[ccp4bb] Cryo-FIB/SEM & Cryo-ET Post-Doctoral Opportunities in New York

[Anthony Fitzpatrick]

The Fitzpatrick lab, a member of the Zuckerman Mind Brain Behavior
Institute at Columbia University, has multiple openings for postdoctoral
research associates to lead projects combining serial-section electron
microscopy, correlative light/electron microscopy, advanced cryo-focused
ion beam specimen preparations, cryo-electron tomography and 3D
processing/subtomogram averaging of neurons, glia, and human brain tissue.



Situated in the heart of Manhattan, the Zuckerman Institute houses sixty
laboratories employing a broad range of interdisciplinary approaches to
transform our understanding of the mind and brain. In this highly
collaborative environment, labs work together to gain critical insights
into human health by exploring how the brain develops, performs, endures
and recovers from trauma or disease.

Members of the lab will have access to a state-of-the-art suite of electron
microscopes and computing resources:



Titan Krios microscope(s) with Gatan BioQuantum energy filter and K3 Summit
direct electron detector



Aquilos cryo-FIB/SEM microscope and a Leica cryo-correlative fluorescence
light microscope (Fitzpatrick Lab)



Nova Nano SEM and a Zeiss SIM/PALM super-resolution light microscope
(Fitzpatrick Lab)



NVIDIA RTX 2080Ti GPU cluster (Fitzpatrick Lab)


We are looking for outstanding scientists who have a strong background in
biophysics, biochemistry or neuroscience. Prior cryo-EM/electron tomography
experience is considered an advantage, but is not essential.


If you’re interested in joining our lab, please send your CV with a brief
description of your current research, as well as 2-3 contacts for
references, to anthony.fitzpatr...@columbia.edu.

Columbia University is an Affirmative Action/Equal Opportunity employer.
Columbia values diversity among its students, staff, and faculty and
strongly welcomes applications from women, persons with disabilities,
protected veterans, and underrepresented minorities.





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Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

[Jonathan Cooper]

 Ian, statistics is not my forte, but I don't think anyone is suggesting that 
the measurement errors of NCS-related reflection amplitudes are correlated. In 
simple terms, since NCS-related F's should be correlated, the working-set 
reflection amplitudes could be correlated with those in the test-set, if the 
latter is chosen randomly, rather than in shells. Am I right in saying that 
R-free not just indicates over-fitting but, also, acts as an unbiased measure 
of the agreement between Fo and Fc? During a well-behaved refinement run, in 
the cycles before any over-fitting becomes apparent, the decrease in R-free 
value will indicate that the changes being made to the model are making it more 
consistent with Fo's. In these stages, any correlation between the test-set and 
the working-set F's due to NCS would be expected to affect the R-free 
(cross-validation bias), making it lower than it would be if the test set had 
been chosen in resolution shells? However, you are always right and, as you 
know, I failed to detect any such effect in my limited tests. Thanks to you and 
others for replying. 

On Tuesday, 4 June 2019, 02:07:10 BST, Edward A. Berry  
wrote:  
 
