Re: [ccp4bb] Virtual Registration for 10th CCP-EM Spring Symposium & BCI User Meeting 30th April - 2nd May 2024

[Tom Burnley - STFC UKRI]

Dear all,

BCI and Spring Symposium is now live!

If you'd like to join virtually any time over the few days please register here 
for full joining instructions:

https://cvent.me/Q1QANv

Or you can drop in following the Zoom links in the full schedule here:

https://www.ccpem.ac.uk/downloads/symposium/2024/outline_ccp-em_symp_schedule_2024.pdf

All the best,

Tom

From: Burnley, Tom (STFC,RAL,SC)
Sent: 28 April 2024 13:23
To: ccpem mailing list ; ccp4bb ; 
3...@ncmir.ucsd.edu <3...@ncmir.ucsd.edu>
Subject: Virtual Registration for 10th CCP-EM Spring Symposium & BCI User 
Meeting 30th April - 2nd May 2024

Hi everyone,

We're looking forward to the 10th CCP-EM Spring Symposium & BCI User Meeting 
next week.

If you aren't able to make it person you can still register as a virtual 
delegate

Registration page:
https://cvent.me/Q1QANv

N.B. virtual registration is free and you'll be able which the live stream (and 
ask questions) for all the talks from our wonderful speakers including

CCP-EM Symposium

Yifan Cheng (UCSF)

Wah Chiu (Stanford)

Dan Clare (DLS)

Hans Elmlund (NIH)

Judy Hirst (MRC-MBU)

Oleg Kovalevskiy (DeepMind)

Martin Pilhofer (ETH Zürich)

Lorenz Lamm (Helmholtz Zentrum München)

Kyle Morris (EBI)

Thomas Mulvaney (CSSB)

Alexis Rohou (Genentech)

Chris Russo (MRC-LMB)

Carsten Sachse (Jülich)

Helen Saibil (Birkbeck)

Filo Sanchez Rodriguez (York)

Sjors Scheres (MRC-LMB)

Sriram Subramaniam (British Columbia)

Rebecca Thompson (TFS)

Peiyi Wang (SUSTech)

Martyn Winn (STFC)

Tzviya Zeev-Ben-Mordehai (Utrecht)

Xiaodong Zhang (Francis Crick Institute)

Ellen Zhong (Princeton)


Confirmed BCI speakers:

Vicki Gold (Exeter)

Mangala Srinivas (Wageningen)

Stefan Raunser (Max Planck Molecular Physiology)

Plus eBIC user meeting round-table discussion

Symposium scientific organisers:
Peijun Zhang (DLS/Oxford)
Peter Rosenthal (Francis Crick Institute)

Biological Cryo-Imaging user meeting organising committee:
Lorna Malone (eBIC, Diamond)
Archana Jadhav (B24, Diamond)

Full details and schedule:
https://www.ccpem.ac.uk/training/spring_symposium_2024/spring_symposium_2024.php

All times are UK (BST) and most talks will be available to view later.

We look forward to welcoming you all either in-person or virtually in 
Nottingham .

Best wishes from CCP-EM & DLS BCI



To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Virtual Registration for 10th CCP-EM Spring Symposium & BCI User Meeting 30th April - 2nd May 2024

[Tom Burnley - STFC UKRI]

Hi everyone,

We're looking forward to the 10th CCP-EM Spring Symposium & BCI User Meeting 
next week.

If you aren't able to make it person you can still register as a virtual 
delegate

Registration page:
https://cvent.me/Q1QANv

N.B. virtual registration is free and you'll be able which the live stream (and 
ask questions) for all the talks from our wonderful speakers including

CCP-EM Symposium

Yifan Cheng (UCSF)

Wah Chiu (Stanford)

Dan Clare (DLS)

Hans Elmlund (NIH)

Judy Hirst (MRC-MBU)

Oleg Kovalevskiy (DeepMind)

Martin Pilhofer (ETH Zürich)

Lorenz Lamm (Helmholtz Zentrum München)

Kyle Morris (EBI)

Thomas Mulvaney (CSSB)

Alexis Rohou (Genentech)

Chris Russo (MRC-LMB)

Carsten Sachse (Jülich)

Helen Saibil (Birkbeck)

Filo Sanchez Rodriguez (York)

Sjors Scheres (MRC-LMB)

Sriram Subramaniam (British Columbia)

Rebecca Thompson (TFS)

Peiyi Wang (SUSTech)

Martyn Winn (STFC)

Tzviya Zeev-Ben-Mordehai (Utrecht)

Xiaodong Zhang (Francis Crick Institute)

Ellen Zhong (Princeton)


Confirmed BCI speakers:

Vicki Gold (Exeter)

Mangala Srinivas (Wageningen)

Stefan Raunser (Max Planck Molecular Physiology)

Plus eBIC user meeting round-table discussion

Symposium scientific organisers:
Peijun Zhang (DLS/Oxford)
Peter Rosenthal (Francis Crick Institute)

Biological Cryo-Imaging user meeting organising committee:
Lorna Malone (eBIC, Diamond)
Archana Jadhav (B24, Diamond)

Full details and schedule:
https://www.ccpem.ac.uk/training/spring_symposium_2024/spring_symposium_2024.php

All times are UK (BST) and most talks will be available to view later.

We look forward to welcoming you all either in-person or virtually in 
Nottingham .

Best wishes from CCP-EM & DLS BCI



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

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[ccp4bb] Final Registration for 10th CCP-EM Spring Symposium & BCI User Meeting 30th April - 2nd May 2024

[Tom Burnley - STFC UKRI]

Hi all,


Quick reminder that in person registration for the Symposium closes tomorrow 
(Friday 29th March).


Virtual registration will remain open but if you would like to attend in person 
please register now if you haven't already.


Registration page:

https://cvent.me/Q1QANv


Please note we have now sold out of our conference accommodation so any new 
delegates will need to arrange their own accommodation.  Hotels are available 
near the conference centre e.g.:



Travelodge Nottingham Wollaton Park (~15mins walk from EMCC conference centre)

https://www.travelodge.co.uk/hotels/474/Nottingham-Wollaton-Park-hotel



Confirmed symposium speakers:

Yifan Cheng (UCSF)

Wah Chiu (Stanford)

Dan Clare (DLS)

Hans Elmlund (NIH)

Judy Hirst (MRC-MBU)

Oleg Kovalevskiy (DeepMind)

Martin Pilhofer (ETH Zürich)

Lorenz Lamm (Helmholtz Zentrum München)

Kyle Morris (EBI)

Thomas Mulvaney (CSSB)

Alexis Rohou (Genentech)

Chris Russo (MRC-LMB)

Carsten Sachse (Jülich)

Helen Saibil (Birkbeck)

Filo Sanchez Rodriguez (York)

Sjors Scheres (MRC-LMB)

Sriram Subramaniam (British Columbia)

Rebecca Thompson (TFS)

Peiyi Wang (SUSTech)

Martyn Winn (STFC)

Tzviya Zeev-Ben-Mordehai (Utrecht)

Xiaodong Zhang (Francis Crick Institute)

Ellen Zhong (Princeton)



Confirmed BCI speakers:

Vicki Gold (Exeter)

Mangala Srinivas (Wageningen)

Stefan Raunser (Max Planck Molecular Physiology)

Plus eBIC user meeting round-table discussion



Symposium scientific organisers:

Peijun Zhang (DLS/Oxford)

Peter Rosenthal (Francis Crick Institute)


Biological Cryo-Imaging user meeting organising committee:

Lorna Malone (eBIC, Diamond)

Archana Jadhav (B24, Diamond)



Full details and schedule:

https://www.ccpem.ac.uk/training/spring_symposium_2024/spring_symposium_2024.php

We look forward to welcoming you all in Nottingham!



Best wishes from CCP-EM & DLS BCI





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

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Re: [ccp4bb] Early bird deadline: Monday 11 March - 10th CCP-EM Spring Symposium 30th April - 2nd May 2024

[Tom Burnley - STFC UKRI]

Hi all,

Final reminder that earlier bird registration for the Symposium/BCI meeting 
closes at the end of today (Mon 11 March)

All the best,

Tom


From: Burnley, Tom (STFC,RAL,SC)
Sent: 08 March 2024 13:55
To: ccpem mailing list 
Cc: ccp4bb ; 3...@ncmir.ucsd.edu <3...@ncmir.ucsd.edu>
Subject: Early bird deadline: Monday 11 March - 10th CCP-EM Spring Symposium 
30th April - 2nd May 2024


Hi all,


Just a reminder that the earlier bird registration for the Symposium closes end 
of Monday 11th, after than the conference fees will increase:



Conference fees

PhD/PDRA Early Bird: £150.00

Standard Early Bird: £200.00

  

PhD/PDRA: £200.00

Standard: £250.00



Registration page:

https://cvent.me/Q1QANv


Please note we have now sold out of our conference accommodation so any new 
delegates will need to arrange their own accommodation.  Hotels are available 
near the conference centre e.g.:



Travelodge Nottingham Wollaton Park (~15mins walk from EMCC conference centre)

https://www.travelodge.co.uk/hotels/474/Nottingham-Wollaton-Park-hotel



Confirmed symposium speakers:

Yifan Cheng (UCSF)

