Re: [ccp4bb] "Atomic resolution"

[Victor Lamzin]

Dear Jacob,

The resolution in reciprocal and real space was addressed by R. W. James 
in his paper 'False Detail in Three-Dimensional Fourier Representations 
of Crystal Structures' piblished in Acta Cryst. (1948). 1, 132-134. 
James showed that atomic density shape in the presence of series 
terminations is described by the Bessel function of zero order:


3*[sin(m) - m*cos(m)]/m^3
where m=2*Pi*r/dmin

This function is equal to 1 at the atomic centre (r=0) and decreases as 
r increases, then it oscillates. The function reduces to 0.5 for 
r/dmin=0.4. Therefore, the two equal atoms to be separated (in a sense 
of having a density in between lower than at their centres) the distance 
between them should be equal (or higher) than 2*dmin*0.4


Main chain C and O atoms separated by 1.23 A should be resolved if dmin 
is better than 1.55 A.


Two carbon sp3 atoms (distance 1.53 A) should be resolved if dmin is 
better than 1.9 A.


Indeed, as Thomas wrote, 1.5 A is about right.

The above is correct in the absence of atomic displacement parameters 
(Bfactor=0), for example for the normalised (sharpened) structure factor 
amplitudes. And, of course, for the complete and error-free diffraction 
data.


Victor



On 11/01/2018 21:07, Keller, Jacob wrote:


The reason behind this query is that I want to illustrate the power of 
prior knowledge in data analysis. I want to say something like “even 
though atoms cannot be directly observed at worse than X resolution, 
which represents Y% of the PDB, all of these data sets have been fit 
correctly with atomic models. This is due entirely to the power of the 
excellent priors which exist in crystallography.”


JPK

+

Jacob Pearson Keller

Research Scientist / Looger Lab

HHMI Janelia Research Campus

19700 Helix Dr, Ashburn, VA 20147

(571)209-4000 x3159

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*From:* Thomas Edwards [mailto:t.a.edwa...@leeds.ac.uk]
*Sent:* Thursday, January 11, 2018 2:59 PM
*To:* Keller, Jacob 
*Cc:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] "Atomic resolution"

Dear Jacob,

Ah... this old chestnut!

Current EM people say that they are at atomic resolution because they 
are building atomic models (naive??).


I have been criticised in the past for using the term with say 2.2A 
diffraction data. By co-authors and reviewers alike. When I was young 
and naive.


My (current) definition would be yours - visible with data.

I think 1.5A is about right for X-ray. Maybe higher res?

I’m sure there are lots of rigorous ways to think. I probably haven’t 
taken that route. However, I think it is a semantic problem that might 
benefit from some disambiguation rather than rigour.


It depends why you are asking the question...

Sorry..!

*/Ed is: Out and about.../*

*/Sent from iPhone6sPlus./*


On 11 Jan 2018, at 19:31, Keller, Jacob > wrote:


Dear Crystallographers,

Has there been a consensus as to what is meant by “atomic
resolution?” Seems like the term is taken by various practitioners
to mean different things.

A related question: at what resolution are atoms “visible” using
only the data? I have an empirical feeling that this would be
around 1.5 Ang Bragg spacings, but on the other hand, one can
contour up most maps and see individual atom peaks. I would be
interested to hear a more rigorous way to think about this.

All the best,

Jacob Keller

+

Jacob Pearson Keller

Research Scientist / Looger Lab

HHMI Janelia Research Campus

19700 Helix Dr, Ashburn, VA 20147

(571)209-4000 x3159

+

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Re: [ccp4bb] "Atomic resolution"

[mesters]

Atomic resolution or "the Sheldrick criterion" starts at 1.2 Å or 
better, 1.5 Å is too optimistic as the Bfactors are not zero as Vicotr 
pointed out, have a look at



 `Atomic resolution': a badly abused term in structural biology
 


and

Responses to/`Atomic resolution': a badly abused term in structural 
biology /






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[ccp4bb] Facility Manager position at Florida State University

[Beth Stroupe]

The Department of Biological Science at Florida State University is 
seeking applications for the position of Facility Manager for the 
Biological Science Imaging Resource (BSIR). The position is available 
starting March 1, 2018. We will begin to review applications in January, 
2018 and continue until the position is filled. The position entails 
day-to-day management of the facility, which maintains a Titan Krios, 
two conventional TEMs, an SEM, confocal and conventional light 
microscopes and specimen preparation equipment. The facility currently 
has two additional personnel, one with responsibility for the 
conventional TEMs and LMs and another with responsibility for the SEM. 
The flagship instrument of the BSIR is a Titan Krios TEM equipped 
currently with a DE-64 direct electron detector. In 2018 a Volta Phase 
plate and a Gatan BioQuantum/K3 will be added to the Titan Krios. In 
additional to overall management of the facility, the Facility Manager 
will have primary responsibility for day to day running of the 
Titan-Krios electron microscope and secondary responsibility for the 
other equipment, which will be the primary responsibility of the other 
facility staff.