 On 05/19/2019 08:21 AM, Ian Tickle wrote:
~~~
>> So there you have it: what matters is that the _errors_ in the NCS-related 
>> amplitudes are uncorrelated, or at least no more correlated than the errors 
>> in the non-NCS-related amplitudes, NOT the amplitudes themselves.

Thanks, Ian!

I would like to think that it is the errors in Fobs that matter (as may be the 
case), because then:
1. ncs would not bias R-free even if you _do_ use ncs constraints/restraints. 
(changes in Fcalc due to a step of refinement would be positively correlated 
between sym-mates, but if the sign of (Fo-Fc) is opposite at the sym-mate, what 
impoves the working reflection would worsen the free)
2. There would be no need to use the same free set when you refine the 
structure against a new dataset (as for ligand studies) since the random errors 
of measurement in Fobs in the two sets would be unrelated.

However when I suggested that in a previous post, I was reminded that errors in 
Fobs account for only a small part of the difference (Fo-Fc). The remainder 
must be due to inability of our simple atomic models to represent the actual 
electron density, or its diffraction; and for a symmetric structure and a 
symmetric model, that difference is likely to be symmetric.  Whether that 
difference represents "noise" that we want to avoid fitting is another 
question, but it is likely that (Fo-Fc) will be correlated with sym-mates. So I 
settled for convincing myself that the changes in Fc brought about by 
refinement would be uncorrelated, and thus the _changes_ in (Fo-Fc) at each 
step would be uncorrelated.

Below are some of the ideas I come up with in trying to think about this, and 
about bias in general. (Not very well organized and not the best of prose, but 
if one is a glutton for punishment, or just wants to see how the mind of a 
madman works . . .)

Warning- some of this is contrary to current consensus opinion and the 
conclusions may be, in the words of a popular autobuilding program, partly 
WRONG!  In particular, the idea that coupling by the G-function does not bias 
R-free, but rather is the only reason that R-free works at all!
- - - - - - - - - -

The differences (Fo-Fc) can be divided between (1) errors in measurement
of reflection intensities and (2)failure of the model to represent the
true structure. The first can be considered "noise" and we would expect
it to be random, with no correlation between symm mates.
However most of the difference between Fc and Fobs is not due to random
noise in the data, but to failures of our model to accurately represent
the real thing. These differences are likely to be ncs-symmetric.
Leaving aside the question of whether or not we want to fit this kind of
"noise" (bringing the model closer to the real structure?), we conclude
that (Fo-Fc) is likely to be correlated between ncs-mates.

But for refinement against the working set to bias the contribution of
sym-related free-set reflections to R-free would require that _changes_
in |Fo-Fc| from a step of refinement would be ncs-correlated. If on the
contrary they are not correlated, i.e. if a change that decreases
|Fo-Fc| for a working reflection is equally likely to decrease or
increase |Fo-Fc| for its sym mate (which may be) in the free set, then
it is hard to see how refinement against the working reflection would
bias R-free.

Under what conditins would |Fo-Fc| for symmetry related reflections be
correlated? This would be the case if change in Fc correlates AND the
sign of (Fo-Fc) correlates. Again, if the difference were only due to
random error in Fobs, then the sign of Fo-Fc of a symmetry related reflection
would be as likely to be the opposite as the same (as the original
reflection) so even if changes in Fc are correlated, what improves the
fit to the 

Re: [ccp4bb] MolProbity website down

[Tristan Croll]

Seems to be working fine: 
https://downforeveryoneorjustme.com/molprobity.biochem.duke.edu. It's 
not a secure site, though: https://molprobity... times out, whereas 
http://molprobity... goes through. Could that be your issue?


On 2019-06-04 13:19, Andrea Pica wrote:

Hi everyone,

it seems that MolProbity website (molprobity.biochem.duke.edu) is not 
reachable.


Anyone knows what happened?

Cheers,

Andrea


--
Andrea Pica. Ph.D.
Postdoctoral Researcher
High-Throughput Crystallization Lab
EMBL Grenoble Outstation
Postal address: European Molecular Biology Laboratory
71, Avenue des Martyrs
CS 90181 38042 Grenoble Cedex 9, France
Delivery address: European Molecular Biology Laboratory
71, Avenue des Martyrs
38000 Grenoble, France
Phone +33 (0) 47 620 7632



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[ccp4bb] MolProbity website down

[Andrea Pica]

Hi everyone,

it seems that MolProbity website (molprobity.biochem.duke.edu) is not 
reachable.


Anyone knows what happened?

Cheers,

Andrea


--
Andrea Pica. Ph.D.
Postdoctoral Researcher
High-Throughput Crystallization Lab
EMBL Grenoble Outstation
Postal address: European Molecular Biology Laboratory
71, Avenue des Martyrs
CS 90181 38042 Grenoble Cedex 9, France
Delivery address: European Molecular Biology Laboratory
