[ccp4bb] Prato cryoEM course 2019 (Tuscany) - few sits still available

[Alex de Marco]

Dear all,

I would like to highlight the fact that we still have a few places
available for the second edition of the “*Prato cryoEM course*” from* 31st to
6th of April 2019*.



We will be taking applications until the end of the year.


The course aims at PhD students and researchers with little experience in
cryoEM or that are planning to use cryoEM to bring their projects to the
next level.

It will comprise a series of lectures covering all steps of Single-particle
cryoEM and Subtomogram Averaging (from sample preparation to data
collection and image processing). Practical sessions will give the students
the opportunity to perform image processing for both single particle and
subtomogram averaging and test multiple software packages.


Confirmed speakers:

*Christos Gastogiannis*, Max Planck Institute for Structural Biology,
Dortmund, Germany

*Misha Kudryashev*, Max Planck Institute for Biophysics, Goethe University
of Frankfurt.

*Timothy Grant*, Janelia Research Campus, Ashburn, VA, USA

*Daniel Castano-Diez*, Biozentrum, University of Basel, Basel, Switzerland

*Carlos Oscar Sorzano*, National Center for Biotechnology, Madrid, Spain

*Alex de Marco*, Monash University, Melbourne, Australia

*Hans Elmlund*, Monash University, Melbourne, Australia

*Dominika Elmlund*, Monash University, Melbourne, Australia


The subscription fees include lunch, coffee brakes and accommodation.

Participants will be required to present a poster and submit a short
motivation letter.



More information about the course can be found on
http://simplecryoem.com/Prato_2019/workshop2019.html


For those who did not submit an abstract and were not accepted feel free to
submit it now if you do want to be considered.




We hope to see you in Tuscany



Alex, Dominika and Hans

-- 

*Alex de Marco, PhD*

Associate Professor



Monash University

*Dept. of Biochemistry and Molecular Biology*

*ARC Centre of Excellence in Advanced Molecular Imaging*

23 Innovation Walk, 3800 Clayton (Australia)

P: +61 3 99053791 <%2B61%2003%2099053791>

M: *+61 4 11041429*

Email: alex.dema...@monash.edu

Web: www.demarco-lab.com



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Re: [ccp4bb] Experimental phasing vs molecular replacement

[Keller, Jacob]

>>That said, model phases are not so bad.  In fact, in all my experiments with 
>>fake data the model-phased 2mFo-DFc map always has the best correlation to 
>>the "true" map.  If you substitute the "true" phases and use the 2mFo-DFc 
>>coefficients you actually make things worse. Counter-intuitive, but true.

I don't understand what you mean by true and fake here--can you clarify? How 
are the true map and phases generated (from an original true model, I assume?), 
and how are the fake data generated? (Also from the true model?) I am wondering 
whether there is some circular reasoning?

JPK



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Re: [ccp4bb] Experimental phasing vs molecular replacement

[James Holton]

It is true that MAD phasing can give you hyper-accurate phases. This is 
because you are measuring the heavy atom signal in both directions on 
the Harker diagram, allowing the phase to be solved analytically.  The 
phasing signal is noisy, of course, but you can fix that either with a 
bigger heavy atom (more signal) or by doing a lot of averaging (less 
noise). You will probably need more than one crystal.


SAD, on the other hand, can never give you very good phases because the 
phase probability distributions are all bimodal. The technology that 
makes SAD practical is solvent flattening, but as soon as you start 
doing things like solvent flattening you are already imposing a model, 
and every model comes with some amount of bias.  How important that bias 
is depends on the question you are trying to answer.


MIR, like MAD, can get arbitrarily accurate phases, but this and every 
other technique requires a high degree of isomorphism.


In practice, essentially all experimental phasing attempts are really 
trying to get you just over that ever-elusive tipping point of phase 
quality where solvent flattening and model building can take you the 
rest of the way.  So, in the end what you have are model phases, just 
like if you had done MR.  It's sad really how fleeting the involvement 
of experimental phases are in essentially all MAD/SAD structure 
determinations.  Pun intended.


That said, model phases are not so bad.  In fact, in all my experiments 
with fake data the model-phased 2mFo-DFc map always has the best 
correlation to the "true" map.  If you substitute the "true" phases and 
use the 2mFo-DFc coefficients you actually make things worse.  
Counter-intuitive, but true.


-James Holton
MAD Scientist

On 12/5/2018 12:07 AM, 香川 亘 wrote:

Dear all,

It is my understanding that experimental phasing (e.g. Se-SAD), in principle, 
yields better electron density maps than molecular replacement for protein 
regions with weak electron densities (partially disordered or flexible).  I 
would appreciate if someone could provide comments on whether my understanding 
is correct or not.  If there any good examples or literatures on this issue I 
would be grateful to know about it.

I thank you in advance.