Wah Chiu (Stanford)

Dan Clare (DLS)

Hans Elmlund (NIH)

Judy Hirst (MRC-MBU)

Oleg Kovalevskiy (DeepMind)

Martin Pilhofer (ETH Zürich)

Lorenz Lamm (Helmholtz Zentrum München)

Kyle Morris (EBI)

Thomas Mulvaney (CSSB)

Alexis Rohou (Genentech)

Chris Russo (MRC-LMB)

Carsten Sachse (Jülich)

Helen Saibil (Birkbeck)

Filo Sanchez Rodriguez (York)

Sjors Scheres (MRC-LMB)

Sriram Subramaniam (British Columbia)

Rebecca Thompson (TFS)

Peiyi Wang (SUSTech)

Martyn Winn (STFC)

Tzviya Zeev-Ben-Mordehai (Utrecht)

Xiaodong Zhang (Francis Crick Institute)

Ellen Zhong (Princeton)



Confirmed BCI speakers:

Vicki Gold (Exeter)

Mangala Srinivas (Wageningen)

Stefan Raunser (Max Planck Molecular Physiology)

Plus eBIC user meeting round-table discussion



Symposium scientific organisers:

Peijun Zhang (DLS/Oxford)

Peter Rosenthal (Francis Crick Institute)


Biological Cryo-Imaging user meeting organising committee:

Lorna Malone (eBIC, Diamond)

Archana Jadhav (B24, Diamond)



Full details and schedule:

https://www.ccpem.ac.uk/training/spring_symposium_2024/spring_symposium_2024.php

We look forward to welcoming you all in Nottingham!



Best wishes from CCP-EM & DLS BCI



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
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[ccp4bb] Early bird deadline: Monday 11 March - 10th CCP-EM Spring Symposium 30th April - 2nd May 2024

[Tom Burnley - STFC UKRI]

Hi all,


Just a reminder that the earlier bird registration for the Symposium closes end 
of Monday 11th, after than the conference fees will increase:



Conference fees

PhD/PDRA Early Bird: £150.00

Standard Early Bird: £200.00

  

PhD/PDRA: £200.00

Standard: £250.00



Registration page:

https://cvent.me/Q1QANv


Please note we have now sold out of our conference accommodation so any new 
delegates will need to arrange their own accommodation.  Hotels are available 
near the conference centre e.g.:



Travelodge Nottingham Wollaton Park (~15mins walk from EMCC conference centre)

https://www.travelodge.co.uk/hotels/474/Nottingham-Wollaton-Park-hotel



Confirmed symposium speakers:

Yifan Cheng (UCSF)

Wah Chiu (Stanford)

Dan Clare (DLS)

Hans Elmlund (NIH)

Judy Hirst (MRC-MBU)

Oleg Kovalevskiy (DeepMind)

Martin Pilhofer (ETH Zürich)

Lorenz Lamm (Helmholtz Zentrum München)

Kyle Morris (EBI)

Thomas Mulvaney (CSSB)

Alexis Rohou (Genentech)

Chris Russo (MRC-LMB)

Carsten Sachse (Jülich)

Helen Saibil (Birkbeck)

Filo Sanchez Rodriguez (York)

Sjors Scheres (MRC-LMB)

Sriram Subramaniam (British Columbia)

Rebecca Thompson (TFS)

Peiyi Wang (SUSTech)

Martyn Winn (STFC)

Tzviya Zeev-Ben-Mordehai (Utrecht)

Xiaodong Zhang (Francis Crick Institute)

Ellen Zhong (Princeton)



Confirmed BCI speakers:

Vicki Gold (Exeter)

Mangala Srinivas (Wageningen)

Stefan Raunser (Max Planck Molecular Physiology)

Plus eBIC user meeting round-table discussion



Symposium scientific organisers:

Peijun Zhang (DLS/Oxford)

Peter Rosenthal (Francis Crick Institute)


Biological Cryo-Imaging user meeting organising committee:

Lorna Malone (eBIC, Diamond)

Archana Jadhav (B24, Diamond)



Full details and schedule:

https://www.ccpem.ac.uk/training/spring_symposium_2024/spring_symposium_2024.php

We look forward to welcoming you all in Nottingham!



Best wishes from CCP-EM & DLS BCI



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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[ccp4bb] Bursary Extension - Monday 4 March 10th CCP-EM Spring Symposium/DLS BCI User Meeting 30th April - 2nd May 2024

[Tom Burnley - STFC UKRI]

Dear all,

** We have additional bursary places and have extended the bursary deadline to 
Monday 4th March **

This is thanks to kind support from: CryoCloud, CryoSol, Dectris, Quantum 
Detectors, Nanosoft, SubAngstrom and Thermo Fisher Scientific.

The bursaries will cover registration fee and two nights accommodation. If you 
are interested please send a 300 word application to ccpemeve...@stfc.ac.uk 
detailing your interest in attending the conference in person, why this can't 
be covered by other funds and how this would benefit you and others.  We will 
confirm all bursary places by 7th March.

** Early bird registration will now close Monday 11th March **

Confirmed symposium speakers:
Yifan Cheng (UCSF)
Wah Chiu (Stanford)
Hans Elmlund (NIH)
Judy Hirst (MRC-MBU)
Oleg Kovalevskiy (DeepMind)
Martin Pilhofer (ETH Zürich)
Lorenz Lamm (Helmholtz Zentrum München)
Kyle Morris (EBI)
Thomas Mulvaney (CSSB)
David Owen (DLS)
Alexis Rohou (Genentech)
Chris Russo (MRC-LMB)
Carsten Sachse (Jülich)
Helen Saibil (Birkbeck)
Filo Sanchez Rodriguez (York)
Sjors Scheres (MRC-LMB)
Sriram Subramaniam (British Columbia)
Rebecca Thompson (TFS)
Peiyi Wang (SUSTech)
Martyn Winn (STFC)
Tzviya Zeev-Ben-Mordehai (Utrecht)
Xiaodong Zhang (Francis Crick Institute)
Ellen Zhong (Princeton)

Confirmed BCI speakers:
Vicki Gold (Exeter)
Mangala Srinivas (Wageningen)
Stefan Raunser (Max Planck Molecular Physiology)
Plus eBIC user meeting round-table discussion

Symposium scientific organisers:
Peijun Zhang (DLS/Oxford)
Peter Rosenthal (Francis Crick Institute)

Biological Cryo-Imaging user meeting organising committee:
Lorna Malone (eBIC, Diamond)
Archana Jadhav (B24, Diamond)

30th April - 2nd May 2024, EMCC, Nottingham, UK

Full details and schedule:
https://www.ccpem.ac.uk/training/spring_symposium_2024/spring_symposium_2024.php

Registration:
https://cvent.me/Q1QANv

We look forward to welcoming you all in Nottingham!

Best wishes from CCP-EM & DLS BCI



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
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[ccp4bb] 10th CCP-EM Spring Symposium 30th April - 2nd May 2024

[Tom Burnley - STFC UKRI]

Dear all,

We are pleased to announce the 10th Annual CCP-EM Spring Symposium!  The 
conference aims to provide a forum to highlight state-of-the-art developments 
in computational cryoEM and related themes, as well as showcasing outstanding 
recent biological applications. We aim to promote an inclusive, friendly 
atmosphere, welcoming those both old and new to the community. Topics include 
instrument technology, sample preparation, image processing, single particle 
reconstruction, tomography and model building.

The meeting also includes the Diamond Light Source Biological Cryo-Imaging User 
Meeting for eBIC & B24 and associated satellite meetings for correlative 
microscopy (eBIC), soft X-ray tomography (B24) & automated live processing for 
SPA and cryoET (eBIC).

The conference will be held as a hybrid meeting, with the physical event at the 
EMCC in Nottingham, plus virtual access online via Zoom. It is kindly sponsored 
by CryoSol, Dectris, Quantum Detectors, Nanosoft, SubAngstrom and Thermo Fisher 
Scientific.

Dates:
30th April - 2nd May 2024

Location:
EMCC, Nottingham, UK

Registration:
https://cvent.me/Q1QANv

Confirmed Symposium speakers include:
Yifan Cheng (UCSF)
Wah Chiu (Stanford)
Martin Pilhofer (ETH Zürich)
Alexis Rohou (Genentech)
Chris Russo (MRC-LMB)
Carsten Sachse (Jülich)
Helen Saibil (Birkbeck)
Sjors Scheres (MRC-LMB)
Sriram Subramaniam (British Columbia)
Tzviya Zeev-Ben-Mordehai (Utrecht)
Xiaodong Zhang (Francis Crick Institute)
Peiyi Wang (SUSTech)

Confirmed BCI speakers:
Vicki Gold (Exeter)
Mangala Srinivas (Wageningen)
Stefan Raunser (Max Planck Molecular Physiology)
Plus eBIC user meeting round-table discussion

Symposium scientific organisers:
Peijun Zhang (DLS/Oxford)
Peter Rosenthal (Francis Crick Institute)

Biological Cryo-Imaging user meeting organising committee:
Lorna Malone (eBIC, Diamond)
Archana Jadhav (B24, Diamond)

More details are available here:
https://www.ccpem.ac.uk/training/spring_symposium_2024/spring_symposium_2024.php

Early bird discounted prices are available for the next month and we have a 
limited number of hotel rooms so please register asap.