71, Avenue des Martyrs
38000 Grenoble, France
Phone +33 (0) 47 620 7632



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Re: [ccp4bb] 40th CCP4 anniversary competition - 10 Golden Tickets deadline 18th June!

[Paula Salgado]

Submissions of the 200 word summary (abstract style) highlighting CCP4 in your 
work together with a link to the paper or software or any relevant form of 
evidence of your contribution. can be sent to me directly to 
paula.salg...@ncl.ac.uk.


Looking forward to the exciting CCP4-linked science coming my way!


Paula


===

Dr Paula S. Salgado
Senior Lecturer in Macromolecular Crystallography
Institute for Cell and Molecular Biosciences
Faculty of Medical Sciences
3rd Floor Cookson Building
Newcastle University
Newcastle upon Tyne, NE2 4HH, UK

Tel: +44 (0)191 208 7432
Fax: +44 (0)191 208 7424
Email: paula.salg...@ncl.ac.uk

From: CCP4 bulletin board  on behalf of Paula Salgado 

Sent: 03 June 2019 15:47:28
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 40th CCP4 anniversary competition - 10 Golden Tickets 
deadline 18th June!


Apologies for the funny format in the flyer - now attached as PDF and JPG, 
hopefully with no issues!


===

Dr Paula S. Salgado
Senior Lecturer in Macromolecular Crystallography
Institute for Cell and Molecular Biosciences
Faculty of Medical Sciences
3rd Floor Cookson Building
Newcastle University
Newcastle upon Tyne, NE2 4HH, UK

Tel: +44 (0)191 208 7432
Fax: +44 (0)191 208 7424
Email: paula.salg...@ncl.ac.uk

From: CCP4 bulletin board  on behalf of Paula Salgado 

Sent: 03 June 2019 15:37:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] 40th CCP4 anniversary competition - 10 Golden Tickets 
deadline 18th June!




This year, CCP4 turns 40 and is celebrating in style with an event in London. 
CCP4 has a strong focus on training the new generation of crystallographers and 
developers so, as part of the celebrations, we are inviting 10 PhD students and 
Post-doctoral researchers to showcase their work using CCP4.



If you are a PhD student or Postdoc protein crystallographer and have published 
work featureing CCP4 as a strong component, or have made a recognised 
contribution to CCP4 software, you could be joining the celebrations at the 
Royal Society, London, on Tuesday 9 July, from 13:00-17:00.



To win, just submit a piece of published work highlighting CCP4, where you are 
the first author. If selected, you will be asked to create a poster to present 
to a wide range of audiences at the event.  Small travel bursaries are 
available to help with costs (details http://www.ccp4.ac.uk/40thccp4golden.htm).


Deadline to apply is June 18th, so hurry! Please share with your students, 
postdocs, colleagues and friends! We want to hear about your great work and 
want you to join the party on July 9th!


Attached is a flyer you can use to help advertise the competition.


Hope to see you at the Royal Society!


Competition details :

http://www.ccp4.ac.uk/40thccp4golden.htm



On behalf of the CCP4 Executive

Paula Salgado


===

Dr Paula S. Salgado
Senior Lecturer in Macromolecular Crystallography
Institute for Cell and Molecular Biosciences
Faculty of Medical Sciences
3rd Floor Cookson Building
Newcastle University
Newcastle upon Tyne, NE2 4HH, UK

Tel: +44 (0)191 208 7432
Fax: +44 (0)191 208 7424
Email: paula.salg...@ncl.ac.uk



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[ccp4bb] COOT crashes when I merge molecules

[Luca Mazzei]

Dear CPP4 people,

COOT (0.8.9.2 EL) crashes everytime I merge my model with the monomer EDO 
(1,2-Ethanediol, cryoprotectant). The same issue does not occur with other 
monomers. I tried to replace EDO.cif in a new monomer (EDQ.cif) and COOT works 
fine.
Any suggestion?

Thanks in advance,

Luca Mazzei

Luca Mazzei - PhD
Department of Pharmacy and Biotechnology
University of Bologna
Viale Giuseppe Fanin, 40 - 40127
Bologna - Italy



Il giorno 4 giu 2019, alle ore 09:02, Darren Hart 
mailto:darren.h...@ibs.fr>> ha scritto:

You have to start it via the menu item, not the command line.

Darren

On 03/06/2019 14:31, Pedro Matias wrote:

Well, I can't get it to work in FC30 - I installed FC30 on a virtual machine 
and managed to install both snapd and pymol-oss but pymol does not run as a 
command.

Am I missing something rather obvious?

Pedro

Às 12:46 de 03/06/2019, Matic Kisovec escreveu:
Hi,

thank you very much for this. Work fine on Ubuntu 19.04.

Kind regrds,
Matic


On 17. 05. 19 20:04, Arunabh Athreya wrote:
Thanks for sharing this.

Get Outlook for Android


From: CCP4 bulletin board  
on behalf of David Schuller 
Sent: Thursday, May 16, 2019 11:41:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PyMOL now packaged as a snap on Linux

It seems to work on Fedora 30 and on Scientific Linux 7 (which means it should 
also work on RHEL7 and Centos 7)

Thank you.



On 5/16/19 10:47 AM, Darren Hart wrote:
Some more info:

https://snapcraft.io/pymol-oss

It seems to work exactly as expected.

Darren


On 16/05/2019 16:05, Folmer Fredslund wrote:
Hi Darren,

That's brilliant!

I'll give it a spin and see how it works.

