for the 
bioinorganic chemistry in the Rutherford group.


--
Dr. James W. Murray
Senior Lecturer, Dept. Life Sciences
Imperial College, London





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[ccp4bb] ERC-funded PhD in cryoEM of archaea in Exeter, UK

[Conners, Becky]

Dear all,

An exciting PhD position is available in my lab. The project focuses on 
investigating the structure and macromolecular organisation of archaeal surface 
layers and filaments and ultimately aims to employ these self-polymerising 
proteins in the design of biohybrid microrobotic drug delivery vehicles. You 
will have the opportunity to work in the unique research environment of the 
Living Systems Institute (LSI) in Exeter (UK). The LSI is a brand new 
interdisciplinary research facility, housing biologists, physicists, 
mathematicians and medical scientists who are pioneering novel approaches to 
investigate the fundamentals of life. You will have access to state-of-the art 
cryoEM equipment, including a fully automated Tecnai T12 screening microscope 
with a Gatan OneView CMOS camera, a 200 kV Talos Arctica equipped with a K2 
direct electron detector and a powerful GPU computer cluster for image 
processing. The position is open as of now.

If you are interested in applying, please follow the link below.

http://www.exeter.ac.uk/studying/funding/award/?id=3473

Cheers,
Bertram


Dr Bertram Daum
Senior Research Fellow
University of Exeter

+441392727455
www.exeter.ac.uk

Living Systems Institute
Stocker Road
Exeter
Devon
EX4 4QD
United Kingdom






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[ccp4bb] Post-doctoral position in structural glycobiology, AFMB, Marseille

[Gerlind Sulzenbacher]

Dear all,

a post-doctoral position funded by  ANR project GAGOsynth is available 
for a structural biologist in the team “Structural Glycobiology and 
Neurobiology” at the AFMB laboratory, Marseille, France. We are seeking 
for an enthusiastic, highly motivated and creative individual with solid 
knowledge and expertise in structural biology and biochemistry to 
investigate the structure-function relationships of enzyme complexes 
involved in heparan sulfate (HS) biosynthesis in collaboration with the 
groups of Hugues Lortat-Jacob and Guy Schoehn at IBS (Grenoble, France). 
In particular, we aim at deciphering how the concerted action of HS 
biosynthetic enzymes can encode defined oligosaccharide motifs along the 
polymer to modulate activity of various protein ligands.


Candidates must have a recent Ph.D. (or being in the process of 
completing one) in a relevant field with a demonstrated record of 
productive research. Experience in protein expression, particularly in 
eukaryotic cells, in biochemistry, and in X-ray crystallography or 
single particle cryo-EM is highly desirable.


Applicants are invited to submit i) a cover letter describing research 
interests, ii) a CV and iii) the names and contact details of three 
references to Yves Bourne (yves.bou...@afmb.univ-mrs.fr)./

/

http://www.afmb.univ-mrs.fr/post-doctoral-position,587/
/

Application deadline: April 30, 2019/
/

--
Gerlind Sulzenbacher
Architecture et Fonction des Macromolécules Biologiques
UMR7257 CNRS, Aix-Marseille Université
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel +33 491 82 55 66
Fax +33 491 26 67 20
E-mail: gerlind.sulzenbac...@afmb.univ-mrs.fr




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