Thanks to the kind support of our sponsors we have a limited number of 
bursaries which will cover registration fees and two night halls accommodation. 
If you are interested please can you send a 300 word application to 
ccpemeve...@stfc.ac.uk detailing your interest in attending the conference in 
person and why a bursary would help (closing date 11 Feb).

We look forward to welcoming you all in Nottingham!

Best wishes from CCP-EM & DLS BCI



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
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[ccp4bb] Fw: [ccp4bb] CCP4 Study Weekend 2024 - In-person registration CLOSES TODAY - 4TH DECEMBER!

[Tom Burnley - STFC UKRI]

Quick reminder - last call for CCP4 Study Weekend in person registration is 
today (Monday 4th Dec)!



From: CCP4 bulletin board  on behalf of Karen McIntyre - 
STFC UKRI <6f4fce69ead1-dmarc-requ...@jiscmail.ac.uk>
Sent: 01 December 2023 14:31
To: ccp4bb 
Subject: Re: [ccp4bb] CCP4 Study Weekend 2024 - In-person registration CLOSES 
MONDAY 4TH DECEMBER!


In-person registration for the CCP4 Study Weekend 2024 closes on Monday 4th 
December (this coming Monday).



Virtual registration will still be available after this date.



Register now if you want to be in the room where it happens!



Regards



Karen McIntyre



CCP4 Project Administrator

CCP4 Equality, Diversity and Inclusion Champion

Member of SCD ED Working Group



Science and Technology Facilities Council

karen.mcint...@stfc.ac.uk

Zoom phone: 01235 44 5790



[cid:image001.png@01DA2463.11ADDC60]



**Hours of work: Monday to Thursday: 8.30am to 1.30pm, Friday 10:30am to 
3.30pm.  Please note that I only work part-time **



From: McIntyre, Karen (STFC,RAL,SC)
Sent: Thursday, November 23, 2023 12:21 PM
To: 'ccp4bb' ; CCP4 WG1 ; 
CCP4 WG2 ; 'cc...@jiscmail.ac.uk' 
; 'c...@jiscmail.ac.uk' ; 
'pheni...@phenix-online.org' ; 
'pdbe-api-us...@ebi.ac.uk' 
Subject: RE: CCP4 Study Weekend 2024 - In-person Early bird registration 
including standard student bursary CLOSES TODAY!
Importance: High



In-person early bird registration for the CCP4 Study Weekend 2024 closes today.



Anyone registering for the in-person event after today will not be eligible for 
a standard student bursary and the price for standard delegates increases by 
£50.



In-person registration will close on Monday 4th December 2023.



Virtual registration will still be available after this date.



Regards



Karen McIntyre



CCP4 Project Administrator

CCP4 Equality, Diversity and Inclusion Champion

Member of SCD ED Working Group



Science and Technology Facilities Council

karen.mcint...@stfc.ac.uk

Zoom phone: 01235 44 5790



[cid:image001.png@01DA2463.11ADDC60]



**Hours of work: Monday to Thursday: 8.30am to 1.30pm, Friday 10:30am to 
3.30pm.  Please note that I only work part-time **



From: McIntyre, Karen (STFC,RAL,SC)
Sent: Tuesday, November 21, 2023 10:34 AM
To: 'ccp4bb' mailto:ccp4bb@jiscmail.ac.uk>>; CCP4 WG1 
mailto:ccp4...@listserv.stfc.ac.uk>>; CCP4 WG2 
mailto:ccp4...@listserv.stfc.ac.uk>>; 
'cc...@jiscmail.ac.uk' mailto:cc...@jiscmail.ac.uk>>; 
'c...@jiscmail.ac.uk' mailto:c...@jiscmail.ac.uk>>; 
'pheni...@phenix-online.org' 
mailto:pheni...@phenix-online.org>>; 
'pdbe-api-us...@ebi.ac.uk' 
mailto:pdbe-api-us...@ebi.ac.uk>>
Subject: RE: CCP4 Study Weekend 2024 - Early bird registration including 
standard student bursary deadline EXTENDED TO FRIDAY 24TH NOVEMBER!
Importance: High



The early bird deadline for in-person registration for the CCP4 Study Weekend 
2024 has been extended until Friday 24th November.



Regards



Karen McIntyre



CCP4 Project Administrator

CCP4 Equality, Diversity and Inclusion Champion

Member of SCD ED Working Group



Science and Technology Facilities Council

karen.mcint...@stfc.ac.uk

Zoom phone: 01235 44 5790



[cid:image001.png@01DA2463.11ADDC60]



**Hours of work: Monday to Thursday: 8.30am to 1.30pm, Friday 10:30am to 
3.30pm.  Please note that I only work part-time **



From: McIntyre, Karen (STFC,RAL,SC)
Sent: Friday, November 17, 2023 12:05 PM
To: 'ccp4bb' mailto:ccp4bb@jiscmail.ac.uk>>; CCP4 WG1 
mailto:ccp4...@listserv.stfc.ac.uk>>; CCP4 WG2 
mailto:ccp4...@listserv.stfc.ac.uk>>; 
'cc...@jiscmail.ac.uk' mailto:cc...@jiscmail.ac.uk>>; 
'c...@jiscmail.ac.uk' mailto:c...@jiscmail.ac.uk>>; 
'pheni...@phenix-online.org' 
mailto:pheni...@phenix-online.org>>; 
'pdbe-api-us...@ebi.ac.uk' 
mailto:pdbe-api-us...@ebi.ac.uk>>
Subject: CCP4 Study Weekend 2024 - Early bird registration including standard 
student bursary deadline ends this SUNDAY!
Importance: High



Dear all,



Registration is open for the 2024 CCP4 study weekend entitled "Decision making 
in MX - how to be a productive structural biologist".



Important Key Dates:

* Early bird registration final date: 19 November 2023;

* We have assisted places available for students registering during early bird 
period i.e. now until 19 November - which cover the cost of registration plus 
one night accommodation meaning students only pay for aqdditional nights 
accommodation @ £63 per night;

* Registration for in-person delegates closes 4 December 2023 (or earlier if 
in-person places sell out although you will be able to join the in-person 
waitlist).



This year we are focusing on decision-making in macromolecular crystallography: 
when to use what automated tool, how to interpret the output and when you need 
to get your hands dirty instead. The frontiers of crystallography now involve 
massive multi-crystal and 

[ccp4bb] CCP-EM Spring Symposium - Starts Today

[Tom Burnley - STFC UKRI]

Dear all,


A quick reminder that the CCP-EM Spring Symposium starts today at 1pm (UK) with 
the Diamond Light Source Biological Cryo-imaging User Meeting.


We have some great speakers over the next three days, see the full schedule (UK 
times):

https://www.ccpem.ac.uk/downloads/symposium/ccp-em_symp_schedule_2023.pdf


…if you’d link to attend virtually you can register for free here:

https://www.ccpem.ac.uk/training/spring_symposium_2023/spring_symposium_2023.php


…or you can join directly via Zoom:

http://ukri.zoom.us/j/98084886151


…and join the conversation / ask questions to speakers via Slack:

http://join.slack.com/t/ccpemspringsy-jsv3489/shared_invite/zt-1ti67pc1d-YXNDRxZWcArCOlszvkjYDw


All the best,


Tom




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[ccp4bb] Final Registration - 9th CCP-EM Spring Symposium 25-27th April 2023

[Tom Burnley - STFC UKRI]

Dear all,

Final reminder that registration for the CCP-EM Symposium closes today (Friday 
24th March).

Registration link and more conference details here…

https://www.ccpem.ac.uk/training/spring_symposium_2023/spring_symposium_2023.php

* Applying for a talk
As in previous years we are seeking a number of additional talks selected from 
submitted abstracts.
If interested, please submit a proposed title and abstract during registration 
for consideration by the scientific organisers or submit a talk title and 
abstract (up to 500 words) directly by email to:

ccpemeve...@stfc.ac.uk.

Please also include your name, position, group and institute.  We are 
particularly interested in abstracts with a computational focus e.g. new 
algorithms or methods for the spring symposium. For the BCI user meeting we 
welcome new results that have been made possible by use of eBIC in the last 
12-18 months.  Deadline for abstract submission is Friday 31st March.

* BCI User Survey
Please can all Diamond users of BCI facilities complete the survey by 11th 
April (see link below).  During the user meeting representatives from eBIC, B24 
and the Membrane Protein Lab (MPL) will discuss topics raised in the User 
Survey and welcome your feedback and support:

https://forms.office.com/pages/responsepage.aspx?id=dLonnQABDU2B_x1yja6N9k2iEV9rkoVBsESt7IZg17BUMk9XVzdDTUoyMTJERUg1N1JZUURFRzZKSy4u

All the best from CCP-EM & DLS BCI




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Re: [ccp4bb] 9th CCP-EM Spring Symposium 25-27th April 2023

[Tom Burnley - STFC UKRI]

Dear all,

Bursaries applications - extended deadline - Friday 17th March

We still have a number of bursaries available thanks to our kind sponsors 
(Quantum Detectors, SPT Labtech & Quantifoil, Evotec, Dectris and Thermo Fisher 
Scientific ).  The bursaries can cover accommodation and registration for those 
who need them to attend in person.  So, if you'd like to join the 200+ in 
person delegates but need a hand covering costs do get in touch.