Best regards
Folmer


tor. 16. maj 2019 13.02 skrev Darren Hart 
mailto:darren.h...@ibs.fr>>:
Since yesterday, PyMOL (open source version v2.3) has been packaged as a
distro-independent "snap" that can be installed easily on linux
platforms - no more cloning from gitlab and compiling after installing
the dependencies.

On Ubuntu, install from software centre or:

sudo snap install pymol-oss

Many distros have the snap architecture already installed. If not, you
just need to install snapd in the regular way first (e.g. on Debian:
sudo apt install snapd).

Hope this is useful for some folks.

Best regards,

Darren



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--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu




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--

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8




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--

**

Dr. Darren J. Hart,

CNRS Research Director, Institut de Biologie Structurale (IBS)
Unité Mixte de Recherche UMR5075 (CEA-CNRS-UGA)

Director, Integrated Structural Biology Grenoble (ISBG)
Unité Mixte de Service UMS3518 (CNRS-UGA-CEA-EMBL)

**

Email: 

[ccp4bb] Structural Biology Postdoctoral position - Dr. Eamonn Reading Lab, King's College London, UK

[Reading, Eamonn]

Dear,

A 3.5-4 year Postdoctoral position is available within the Reading Group at 
King's College London on:

Structural dynamics of membrane proteins in their native environment: focus on 
bacterial antibiotic resistance

In this project the post holder will develop chemical biology and structural 
mass spectrometry methods (primarily hydrogen/deuterium exchange mass 
spectrometry) to achieve structural and dynamic insight into membrane proteins 
within native lipid membrane environments. This would be a huge step forward in 
understanding how membrane proteins shape the function of cells for the 
determination of native membrane protein structural biology information.

Please contact Eamonn Reading (eamonn.read...@kcl.ac.uk) for more information 
or an informal discussion.

Link to advert: tinyurl.com/y4karkyn 

Twitter: @EReadingGroup

Kind Regards,



Dr. Eamonn Reading | UKRI Future Leaders Fellow | King's College London


Address: Department of Chemistry, Britannia House, 7 Trinity Street, King's 
College London, London, SE1 1DB

Tel: 020 7848 7508 | E-mail: 
eamonn.read...@kcl.ac.uk




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Re: [ccp4bb] PyMOL now packaged as a snap on Linux

[Darren Hart]

You have to start it via the menu item, not the command line.

Darren

On 03/06/2019 14:31, Pedro Matias wrote:


Well, I can't get it to work in FC30 - I installed FC30 on a virtual 
machine and managed to install both snapd and pymol-oss but pymol does 
not run as a command.


Am I missing something rather obvious?

Pedro

Às 12:46 de 03/06/2019, Matic Kisovec escreveu:

Hi,

thank you very much for this. Work fine on Ubuntu 19.04.

Kind regrds,
Matic


On 17. 05. 19 20:04, Arunabh Athreya wrote:

Thanks for sharing this.

Get Outlook for Android 


*From:* CCP4 bulletin board  on behalf of 
David Schuller 

*Sent:* Thursday, May 16, 2019 11:41:19 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] PyMOL now packaged as a snap on Linux
It seems to work on Fedora 30 and on Scientific Linux 7 (which means 
it should also work on RHEL7 and Centos 7)


Thank you.



On 5/16/19 10:47 AM, Darren Hart wrote:

Some more info:

https://snapcraft.io/pymol-oss

It seems to work exactly as expected.

Darren


On 16/05/2019 16:05, Folmer Fredslund wrote:

Hi Darren,

That's brilliant!

I'll give it a spin and see how it works.

Best regards
Folmer


tor. 16. maj 2019 13.02 skrev Darren Hart >:


Since yesterday, PyMOL (open source version v2.3) has been
packaged as a
distro-independent "snap" that can be installed easily on linux
platforms - no more cloning from gitlab and compiling after
installing
the dependencies.

On Ubuntu, install from software centre or:

sudo snap install pymol-oss

Many distros have the snap architecture already installed. If
not, you
just need to install snapd in the regular way first (e.g. on
Debian:
sudo apt install snapd).

Hope this is useful for some folks.

Best regards,

Darren



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--




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--
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu



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--

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
  Fax   : (351-21) 441-1277 or 443-3644

email :mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



--

**

Dr. Darren J. Hart,

CNRS Research Director, Institut de Biologie Structurale (IBS)
Unité Mixte de Recherche UMR5075 (CEA-CNRS-UGA)

Director, Integrated Structural Biology Grenoble (ISBG)
Unité Mixte de Service UMS3518 (CNRS-UGA-CEA-EMBL)

**

Email: darren.h...@ibs.fr

Tel: +33 4 57 42 85 86

Physical address: IBS/ISBG, 71 avenue des Martyrs, 38000 Grenoble, France

Postal address: IBS/ISBG, 71 avenue des Martyrs, CS 20192, 38042 
Grenoble, Cedex 9, France


**