Minimum qualifications for this job level are a Master’s degree in an 
appropriate field of specialization or equivalent qualifications based 
on professional experience and otherwise qualified to perform assigned 
duties. Strong written and oral communication skills are required.

Preferred qualifications are a PhD in an appropriate science field 
(chemistry, biology, engineering, etc.) and experience with the 
operation of a Titan Krios, operation of Leginon data acquisition 
software as well as high performance computing. The committee will 
consider applications from candidates having experience with other high 
end FEI TEMs.

How to apply:  Go to http://hr.fsu.edu/index.cfm?page=ers/ers_home. 
 
Browse Job Openings and select job 42816 and follow the instructions.

Inquiries should be made to Dr. Kenneth Taylor at taylor at bio.fsu.edu 
 

[ccp4bb] DL_Software Training Workshop 19-22 February @ STFC Daresbury Laboratory

[Ilian Todorov]

Dear colleagues,

There will be a 4-day DL_Software training event at Daresbury Laboratory, 19-22 
February 2018.  For details and registration follow the link - 
http://www.ccp5.ac.uk/events/training_workshop_2018_daresbury.shtml

DL_Software (http://www.ccp5.ac.uk/software) is the collective term for a range 
of scientific software packages developed at Daresbury Laboratory, spanning 
across multi- length and time scales.  This is an opportunity for current and 
potential users of DL_Software to learn how to use these programs and what 
methodologies and algorithms they include. The workshop also offers 
demonstrations and hands-on sessions giving users the opportunity to compile, 
run and experiment with the programs as well as interact with their developers.

Day 1 to Day 3 is the lecture and training sessions for DL_POLY, DL_FIELD, 
ATEN, ChemShell and DL_MESO.

Day 4 is the user-led hands-on session where attendees will provide opportunity 
to seek advice and guidance on aspects of work such as running simulations, 
models set up, scriptings, etc...

DL_MONTE training will run as parallel sessions on Day 3 and Day 4. These 
sessions will include lectures, demonstrations and hands-on tutorials.

For those with supervisory roles, please pass on this email to your students or 
postdocs who may find this Workshop useful for their research.

Regards,

Ilian Todorov

Re: [ccp4bb] "Atomic resolution"

[Ivan Shabalin]

Perpetual topic!

The variety of opinions is amazing. Let me add my opinion here.

I like the definition set by Z. Dauter, G. Murshudov, and K. Wilson in 
the International tables for Crystallography volume F (2001 edition), 
section 18.4.1 "Definition of atomic resolution".


They define the atomic resolution as: when there are sufficient 
accurately measured observables to justify the refinement of the ordered 
part of the structure with full anisotropic ADPs.


Of course, it has a different meaning than the optical resolution, but 
these tend to coincide.


There is no magic number that fits all structures. It depends on the 
quality of data, completeness (especially in the highest shell), and 
solvent content. 1.2 A is a rather conservative estimate.


To decide whether to use anisotropic ADPs or not, I like utilizing the 
Hamilton R-value ratio test.  Basically, once you introduce extra 
parameters, the drop of the R-free should be significant in relation to 
the increase in the number of parameters.


The concept is very well explained in:

To B or not to B: a question of resolution?
https://www.ncbi.nlm.nih.gov/pubmed/22505267

The test is implemented in HKL3000, and probably, in other software.

If using the Hamilton test is not possible, i substitute the test with 
two independent considerations (both are present in Hamilton test):


1) (Number of Unique reflections)/(Number of non-hydrogen atoms)> 18 
should put me on rather safe side. This ratio stands for 
"data-to-parameter ratio" = 2 or higher. One atom is defined by 9 
parameters.


2) Drop of R-free has to be meaningful (significant). My rule of thumb 
is that at least 0.5% percent is good. 1% is safer.


Ivan




With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908

On 01/11/2018 02:30 PM, Keller, Jacob wrote:

Dear Crystallographers,

Has there been a consensus as to what is meant by “atomic resolution?” 
Seems like the term is taken by various practitioners to mean different 
things.