Wataru Kagawa


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Re: [ccp4bb] Sir Prof. Aaron Klug 1926 - 2018

[William G. Scott]

Dear Miri:

Thanks very much for your very thoughtful CCP4 post. Since I was one of his 
last (and perhaps least) postdocs, I felt a bit self-conscious and inadequate 
initiating discussion. I am very grateful to you for doing so.

I would like to point out, for those who are interested, that Ken Holmes (a 
close colleague of Aaron’s) recently published an excellent and definitive 
biography entitled "Aaron Klug: A Long Way from Durban." It is extremely 
well-written, accurate and comprehensive. I got ahold of it here: 
https://www.amazon.com/Aaron-Klug-Long-Durban-Biography/dp/1107147379/ref=mt_hardcover
  

Aaron's many contributions to our field included pioneering work on virus 
structures, which began in collaboration with Rosalind Franklin, structures of 
tRNA, the nucleosome, a ribozyme, discovery of zinc finger transcription 
factors and of course 3D image reconstruction. He initially learned 
crystallography from R. W. James in Cape Town. He also made contributions to 
many aspects of crystallography, including direct methods and heavy-atom 
phasing.

From my personal perspective, he was truly an exceptional mentor. Despite 
obligations that included directorship of the MRC-LMB and then Pres. of the 
Royal Society, he always had time and a keen interest in what each of us in his 
small group was doing. When I first arrived (in 1993), I was supposed to work 
on a structure of a zinc finger/RNA complex, but he quickly deduced that my 
heart was still invested in getting a ribozyme structure, which I had struggled 
with for several years previously. He immediately appreciated its significance 
and encouraged me to make a fresh start of it, which eventually succeeded.

At about the time I got the ribozyme phasing to work, my mother, back in 
Chicago, was treated for lung cancer. Aaron was very supportive and encouraged 
my frequent trips home to visit. When she recovered, he hosted her (along with 
me) for lunch in London at the Royal Society, which she (and I) greatly enjoyed 
and appreciated. (Perhaps because of this in some small part, she beat the odds 
and survived.) It remained one of her fondest memories.

I last saw Aaron about 10 years ago when I gave a presentation at the LMB, and 
he was still very much engaged and helpfully critical of our work. His 
extraordinary intellect, informed by his remarkable dignity and humanity, is as 
much a legacy as his many exceptional contributions to science. 

Yours sincerely,

William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064  
USA

http://scottlab.ucsc.edu

> On Dec 5, 2018, at 5:07 AM, Miri Hirshberg 
> <02897e8e9f0f-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Weds., Dec. 5th 2018
> London
> 
> 
> Prof. Klug died November 20th, 2018, and was buried on November 26th 
> in Cambridge, UK.
> https://www2.mrc-lmb.cam.ac.uk/aaron-klug-1926-2018/
> 
> He was among the founders of Structural Biology as we know it today.
> 
> The title of his 1982 Nobel Prize lecture
> 
> 'From Macromolecules To Biological Assemblies'
> 
> sums part of his vast body of scientific work, from X-ray
> crystallography to EM, nucleic acid structures to the Human Genome
> Project. He also was a supporter of the PDB and the work carried out in
> PDBe. 
> 
> I was privileged to have met him personally, over cups of tea,
> both at Stanford California and in the LMB. His brilliant
> scientific mind went hand in hand with his pleasant,civilised,
> sometimes funny and immensely interesting persona.   
> 
> It is never too late to pay respects.
> May he rest in peace
> 
> Miri Hirshberg
> 
> 
> 
> 
> 
> 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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Re: [ccp4bb] ccp4 release 7.0 update 061

[Ville Uski]

On Wed, Dec 05, 2018 at 08:48:59AM -0800, Steven Rees wrote:
> The link for the latest CCP4 downloads seems to be down (
> http://www.ccp4.ac.uk/download/). The Cached version loads fine (from Dec
> 3), but no server can be found for the download links from this version. Is
> anyone else having this issue?

Hi Steve

bots have been causing this issue every now and then. Sorry about it. The 
download
pages should now be available again.

All the best
Ville



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Re: [ccp4bb] ccp4 release 7.0 update 061

[Steven Rees]

The link for the latest CCP4 downloads seems to be down (
http://www.ccp4.ac.uk/download/). The Cached version loads fine (from Dec
3), but no server can be found for the download links from this version. Is
anyone else having this issue?