Please can you now send the bursaries applications directly to 
ccpemeve...@stfc.ac.uk (include name/group/position/institute and a short 
justification).

We will confirm bursary awards next week.

All the best from CCP-EM & DLS BCI


From: Collaborative Computational Project in Electron cryo-Microscopy 
 on behalf of Tom Burnley - STFC UKRI 
<740061e4cf9b-dmarc-requ...@jiscmail.ac.uk>
Sent: 10 March 2023 08:59
To: cc...@jiscmail.ac.uk 
Subject: Re: [ccpem] 9th CCP-EM Spring Symposium 25-27th April 2023

Dear all,

Final reminder that the early bird registration for the CCP-EM Symposium closes 
today (Friday 10th March).  After today the registration fees increase.

Registration link and more conference details here…

https://www.ccpem.ac.uk/training/spring_symposium_2023/spring_symposium_2023.php

* Bursaries applications - last call
We have a number of bursaries available thanks to our kind sponsors (Quantum 
Detectors, SPT Labtech & Quantifoil, Evotec, Dectris and Thermo Fisher 
Scientific ).  The bursaries can cover accommodation and registration for those 
who need them to attend in person.  Please submit any bursary requests by the 
end of today (Friday 10th March, see registration site for more details).  We 
will confirm bursary awards next week.

* Applying for a talk
As in previous years we are seeking a number of additional talks selected from 
submitted abstracts.
If interested, please submit a proposed title and abstract during registration 
for consideration by the scientific organisers or submit a talk title and 
abstract (up to 500 words) directly by email to:

ccpemeve...@stfc.ac.uk.

Please also include your name, position, group and institute.  We are 
particularly interested in abstracts with a computational focus e.g. new 
algorithms or methods for the spring symposium. For the BCI user meeting we 
welcome new results that have been made possible by use of eBIC in the last 
12-18 months.

* BCI User Survey
Please can all Diamond users of BCI facilities complete the survey by 11th 
April (see link below).  During the user meeting representatives from eBIC, B24 
and the Membrane Protein Lab (MPL) will discuss topics raised in the User 
Survey and welcome your feedback and support:

https://forms.office.com/pages/responsepage.aspx?id=dLonnQABDU2B_x1yja6N9k2iEV9rkoVBsESt7IZg17BUMk9XVzdDTUoyMTJERUg1N1JZUURFRzZKSy4u

All the best from CCP-EM & DLS BCI


From: Collaborative Computational Project in Electron cryo-Microscopy 
 on behalf of Tom Burnley - STFC UKRI 
<740061e4cf9b-dmarc-requ...@jiscmail.ac.uk>
Sent: 07 March 2023 14:15
To: cc...@jiscmail.ac.uk 
Subject: Re: [ccpem] 9th CCP-EM Spring Symposium 25-27th April 2023

Dear all,

Quick reminder that the early bird registration for the CCP-EM Symposium closes 
this Friday (10th March).  After that the registration fees increase.

Registration link and more conference details here…

https://www.ccpem.ac.uk/training/spring_symposium_2023/spring_symposium_2023.php

Also, we are close to selling out the available accommodation so if you are 
planning on coming in person please register soon.

Finally, we have a number of bursaries available thanks to our kind sponsors 
(Quantum Detectors, SPT Labtech & Quantifoil, Evotec and Thermo Fisher 
Scientific ).  The bursaries can cover accommodation and registration for those 
who need them to attend in person.  Please submit any bursary requests by 
Friday 10th March (see registration site for more details).  We will confirm 
bursary awards next week.

All the best from CCP-EM & DLS BCI


From: Burnley, Tom (STFC,RAL,SC)
Sent: 13 February 2023 13:57
To: ccpem mailing list ; ccpem mailing list 
; 3...@ncmir.ucsd.edu <3...@ncmir.ucsd.edu>
Subject: 9th CCP-EM Spring Symposium 25-27th April 2023

Dear CCP-EM,

We are pleased to announce the 9th Annual CCP-EM Spring Symposium. The 
conference aims to provide a forum to highlight state-of-the-art developments 
in computational cryoEM and related themes, as well as showcasing outstanding 
recent biological applications. We aim to promote an inclusive, friendly 
atmosphere, welcoming those both old and new to the community. Topics include 
instrument technology, sample preparation, image processing, single particle 
reconstruction, tomography and model building.

The meeting also includes the Diamond Light Source Biological Cryo-Imaging User 
Meeting for eBIC & 

Re: [ccp4bb] 9th CCP-EM Spring Symposium 25-27th April 2023

[Tom Burnley - STFC UKRI]

Dear all,

Final reminder that the early bird registration for the CCP-EM Symposium closes 
today (Friday 10th March).  After today the registration fees increase.

Registration link and more conference details here…

https://www.ccpem.ac.uk/training/spring_symposium_2023/spring_symposium_2023.php

* Bursaries applications - last call
We have a number of bursaries available thanks to our kind sponsors (Quantum 
Detectors, SPT Labtech & Quantifoil, Evotec, Dectris and Thermo Fisher 
Scientific ).  The bursaries can cover accommodation and registration for those 
who need them to attend in person.  Please submit any bursary requests by the 
end of today (Friday 10th March, see registration site for more details).  We 
will confirm bursary awards next week.

* Applying for a talk
As in previous years we are seeking a number of additional talks selected from 
submitted abstracts.
If interested, please submit a proposed title and abstract during registration 
for consideration by the scientific organisers or submit a talk title and 
abstract (up to 500 words) directly by email to:

ccpemeve...@stfc.ac.uk.

Please also include your name, position, group and institute.  We are 
particularly interested in abstracts with a computational focus e.g. new 
algorithms or methods for the spring symposium. For the BCI user meeting we 
welcome new results that have been made possible by use of eBIC in the last 
12-18 months.

* BCI User Survey
Please can all Diamond users of BCI facilities complete the survey by 11th 
April (see link below).  During the user meeting representatives from eBIC, B24 
and the Membrane Protein Lab (MPL) will discuss topics raised in the User 
Survey and welcome your feedback and support:

https://forms.office.com/pages/responsepage.aspx?id=dLonnQABDU2B_x1yja6N9k2iEV9rkoVBsESt7IZg17BUMk9XVzdDTUoyMTJERUg1N1JZUURFRzZKSy4u

All the best from CCP-EM & DLS BCI


From: Collaborative Computational Project in Electron cryo-Microscopy 
 on behalf of Tom Burnley - STFC UKRI 
<740061e4cf9b-dmarc-requ...@jiscmail.ac.uk>
Sent: 07 March 2023 14:15
To: cc...@jiscmail.ac.uk 
Subject: Re: [ccpem] 9th CCP-EM Spring Symposium 25-27th April 2023

Dear all,

Quick reminder that the early bird registration for the CCP-EM Symposium closes 
this Friday (10th March).  After that the registration fees increase.

Registration link and more conference details here…

https://www.ccpem.ac.uk/training/spring_symposium_2023/spring_symposium_2023.php

Also, we are close to selling out the available accommodation so if you are 
planning on coming in person please register soon.

Finally, we have a number of bursaries available thanks to our kind sponsors 
(Quantum Detectors, SPT Labtech & Quantifoil, Evotec and Thermo Fisher 
Scientific ).  The bursaries can cover accommodation and registration for those 
who need them to attend in person.  Please submit any bursary requests by 
Friday 10th March (see registration site for more details).  We will confirm 
bursary awards next week.

All the best from CCP-EM & DLS BCI


From: Burnley, Tom (STFC,RAL,SC)
Sent: 13 February 2023 13:57
To: ccpem mailing list ; ccpem mailing list 
; 3...@ncmir.ucsd.edu <3...@ncmir.ucsd.edu>
Subject: 9th CCP-EM Spring Symposium 25-27th April 2023

Dear CCP-EM,

We are pleased to announce the 9th Annual CCP-EM Spring Symposium. The 
conference aims to provide a forum to highlight state-of-the-art developments 
in computational cryoEM and related themes, as well as showcasing outstanding 
recent biological applications. We aim to promote an inclusive, friendly 
atmosphere, welcoming those both old and new to the community. Topics include 
instrument technology, sample preparation, image processing, single particle 
reconstruction, tomography and model building.

The meeting also includes the Diamond Light Source Biological Cryo-Imaging User 
Meeting for eBIC & B24 and two satellite meetings for SPT Labtech & eBIC for 
Industry.

The conference will be held as a hybrid meeting, with the physical event at the 
EMCC in Nottingham, plus virtual access online via Zoom. It is kindly sponsored 
by Quantum Detectors, SPT Labtech & Quantifoil, and Thermo Fisher Scientific.