A related question: at what resolution are atoms “visible” using only 
the data? I have an empirical feeling that this would be around 1.5 Ang 
Bragg spacings, but on the other hand, one can contour up most maps and 
see individual atom peaks. I would be interested to hear a more rigorous 
way to think about this.


All the best,

Jacob Keller

+

Jacob Pearson Keller

Research Scientist / Looger Lab

HHMI Janelia Research Campus

19700 Helix Dr, Ashburn, VA 20147

(571)209-4000 x3159

+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of 
this message with any third party, without a written consent of the 
sender. If you received this message by mistake, please reply to this 
message and follow with its deletion, so that we can ensure such a 
mistake does not occur in the future.

[ccp4bb] Three year postdoctoral position in Grenoble

[Trevor Forsyth]

 Postdoctoral research fellow in Structural Biology M/F

(see https://www.ill-recruits.eu/generator.php?id=619)

A postdoctoral scientist is sought to participate in an international 
project that connects the ILL (France), Hamburg/DESY (Germany), New York 
University (USA), and the University of Canterbury (New Zealand). The 
project is funded by a prestigious grant from the Human Frontier Science 
Program (HFSP) to Keele University (UK) and will link to the one of the 
most important European facility developments in a generation – the 
creation of an X-ray laser source (XFEL, Hamburg).  HFSP grants are 
awarded to teams having strong complementary expertise and who propose 
highly innovative research. This intercontinental collaboration links 
established neutron and X-ray approaches for the study of biological 
systems with those now emerging at X-ray free-electron lasers (XFELs) 
facilities and addresses the challenge of imaging single fibrous 
biological macromolecules.


*Duties:*
The scientist will be located within ILL’s Life Sciences Group and play 
a crucial role in the preparation of samples as well as carrying out 
experiments at the ILL and ESRF in Grenoble, the LCLS FEL source at 
Stanford University (USA), and the new XFEL facility in Hamburg. The 
main tasks will be to:


 * Carry out extensive sample preparation work – proteins, nucleic
   acids, filamentous complexes
 * Perform diffraction experiments at different facilities such as ILL
   and ESRF in Grenoble - France, X-FEL in Hamburg, and Stanford
 * Analyse data as required
 * Prepare papers for scientific press
 * Contribute to workshops, conferences, etc.

*Qualifications and experience:*
Candidates should have an appropriate undergraduate background (eg 
physical or life sciences) and a PhD in a relevant area. They should be 
competent in molecular biology and biochemistry techniques, sample 
preparation and should also be familiar with data collection (eg 
crystallography, SAXS/SANS) methods and have a good general grasp of 
biophysical techniques.


*Language skills:*
As an international research centre, we are particularly keen to ensure 
that we also attract applicants from outside France. You must have a 
sound knowledge of English and be willing to learn French (a language 
course will be paid for by the ILL). Knowledge of German would be an 
advantage.


*Notes:*
Post-Doctoral contract of 18 months, renewable for a further 6 to 
18-month period.
*Only candidates holding a PhD obtained less than 2 years ago are 
eligible for post-doctoral positions.*
Further information can be obtained contacting Prof. Trevor Forsyth at 
the ILL or at Keele University**


*Benefits:*
Generous company benefits (expatriation allowance), relocation 
assistance and language courses may be offered (for more information, 
please consult our employment conditions 
).


*How to apply:*
Please see https://www.ill-recruits.eu/generator.php?id=619. 
Applications should be submitted online with a CV, list of publications, 
and the names of 3 referees, including one from your present work place, 
no later than *04.03.2018*, via our website: www.ill.eu/careers 
 (Vacancy reference: *17/PostDoc11*).


*Interviews will take place from mid-March 2018 onwards.*

closing date for submissions: *04/03/2018 *Ref. #: *17/Postdoc11 *
We care about Equal Opportunity and Diversity; therefore we encourage 
both men and women with relevant qualifications to apply.


--
___
Trevor Forsyth
Professor of Biophysics
Institut Laue Langevin/Keele University
71 avenue des Martyrs, CS 20156, Grenoble Cedex 9
Email tfors...@ill.eu or v.t.fors...@keele.ac.uk
Tel: +33(0)476207158
Secretary: Alison Mader
Email: ma...@ill.eu
Tel: +33(0)476207635
___

[ccp4bb] Structural Biology Post-doctoral Fellow Position in Purdue University

[Das, Chittaranjan]