Regards,
Steve

On Wed, Aug 15, 2018 at 8:12 AM Charles Ballard - UKRI STFC <
charles.ball...@stfc.ac.uk> wrote:

> Dear All
>
> ccp4 update 061 to release 7.0 is now available.  It contains
>
> * DIALS 1.10.4 and XIA2 0.5.582
>  - release notes: https://github.com/dials/dials/releases/tag/v1.10.0
>
> * molprobity 4.4
>  - scripts molprobity.molprobity, molprobity.clashscore,
> molprobity.cablam, probe, reduce, etc
>  - http://molprobity.biochem.duke.edu/
>  - thank you to Jane Richardson, Nigel Moriarty, Randy Read
>
> * lorestr
>  - update to use bundled molprobity.
>
> This is available as an update to current installations, and as a direct
> download from the ccp4 site.
>
> Coming soon:
>
>  * major update to monomer library
>  * molprobity integration to ccp4i2
>  * DIALS gui update
>  * additional reference structures for buccaneer.
>
> All the best
>
> Charles
> 
>
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>



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Re: [ccp4bb] pyruvoyl modification and coot

[Paul Emsley]

On 05/12/2018 00:44, Jungwook Kim wrote:
I am about to refine a structure containing an N-terminal pyruvoyl residue (naturally derived from serine), 
which is commonly seen in many decarboxylases.


File -> Get Monomer -> PYR

Edit -> Merge Molecules -> [Merge the PYR molecule into your protein molecule]

Renumber the PYR residue and change the chain-id as needed

Extensions -> Modules -> CCP4 -> CCP4 -> Make a Link via Acedrg

Delete Atom: O2 -> Pick 2 Atoms -> Click on C1 of PYR and N of your N-terminal 
residue [*]

This will generate a dictionary that should be usable in Refmac and Coot.


Paul.

[*] I am guessing that this is the link that you want to make, I didn't look it 
up :-)



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[ccp4bb] Sir Prof. Aaron Klug 1926 - 2018

[Miri Hirshberg]

Weds., Dec. 5th 2018
London


Prof. Klug died November 20th, 2018, and was buried on November 26th 
in Cambridge, UK.
https://www2.mrc-lmb.cam.ac.uk/aaron-klug-1926-2018/
 
He was among the founders of Structural Biology as we know it today.

The title of his 1982 Nobel Prize lecture
 
 'From Macromolecules To Biological Assemblies'
 
sums part of his vast body of scientific work, from X-ray
crystallography to EM, nucleic acid structures to the Human Genome
Project. He also was a supporter of the PDB and the work carried out in
PDBe. 

I was privileged to have met him personally, over cups of tea,
both at Stanford California and in the LMB. His brilliant
scientific mind went hand in hand with his pleasant,civilised,
sometimes funny and immensely interesting persona.   

It is never too late to pay respects.
May he rest in peace
 
Miri Hirshberg
 
 



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Re: [ccp4bb] Experimental phasing vs molecular replacement

[Frederic Vellieux]

Hello,

I think what you are alluding to is model bias in (macromolecular) 
crystallography. What you should consult are the publications associated 
with this topic, and those on the map coefficients used to compute 
electron density maps (e.g. SIGMAA weighting), OMIT maps, current 
refinement techniques...


"Heavy-atom" phasing also suffers (or may suffer) from "imperfections" 
due to the heavy atom model used for phasing. Some of us remember 
ripples in electron density maps.


Fred.

On 2018-12-05 09:07, 香川 亘 wrote:

Dear all,

It is my understanding that experimental phasing (e.g. Se-SAD), in
principle, yields better electron density maps than molecular
replacement for protein regions with weak electron densities
(partially disordered or flexible).  I would appreciate if someone
could provide comments on whether my understanding is correct or not.
If there any good examples or literatures on this issue I would be
grateful to know about it.

I thank you in advance.

Wataru Kagawa


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[ccp4bb] New PDB archive reference paper now in NAR 2019 Database issue

[John Berrisford]

An important   new publication
describing the activities and development of the Protein Data Bank (PDB),
and authored by the whole wwPDB consortium, has been recently released in
the 2019 Database issue of Nucleic Acids Research.

Please see the following news release from the
 wwPDB
website:

"  Protein Data Bank: the single global
archive for 3D macromolecular structure data has been published in the 2019
Database issue of Nucleic Acids Research. The paper was authored by "wwPDB
Consortium" to underscore the importance of the global wwPDB partnership in
managing the PDB archive.

This article describes the development of the PDB under the stewardship of
wwPDB, such as new archival content, master format and dictionary and major
remediation efforts. The publication also emphasizes the importance of
continued community interactions, the scientific and technical challenges
the PDB faces, and charts the road ahead."

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

  http://www.pdbe.org

 
http://www.facebook.com/proteindatabank

  http://twitter.com/PDBeurope

 




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[ccp4bb] Experimental phasing vs molecular replacement

[香川 亘]

Dear all,

It is my understanding that experimental phasing (e.g. Se-SAD), in principle, 
yields better electron density maps than molecular replacement for protein 
regions with weak electron densities (partially disordered or flexible).  I 
would appreciate if someone could provide comments on whether my understanding 
is correct or not.  If there any good examples or literatures on this issue I 
would be grateful to know about it.

I thank you in advance.

Wataru Kagawa 


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