Registration is open now:
https://cvent.me/5rk8kR

More details and schedule are available here:
https://www.ccpem.ac.uk/training/spring_symposium_2023/spring_symposium_2023.php

Confirmed Symposium speakers include:
Alan Brown (Harvard)
Beatriz Costa Gomes (Turing)
Tristan Croll (Altos)
Ieva Drulyte (TFS)
Rene Frank (Leeds)
Michael Grange (Franklin)
Matt Iadanza (STFC)
Kiarash Jamali (MRC-LMB)
Gerard Kleywegt (EBI)
Sam Lacey (Human Technopole)
Bonnie Murphy (Max Planck)
Randy Read (Cambridge)
Ricardo Righetto (Basel)
Elizabeth Villa (UCSD)* remote
Janet Vonck (Max Planck Biophysics)

Confirmed BCI speakers:
Bridget Carragher (Chan Zuckerberg Imaging Institute)
Victoria Garcia Gi

[ccp4bb] 9th CCP-EM Spring Symposium 25-27th April 2023

[Tom Burnley - STFC UKRI]

Dear all,

We are pleased to announce the 9th Annual CCP-EM Spring Symposium. The 
conference aims to provide a forum to highlight state-of-the-art developments 
in computational cryoEM and related themes, as well as showcasing outstanding 
recent biological applications. We aim to promote an inclusive, friendly 
atmosphere, welcoming those both old and new to the community. Topics include 
instrument technology, sample preparation, image processing, single particle 
reconstruction, tomography and model building.

The meeting also includes the Diamond Light Source Biological Cryo-Imaging User 
Meeting for eBIC & B24 and two satellite meetings for SPT Labtech & eBIC for 
Industry.

The conference will be held as a hybrid meeting, with the physical event at the 
EMCC in Nottingham, plus virtual access online via Zoom. It is kindly sponsored 
by Quantum Detectors, SPT Labtech & Quantifoil, and Thermo Fisher Scientific.

Registration is open now:
https://cvent.me/5rk8kR

More details and schedule are available here:
https://www.ccpem.ac.uk/training/spring_symposium_2023/spring_symposium_2023.php

Confirmed Symposium speakers include:
Alan Brown (Harvard)
Beatriz Costa Gomes (Turing)
Tristan Croll (Altos)
Ieva Drulyte (TFS)
Rene Frank (Leeds)
Michael Grange (Franklin)
Matt Iadanza (STFC)
Kiarash Jamali (MRC-LMB)
Gerard Kleywegt (EBI)
Sam Lacey (Human Technopole)
Bonnie Murphy (Max Planck)
Randy Read (Cambridge)
Ricardo Righetto (Basel)
Elizabeth Villa (UCSD)* remote
Janet Vonck (Max Planck Biophysics)

Confirmed BCI speakers:
Bridget Carragher (Chan Zuckerberg Imaging Institute)
Victoria Garcia Giner (Imperial College London)
Peter Wing (Nuffield Department of Medicine, Oxford)
Elizabeth Wright (UW-Madison)
Plus eBIC user meeting round-table discussion
Symposium scientific organisers:
Vicki Gold (Exeter)
Stephan Meuch (Leeds)

Biological Cryo-Imaging user meeting organising committee:
Lorna Malone (eBIC, Diamond)
Archana Jadhav (B24, Diamond)
Rachel Freeman (Industrial liaison office, Diamond)

Early bird discounted prices are available for the next month and we have a 
limited number of hotel rooms so please register asap.

We look forward to welcoming you all in Nottingham!

Best wishes from CCP-EM & DLS BCI



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[ccp4bb] CCP-EM Spring Symposium VIII 2022 3-5th May 2022

[Tom Burnley - STFC UKRI]

Dear CCP-EM,

CCP-EM are pleased to announce the eighth annual 'CCP-EM Spring Symposium', 
3-5th May 2022.  The conference aims to provide a forum to highlight state of 
the art developments in computational cryoEM and related themes as well as 
showcasing outstanding recent biological applications.  We aim to promote an 
inclusive, friendly atmosphere welcoming both old and new to the community.  
Topics include instrument technology, sample preparation, image processing, 
single particle reconstruction, tomography and model building.  The schedule 
will also include the Diamond Light Source biological cryo-imaging user meeting 
for eBIC & B24.

The conference will be held as a hybrid meeting with the physical event at the 
EMCC in Nottingham and online via Zoom and is kindly sponsored by SPT Labtech 
and Quantifoil.

Registration is open now:
https://cvent.me/449Ozw

More details and schedule are available here:
https://www.ccpem.ac.uk/training/spring_symposium_2022/spring_symposium.php

Confirmed speakers include:
Becky Thompson (Leeds)
Christiane Berger-Schaffitzel (Bristol)
Dari Kimanius (MRC-LMB)
Dorothee Liebschner (Berkeley Lab)
Florian Schur (IST-Austria)
Giulia Zanetti (Birkbeck)
Goedele Maertens (Imperial)
Holger Stark (MPI Biophysical Chemistry)
Katerina Naydenova (MRC-LMB)
Peter Rosenthal (Crick)
Ruben Sanchez-Garcia (Oxford)
Tim Grant (UW-Madison)
Tom Deegan (Edinburgh)
Ulrich Lorenz (EPFL)
Wim Hagen (EMBL)
What’s new at CCP-EM, EBI, RFI and eBIC

Scientific organisers:
Doryen Bubeck (Imperial)
Paula da Fonseca (Glasgow)

Best wishes from the CCP-EM team

This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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[ccp4bb] CCP-EM Spring Symposium Starts Today!

[Tom Burnley - STFC UKRI]

Dear all,

A quick reminder that the CCP-EM Spring Symposium starts today.  Full schedule 
is here:

https://www.ccpem.ac.uk/downloads/symposium/ccp-em_symp_schedule_2021.pdf

and registration is free and open here:

https://ukri.zoom.us/webinar/register/WN_p_s9-m73TnK0VYdjWT1stg

All the best,

Tom

This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses. Opinions, conclusions 
or other information in this message and attachments that are not related 
directly to UKRI business are solely those of the author and do not represent 
the views of UKRI.




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[ccp4bb] CCP-EM Spring Symposium - 20-23th April 2021

[Tom Burnley - STFC UKRI]

Dear all,

A quick reminder that the CCP-EM Spring Symposium will take place online next 
week.

The conference will be held as a Zoom webinar series on 20-23th April 2021 and 
is kindly supported by Quantifoil.  Registration is free and available here:
https://ukri.zoom.us/webinar/register/WN_p_s9-m73TnK0VYdjWT1stg

The full schedule is now available here:
https://www.ccpem.ac.uk/downloads/symposium/ccp-em_symp_schedule_2021.pdf

The Diamond Light Source Biological Cryo-imaging User Meeting for eBIC & B24 
will take place on Tuesday 20th.  This includes the eBIC user meeting in which 
eBIC representatives will discuss topics raised in the eBIC User Survey.  
Feedback is most welcome but do please complete in advance so eBIC staff can 
answer your questions:
https://www.surveymonkey.co.uk/r/JGBJLMS

Confirmed speakers include:
Alberto Bartesaghi (Duke)
Francesca Coscia (Human Technopole)
Hans Elmlund (Monash)
Radoslav Enchev (Crick)
Misha Kudryashev (Max Planck Institute of Biophysics)
Takanori Nakane (MRC-LMB)
Carlos Oscar Sorzano (CSIC)
Lori Passmore (MRC-LMB)
Maya Topf (Birkbeck / CSSB Hamburg)
Matthias Wolf (OIST)
Peijun Zhang (DLS / Oxford)
Ellen Zhong (MIT)
Plus what’s new at CCP-EM, EBI and eBIC

Scientific organisers:
Giulia Zanetti (ISMB Birkbeck College)
Christopher Aylett (Imperial College London)

DLS user meeting confirmed speakers:
Jim Naismith (Rosalind Franklin Institute)
Sjors Scheres (MRC-LMB)

Timings (UK):
20-22 April: 14:00-17:30
23 April: 10:30-15:30

Best wishes from CCP-EM

This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses. Opinions, conclusions 
or other information in this message and attachments that are not related 
directly to UKRI business are solely those of the author and do not represent 
the views of UKRI.




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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

[Tom Burnley - UKRI STFC]

Hi Herman,


Just a couple of tips for Refmac...


1) increase number of cycles - we find some cases require a lot of cycles, more 
than you may be used from MX refinement.


2) optimise weight - this is important and at present the autoweighting option 
is not as reliable for EM refinement as MX.


You could run these in parallel whilst exploring the other very nice tools 
suggested !


Cheers,


Tom


From: CCP4 bulletin board  on behalf of Schreuder, 
Herman /DE 
Sent: 30 July 2020 13:28:00
To: ccp4bb
Subject: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real 
real-space-refinement

Hi everybody,

Thank you very much for the many tips! I discovered that in Coot by clicking on 
the N- and C-terminus of a protein chain, one can indeed run a real-space 
refinement on the complete chain and the same is true for a rigid body fit. 
However, subsequent refinement with Refmac did not converge, so it looks like I 
still have to go manually through the chains. ☹
Still on my to do list are:
- test Isolde
- test Main
- test the wiggle-fit option in Coot.

Although the Refmac procedure consisting of converting the cryo-EM map into 
structure factors and running a "crystallographic" refinement on it seems to 
work, in my opinion the future will be a robust real-space refinement on the 
cryo-EM map itself, instead of a refinement on derived structure factors. 
However, this is my personal opinion.