We are seeking a postdoctoral fellow to join the Das laboratory in the 
Department of Chemistry, Purdue University, West Lafayette, IN, USA. Our lab 
investigates the structure and mechanism of action of bacterial effectors and 
their complexes with host targets with an emphasis on deubiquitinating and 
ubiquitin ligating enzymes. These effectors are used by intracellular pathogens 
to manipulate host ubiquitin signaling, often employing radically different 
biochemical mechanism than observed in eukaryotic organisms. A striking example 
is the E1,E2-independent ubiquitination of host proteins by the SdeA ligase 
effector of Legionella pneumophila.  See the following links to publications in 
this area:

1. http://www.pnas.org/content/112/49/15090.long

2. https://www.nature.com/articles/nature17657

3. http://pubs.acs.org/doi/abs/10.1021/acs.biochem.7b00664



This position offers a significant opportunity to develop academic career of a 
really motivated Ph.D scholar by working at the interface between two labs, our 
lab in the Chemistry Department (X-ray crystallography and enzyme mechanism) 
and the Luo Lab in the Biology Department here at Purdue, the latter is a 
world-class lab in Legionella effector biology 
(http://bilbo.bio.purdue.edu/luolab/). Collaboration between our labs allows 
development of structural insights in the context of the relevant biology.  
Applicants should hold a Ph.D. degree in relevant areas of chemistry, 
biochemistry, or biophysics as well as have significant experience in x-ray 
crystallography. This project also involves cryo-EM studies (in collaboration 
with Wen Jiang at Purdue) on protein-protein complexes involving these 
effectors.

If interested, please send your CV to c...@purdue.edu.?

[ccp4bb] 3D Visualization Postdoc at RCSB PDB: San Diego, California

[Jose Duarte]

The University of California, San Diego seeks to fill an opening for a
Postdoctoral Researcher in the RCSB Protein Data Bank.

*Job description*

Your challenge is to develop web-based, innovative scientific visualization
tools for 3D biomolecular structures to help accelerate research and
training in biology, medicine, and related disciplines.

Areas of focus include:

• Innovative representations for 3D structural data

• Visualizations for comparative analyses

• Multiscale rendering for exploring large structures



Your work will reach an audience of more than 1 million RCSB PDB Data
Consumers when deployed as interactive features for the RCSB PDB website (
http://www.rcsb.org).

*Requirements*

The successful candidate holds a Ph.D. in one or more of the following
research areas:

• Structural Bioinformatics, or related field with a focus on software
development

• Computer Science with a focus on scientific visualization



-Demonstrated proficiency in JavaScript as a general-purpose programming
language and experience with state of the art software development tools.

-Strong skills in problem solving and algorithm design are required.

-High productivity demonstrated by publications and contributions to open
source software projects.

-Experience in the development of modern web applications, user interface
design, or scientific visualization is a plus.

-Excellent written and oral communication skills.

*Compensation*

Compensation depends on postdoctoral experience level in accordance with UC
Salary Scale (12/1/16). Please see chart at
http://postdoc.ucsd.edu/appointment-guidelines/index.html

*About UC San Diego, San Diego Supercomputer Center and the Protein Data
Bank*

The position is available immediately in the San Diego Supercomputer Center
(SDSC).
As an Organized Research Unit of UC San Diego, SDSC is a world leader in
data-intensive computing and cyber infrastructure, providing resources,
services, and expertise to the US national research community, including
industry and academia.

The RCSB PDB (http://www.rcsb.org) represents the preeminent source of
experimentally determined macromolecular structure information for research
and teaching in fundamental biology, medicine, and bioenergy. With more
than 1 million users from over 160 countries around the world, the RCSB PDB
is one of the leading worldwide Biological Databases. Our group is
responsible for RCSB Protein Data Bank (PDB) west-coast operations.

*Application*

To be considered, please submit your CV and cover letter (optional) with
contact information to Cole Christie at cole.chris...@rcsb.org.

UC San Diego is an equal opportunity employer, both foreign and domestic
applicants are encouraged to apply.

[ccp4bb] BUCCANEER label choose

[张士军]

Dear all

  I am confusing how to choose or enter the labels when I do density 
modification and autobuilding with ccp4 parrot and buccaneer or ARP/wARP, there 
are three different options like "use Free R-flag ","use map coefficient" and 
"use PHI/FOM instead of HL coefficient" in the figure I attached. What they are 
mean, which one I should choose when I just want to do density modification 
after SAD or MR,and how to do when autobuilding? Even though when I choose"use 
map coefficient", it appeared HLA,HLB,HLC,HLD,and when I choose "use PHI/FOM 
instead of HL coefficient", it appeared PHI,FOM, how to enter these labels? 
Thanks a lot !!!

Best Regards

Shijun