Best regards,
Herman

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board  Im Auftrag von Tom Burnley - 
UKRI STFC
Gesendet: Mittwoch, 29. Juli 2020 18:51
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

EXTERNAL : Real sender is  owner-ccp...@jiscmail.ac.uk



Hi Herman,


There is lots of information on CCP-EM's modelling tools here:


https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ccpem.ac.uk_training_icknield-5F2019_icknield-5F2019.php=DwIFAg=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=aaxzRy8JT0AM0_MqNvU2fr6IB4wIbkY8SsgvQkYcw_w=D5VOMK2Fz8AOV1PCvJpD9tm914KUxJlsRNRWXYPb7tI=


This includes a tutorial on Refmac.  As you note this is done in reciprocal 
space but the CCP-EM pipeline handles conversions from MRC to MTZ format (and 
runs Refmac via CCP4).


All the best,


Tom


From: CCP4 bulletin board  on behalf of Boaz Shaanan 

Sent: 29 July 2020 16:31:46
To: ccp4bb
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

Hi,
Try searching ccp-em.
Boaz

Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel

On Jul 29, 2020 18:29, "Schreuder, Herman /DE"  
wrote:
Coot does it, but if one wants to do it for a complete protein, it is a lot of 
clicking. On the other hand, I have not tried to just select the N- and 
C-terminus for real-space refinement to see what happens. I would prefer to 
have some script to do it.
Best, Herman

Von: Eleanor Dodson 
Gesendet: Mittwoch, 29. Juli 2020 17:23
An: Schreuder, Herman /DE 
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement


EXTERNAL : Real sender is 
eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>

Wont coot do that?
Eleanor

On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:
Dear BB,

I would like to do a real real-space-refinement of a protein against a cryo-EM 
map; not the mtz-based Refmac approach. A quick internet search produced a lot 
of Phenix hits, but little ccp4 hits. Does somebody know how to do this using 
ccp4 programs, or has someone a Coot script to do this?

Thank you for your help!
Herman



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ht

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

[Tom Burnley - UKRI STFC]

Hi Herman,


There is lots of information on CCP-EM's modelling tools here:


https://www.ccpem.ac.uk/training/icknield_2019/icknield_2019.php


This includes a tutorial on Refmac.  As you note this is done in reciprocal 
space but the CCP-EM pipeline handles conversions from MRC to MTZ format (and 
runs Refmac via CCP4).


All the best,


Tom


From: CCP4 bulletin board  on behalf of Boaz Shaanan 

Sent: 29 July 2020 16:31:46
To: ccp4bb
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

Hi,
Try searching ccp-em.
Boaz

Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel

On Jul 29, 2020 18:29, "Schreuder, Herman /DE"  
wrote:
Coot does it, but if one wants to do it for a complete protein, it is a lot of 
clicking. On the other hand, I have not tried to just select the N- and 
C-terminus for real-space refinement to see what happens. I would prefer to 
have some script to do it.
Best, Herman

Von: Eleanor Dodson 
Gesendet: Mittwoch, 29. Juli 2020 17:23
An: Schreuder, Herman /DE 
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement


EXTERNAL : Real sender is 
eleanor.dod...@york.ac.uk

Wont coot do that?
Eleanor

On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:
Dear BB,

I would like to do a real real-space-refinement of a protein against a cryo-EM 
map; not the mtz-based Refmac approach. A quick internet search produced a lot 
of Phenix hits, but little ccp4 hits. Does somebody know how to do this using 
ccp4 programs, or has someone a Coot script to do this?

Thank you for your help!
Herman



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[ccp4bb] 27th April - 1st May - CCP-EM Spring Symposium // Online

[Tom Burnley - UKRI STFC]

Dear all,

This might be of interest to crystallographers also interested in cryoEM...

We are delighted to announce that we will host an online version of the CCP-EM 
Spring Symposium and Diamond Light Source Biological Cryo-imaging User Meeting 
for eBIC and B24.  Confirmed speakers include:

Chris Russo (MRC-LMB)
Joe Atherton (KCL)
Rouslan Efremov (VIB-VUB Center for Structural Biology)
Vicki Gold (University of Exeter)
Alex Noble (NYSBC)
Dimitry Tegunov (Max Planck Institute for Biophysical Chemistry)
Hongyi Xu (Stockholm University)
Miroslava Schaffer (Max Planck Institute for Biochemistry)

Plus many more great speakers covering all aspects of cryoEM methods.  The full 
schedule can be found here:

https://www.ccpem.ac.uk/training/spring_symposium_2020/spring_symposium.php

The meeting will hosted via Zoom and is free of charge but you will need to 
pre-register here:

https://ukri.zoom.us/webinar/register/WN_7ZSLh1xWQcqjqtIE_I2Sjg

We’d like to encourage audience participation so during the talks please 
suggest questions to the session chair via the Zoom chat function and they will 
field these questions to the speaker at the end of the talk.

We are indebted to the speakers for their kind support in unusual circumstances 
and also the hard work of the Scientific Organisers Helen Saibil (Birkbeck) and 
Christos Savva (Leicester) to put together such a rich programme.  We’d like to 
thank them all for their help!

Best wishes from CCP-EM,

Tom, Colin, Agnel, Jola, Helen and Martyn




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Re: [ccp4bb] Job Posting - Computational Scientist in CCP-EM Core Team

[Tom Burnley - UKRI STFC]

Dear all,


Just a reminder that this Sunday 29th March is the closing date to apply for 
the position below.


All the best and stay safe,

Tom and the rest of the CCP-EM team


From: Burnley, Tom (STFC,RAL,SC)
Sent: 28 February 2020 13:38
To: ccpem mailing list; 3...@ncmir.ucsd.edu; ccp4bb
Subject: Job Posting - Computational Scientist in CCP-EM Core Team


Dear all,

We are recruiting for a new member of the CCP-EM team:

https://www.harwellhub.com/Jobs/2020/February/Computation-Scientist-CCP-EM-Software-Developer-fo

This is a really exciting software development post working in collaboration 
with Sjors Scheres (MRC-LMB, RELION) and Gerard Bricogne (Global Phasing, 
SHARP, BUSTER, autoPROC and STARANISO).

It is an open-ended (i.e. not fixed-term) staff scientist position based in the 
CCP-EM core team at the Rutherford Appleton Laboratory in Oxfordshire, UK.

A detailed description is given in the link above but feel free to contact me 
directly for any further information or informal enquiries.  Closing date is 
Sunday 29th March.

All the best,

Tom and the rest of the CCP-EM team




In collaboration with the Scheres group and Global Phasing we will develop a 
new software framework to combine tools for image processing and 3D volume 
reconstruction in RELION with the existing tools in CCP-EM for model building, 
refinement and validation. This will provide an open API to allow integration 
of third-party algorithms, including software from Global Phasing. This 
pipeline framework will create/enable:

Enhanced on-the-fly processing for use in data acquisition.
Complete data processing pipeline from images to refined atomic models.
Modern and flexible user interface.
Rich metadata capture suitable for internal record keeping, deposition to 
EMDB/PDB, and use in the development of ML-based algorithms.

Specific responsibilities include:

Reviewing existing codebases and investigating use of suitable third-party 
libraries
Designing and implementing new software framework for pipeline
Developing new user interfaces and visualisation tools
Liaising with partners to test framework outputs including: eBIC for on-the-fly 
processing; EBI/EMDB for validation and deposition; STFC Scientific Machine 
Learning Group for use in ML; pharmaceutical licence holders for provision of 
end-to-end pipelines (images to models); Global Phasing for integration of 
external processing routines
Assisting Global Phasing with investigations and implementations of 
Bayesian-based algorithms.

On a day-to-day basis, duties will also include:

Developing and maintaining software architecture
Open communication with collaborators via site visits and video conferencing
Keeping up to date with the latest methodology developments in cryoEM
Presenting work through international meetings and publications.

Please contact Tom Burnley (tom.burn...@stfc.ac.uk) if you have any queries 
about this vacancy.
£38,318 - £46,576/Year

About You

You will be a highly motivated and experienced computational scientist with a 
track record of effective software engineering. Previous experience with Python 
is highly desirable, as is knowledge and experience of cryoEM data processing 
and structural biology.

The post requires extensive interactions with the community of scientists and 
developers, and therefore you need good communication skills and should be 
comfortable making scientific presentations and teaching. This role will also 
require regular travel to other partner sites.






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[ccp4bb] Job Posting - Computational Scientist in CCP-EM Core Team

[Tom Burnley - UKRI STFC]

Dear all,

We are recruiting for a new member of the CCP-EM team:

https://www.harwellhub.com/Jobs/2020/February/Computation-Scientist-CCP-EM-Software-Developer-fo

This is a really exciting software development post working in collaboration 
with Sjors Scheres (MRC-LMB, RELION) and Gerard Bricogne (Global Phasing, 
SHARP, BUSTER, autoPROC and STARANISO).

It is an open-ended (i.e. not fixed-term) staff scientist position based in the 
CCP-EM core team at the Rutherford Appleton Laboratory in Oxfordshire, UK.

A detailed description is given in the link above but feel free to contact me 
directly for any further information or informal enquiries.  Closing date is 
Sunday 29th March.

All the best,

Tom and the rest of the CCP-EM team




In collaboration with the Scheres group and Global Phasing we will develop a 
new software framework to combine tools for image processing and 3D volume 
reconstruction in RELION with the existing tools in CCP-EM for model building, 
refinement and validation. This will provide an open API to allow integration 
of third-party algorithms, including software from Global Phasing. This 
pipeline framework will create/enable:

Enhanced on-the-fly processing for use in data acquisition.
Complete data processing pipeline from images to refined atomic models.
Modern and flexible user interface.
Rich metadata capture suitable for internal record keeping, deposition to 
EMDB/PDB, and use in the development of ML-based algorithms.

Specific responsibilities include:

Reviewing existing codebases and investigating use of suitable third-party 
libraries
Designing and implementing new software framework for pipeline
Developing new user interfaces and visualisation tools
Liaising with partners to test framework outputs including: eBIC for on-the-fly 
processing; EBI/EMDB for validation and deposition; STFC Scientific Machine 
Learning Group for use in ML; pharmaceutical licence holders for provision of 
end-to-end pipelines (images to models); Global Phasing for integration of 
external processing routines
Assisting Global Phasing with investigations and implementations of 
Bayesian-based algorithms.

On a day-to-day basis, duties will also include:

Developing and maintaining software architecture
Open communication with collaborators via site visits and video conferencing
Keeping up to date with the latest methodology developments in cryoEM
Presenting work through international meetings and publications.

Please contact Tom Burnley (tom.burn...@stfc.ac.uk) if you have any queries 
about this vacancy.
£38,318 - £46,576/Year

About You

You will be a highly motivated and experienced computational scientist with a 
track record of effective software engineering. Previous experience with Python 
is highly desirable, as is knowledge and experience of cryoEM data processing 
and structural biology.

The post requires extensive interactions with the community of scientists and 
developers, and therefore you need good communication skills and should be 
comfortable making scientific presentations and teaching. This role will also 
require regular travel to other partner sites.






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[ccp4bb] Last day for early bird registration - CCP-EM Spring Symposium VI - 27-29th April 2020

[Tom Burnley - UKRI STFC]

Dear all,

Final day for CCP-EM Spring Symposium early bird registration!

Last day for early bird registration is today - Friday, 21st February.  After 
that the registration fee will increase!

Full details are available here:

http://www.cvent.com/d/8hqsdb

CCP-EM are proud to announce the sixth annual 'CCP-EM Spring Symposium'.  The 
conference aims to provide a forum to highlight state of the art developments 
in computational cryoEM and related themes as well as showcasing outstanding 
recent biological applications.  We aim to promote an inclusive, friendly 
atmosphere welcoming both old and new to the community.  Topics include 
instrument technology, sample preparation, image processing, single particle 
reconstruction, tomography and model building.  The schedule will also include 
the Diamond Light Source biological cryo-imaging user meeting for eBIC & B24.

The conference will be held 27-29th April 2020 at Nottingham University East 
Midlands Conference Centre.  Please note the change of venue (and caterers!) 
from last year.  Confirmed speakers include:

Gabriel Lander (Scripps)
Chris Russo (MRC-LMB)

Joe Atherton (KCL)
Chris Booth (Gatan)
Chun-wa Chung (GlaxoSmithKline)
Rouslan Efremov (VIB-VUB Center for Structural Biology)
Vicki Gold (University of Exeter)
Jeroen Keizer (Thermo Fisher Scientific)
Greg McMullan (MRC-LMB)
Alex Noble (NYSBC)
Gaia Pigino (Max Planck Institute of Molecular Cell Biology and Genetics)
Miroslava Schaffer (Max Planck Institute of Biochemistry)
Dimitry Tegunov (Max Planck Institute for Biophysical Chemistry)
Hongyi Xu (Stockholm University)

Plus what’s new at CCP-EM, EBI and eBIC

Scientific organisers:
Helen Saibil (Birkbeck)
Christos Savva (University of Leicester)

Best wishes from CCP-EM,

Tom, Colin, Agnel, Jola, Helen and Martyn




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[ccp4bb] CCP-EM Icknield Model Building Workshop - Registration Closes Tomorrow (Friday 21st Feb)

[Tom Burnley - UKRI STFC]

Dear all,

*** Reminder - please note registration closes tomorrow - Friday 21st Feb ***

We are pleased to announce our annual 'Icknield Model Building Workshop' will 
take place 16-20 March at RAL/Diamond Light Source, Oxfordshire, UK

This is a comprehensive course for EM model building covering advanced use of 
ARP/wARP, Buccaneer, CCP-EM, Coot, FlexEM, ISOLDE, LocScale, MolProbity, Refmac 
and new validation tools.  The course is designed such that applicants bring 
their own 'live' high resolution datasets to work on with the developers during 
the workshop.

Full details and registration:

http://www.cvent.com/d/fnqm5n

Confirmed tutors include:

Grzegorz Chojnowski (EMBL)
Tristan Croll (Cambridge)
Kevin Cowtan (York)
Judit Debreczeni (AstraZeneca)
Sony Malhotra (Birkbeck)
Garib Murshudov (MRC-LMB)
Rob Nicholls (MRC-LMB)
Maya Topf (Birkbeck)
Rangana Warshamanage (MRC-LMB)
Arjen Jakobi (TU Delft)
Tom Burnley (CCP-EM)
Agnel Joseph (CCP-EM)

The course will be held at the RAL / Diamond campus, Harwell, UK, site of the 
eBIC national facility.  Registration is £300 and we will provide food and 
accommodation at the Bear Hotel in nearby Wantage for nights of 16th (if 
required), 17th, 18th and 19th March.

The course is best suited for ‘high’ resolution datasets (<4Å) and details of 
the datasets will be asked for during registration (any details provided will 
be treated with absolute confidence).

There is a maximum of 50 places to register interest.  We will select the most 
suitable 20 applicants for each course and the course fees will be requested 
once the application is accepted.

Registration for the workshop will close either when all registration places 
are taken or by 21th Feb.  Successful applications will be informed shortly 
afterwards.

All the best,

Tom




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[ccp4bb] 2 days remaining for early bird registration - CCP-EM Spring Symposium VI - 27-29th April 2020

[Tom Burnley - UKRI STFC]

Dear all,

Two more days left for CCP-EM Spring Symposium early bird registration.

Last day for early bird registration is tomorrow - Friday, 21st February.  
After that the registration fee will increase!

Full details are available here:

http://www.cvent.com/d/8hqsdb

CCP-EM are proud to announce the sixth annual 'CCP-EM Spring Symposium'.  The 
conference aims to provide a forum to highlight state of the art developments 
in computational cryoEM and related themes as well as showcasing outstanding 
recent biological applications.  We aim to promote an inclusive, friendly 
atmosphere welcoming both old and new to the community.  Topics include 
instrument technology, sample preparation, image processing, single particle 
reconstruction, tomography and model building.  The schedule will also include 
the Diamond Light Source biological cryo-imaging user meeting for eBIC & B24.

The conference will be held 27-29th April 2020 at Nottingham University East 
Midlands Conference Centre.  Please note the change of venue (and caterers!) 
from last year.  Confirmed speakers include:

Gabriel Lander (Scripps)
Chris Russo (MRC-LMB)

Joe Atherton (KCL)
Chris Booth (Gatan)
Chun-wa Chung (GlaxoSmithKline)
Rouslan Efremov (VIB-VUB Center for Structural Biology)
Vicki Gold (University of Exeter)
Jeroen Keizer (Thermo Fisher Scientific)
Greg McMullan (MRC-LMB)
Alex Noble (NYSBC)
Gaia Pigino (Max Planck Institute of Molecular Cell Biology and Genetics)
Miroslava Schaffer (Max Planck Institute of Biochemistry)
Dimitry Tegunov (Max Planck Institute for Biophysical Chemistry)
Hongyi Xu (Stockholm University)

Plus what’s new at CCP-EM, EBI and eBIC

Scientific organisers:
Helen Saibil (Birkbeck)
Christos Savva (University of Leicester)

Best wishes from CCP-EM,

Tom, Colin, Agnel, Jola, Helen and Martyn





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[ccp4bb] Early bird registration extended - CCP-EM Spring Symposium VI - 27-29th April 2020

[Tom Burnley - UKRI STFC]

Dear all,

Please note we have extended the early bird registration period for the CCP-EM 
Spring Symposium untill this Friday, 21st February.  After that the 
registration fee will increase!

Full details are available here:

http://www.cvent.com/d/8hqsdb

CCP-EM are proud to announce the sixth annual 'CCP-EM Spring Symposium'.  The 
conference aims to provide a forum to highlight state of the art developments 
in computational cryoEM and related themes as well as showcasing outstanding 
recent biological applications.  We aim to promote an inclusive, friendly 
atmosphere welcoming both old and new to the community.  Topics include 
instrument technology, sample preparation, image processing, single particle 
reconstruction, tomography and model building.  The schedule will also include 
the Diamond Light Source biological cryo-imaging user meeting for eBIC & B24.

The conference will be held 27-29th April 2020 at Nottingham University East 
Midlands Conference Centre.  Please note the change of venue (and caterers!) 
from last year.  Confirmed speakers include:

Gabriel Lander (Scripps)
Chris Russo (MRC-LMB)

Joe Atherton (KCL)
Chris Booth (Gatan)
Chun-wa Chung (GlaxoSmithKline)
Rouslan Efremov (VIB-VUB Center for Structural Biology)
Vicki Gold (University of Exeter)
Jeroen Keizer (Thermo Fisher Scientific)
Greg McMullan (MRC-LMB)
Alex Noble (NYSBC)
Gaia Pigino (Max Planck Institute of Molecular Cell Biology and Genetics)
Miroslava Schaffer (Max Planck Institute of Biochemistry)
Dimitry Tegunov (Max Planck Institute for Biophysical Chemistry)
Hongyi Xu (Stockholm University)

Plus what’s new at CCP-EM, EBI and eBIC

Scientific organisers:
Helen Saibil (Birkbeck)
Christos Savva (University of Leicester)

Best wishes from CCP-EM,

Tom, Colin, Agnel, Jola, Helen and Martyn





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[ccp4bb] CCP-EM Icknield Model Building Workshop

[Tom Burnley - UKRI STFC]

Dear all,

We are pleased to announce our annual 'Icknield Model Building Workshop' will 
take place 16-20 March at RAL/Diamond Light Source, Oxfordshire, UK

This is a comprehensive course for EM model building covering advanced use of 
ARP/wARP, Buccaneer, CCP-EM, Coot, FlexEM, ISOLDE, LocScale, MolProbity, Refmac 
and new validation tools.  The course is designed such that applicants bring 
their own 'live' high resolution datasets to work on with the developers during 
the workshop.

Full details and registration:

http://www.cvent.com/d/fnqm5n

Confirmed tutors include:

Grzegorz Chojnowski (EMBL)
Tristan Croll (Cambridge)
Kevin Cowtan (York)
Judit Debreczeni (AstraZeneca)
Sony Malhotra (Birkbeck)
Garib Murshudov (MRC-LMB)
Rob Nicholls (MRC-LMB)
Maya Topf (Birkbeck)
Rangana Warshamanage (MRC-LMB)
Arjen Jakobi (TU Delft)
Tom Burnley (CCP-EM)
Agnel Joseph (CCP-EM)

The course will be held at the RAL / Diamond campus, Harwell, UK, site of the 
eBIC national facility.  Registration is £300 and we will provide food and 
accommodation at the Bear Hotel in nearby Wantage for nights of 16th (if 
required), 17th, 18th and 19th March.

The course is best suited for ‘high’ resolution datasets (<4Å) and details of 
the datasets will be asked for during registration (any details provided will 
be treated with absolute confidence).

There is a maximum of 50 places to register interest.  We will select the most 
suitable 20 applicants for each course and the course fees will be requested 
once the application is accepted.

Registration for the workshop will close either when all registration places 
are taken or by 21th Feb.  Successful applications will be informed shortly 
afterwards.

All the best,

Tom




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[ccp4bb] Registration Open - CCP-EM Spring Symposium VI - 27-29th April 2020

[Tom Burnley - UKRI STFC]

Dear all,

Registration is now open for the CCP-EM Spring Symposium and full details are 
available here:

http://www.cvent.com/d/8hqsdb

CCP-EM are proud to announce the sixth annual 'CCP-EM Spring Symposium'.  The 
conference aims to provide a forum to highlight state of the art developments 
in computational cryoEM and related themes as well as showcasing outstanding 
recent biological applications.  We aim to promote an inclusive, friendly 
atmosphere welcoming both old and new to the community.  Topics include 
instrument technology, sample preparation, image processing, single particle 
reconstruction, tomography and model building.  The schedule will also include 
the Diamond Light Source biological cryo-imaging user meeting for eBIC & B24.

The conference will be held 27-29th April 2020 at Nottingham University East 
Midlands Conference Centre.  Please note the change of venue (and caterers!) 
from last year.  Confirmed speakers include:

Gabriel Lander (Scripps)
Chris Russo (MRC-LMB)

Joe Atherton (KCL)
Chris Booth (Gatan)
Chun-wa Chung (GlaxoSmithKline)
Rouslan Efremov (VIB-VUB Center for Structural Biology)
Vicki Gold (University of Exeter)
Jeroen Keizer (Thermo Fisher Scientific)
Greg McMullan (MRC-LMB)
Alex Noble (NYSBC)
Gaia Pigino (Max Planck Institute of Molecular Cell Biology and Genetics)
Miroslava Schaffer (Max Planck Institute of Biochemistry)
Dimitry Tegunov (Max Planck Institute for Biophysical Chemistry)
Hongyi Xu (Stockholm University)

Plus what’s new at CCP-EM, EBI and eBIC

Scientific organisers:
Helen Saibil (Birkbeck)
Christos Savva (University of Leicester)

** Finally please note the reduced early bird registration fee available until 
Friday 14th February. **

Best wishes from CCP-EM,

Tom, Colin, Agnel, Jola, Helen and Martyn
_




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[ccp4bb] Save the date - CCP-EM Spring Symposium VI - 27-29th April 2020

[Tom Burnley - UKRI STFC]

Save the date - CCP-EM Spring Symposium - 27-29th April 2020

*** Registration will open soon ***

CCP-EM are proud to announce the sixth annual 'CCP-EM Spring Symposium'.  The 
conference aims to provide a forum to highlight state of the art developments 
in computational cryoEM and related themes as well as showcasing outstanding 
recent biological applications.  We aim to promote an inclusive, friendly 
atmosphere welcoming both old and new to the community.  Topics include 
instrument technology, sample preparation, image processing, single particle 
reconstruction, tomography and model building.  The schedule will also include 
the Diamond Light Source biological cryo-imaging user meeting for eBIC & B24.

The conference will be held 27-29th April 2020 at Nottingham University East 
Midlands Conference Centre (note change of venue from last year).  Confirmed 
speakers include:

Gabriel Lander (Scripps)
Chris Russo (MRC-LMB)

Joe Atherton (Birkbeck)
Chris Booth (Gatan)
Chun-wa Chung (GlaxoSmithKline)
Rouslan Efremov (VIB-VUB Center for Structural Biology)
Vicki Gold (University of Exeter)
Jeroen Keizer (Thermo Fisher Scientific)
Greg McMullan (MRC-LMB)
Alex Noble (NYSBC)
Gaia Pigino (Max Planck Institute of Molecular Cell Biology and Genetics)
Miroslava Schaffer (Max Planck Institute of Biochemistry)
Dimitry Tegunov (Max Planck Institute for Biophysical Chemistry)
Hongyi Xu (Stockholm University)

Plus what’s new at CCP-EM, EBI and eBIC

Scientific organisers:
Helen Saibil (Birkbeck)
Christos Savva (University of Leicester)

Best wishes from CCP-EM,

Tom, Colin, Agnel, Jola, Helen and Martyn





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[ccp4bb] CCP-EM Spring Symposium - *Final Day* for Registration (Friday 29th March)

[Tom Burnley - UKRI STFC]

Dear all,

Just a quick final reminder that registration for the Spring Symposium closes 
today Friday (29th March).

Full details and talk titles can be found here:

http://www.cvent.com/d/xbqsqk

The Spring Symposium aims to provide a forum to highlight state of the art 
developments in computational cryo-EM and related themes as well as showcasing 
outstanding recent applications. We aim to promote an inclusive, friendly 
atmosphere welcoming both old and new to the community and there is the 
opportunity to present your work via a poster or a selected talk.

Topics include instrument technology, sample preparation, image processing, 
single particle reconstruction, tomography and model building.

The conference will be held 29th April - 1st May at the University of 
Nottingham, UK & the first day (29th April) will include the Biological 
Cryo-imaging User Meeting for eBIC & B24.

Confirmed speakers & talk titles include:

John Rubinstein (University of Toronto) - CryoEM for scarce and unstable 
membrane protein complexes
Sjors Scheres (MRC-LMB) - Developments in RELION-3

David Bhella (University of Glasgow) - The Scottish Centre for Macromolecular 
Imaging - early adopters of the JEOL CryoARM300
Thomas Braun (University of Basel) - TBC
Doryen Bubeck (Imperial College London) - CryoEM of the membrane attack complex 
reveals how proteins cross lipid bilayers
Felix Weis (EMBL) - How to get the maximum out of your cryo-EM data collection 
session
Wanda Kukulski (MRC-LMB) - Cellular membrane architectures studied by 
correlative microscopy and electron cryo-tomography
Stephen Muench (University of Leeds) - New approaches to grid preparation in 
cryo Electron Microscopy
Stefan Pfeffer (University of Heidelberg) - Structural insights into the 
co-translational machinery for protein folding and maturation
Shaun Rawson (Harvard Medical School) - Rapid evaluation of EM datasets
Sonja Welsch (Thermo Fisher Scientific) - News on Thermo Fisher Scientific’s 
2019 developments for cryoTEM
Pamela Williams (Astex Pharmaceuticals) - TBC

Michele Darrow (TTP Labtech) - Chameleon: Next Generation Sample Preparation 
for CryoEM based on Spotiton
Giulia Weissenberger (CryoSol) - VitroJet: Next Generation Sample Preparation 
for cryo-EM

Plus: what's new at CCP-EM, EBI and eBIC, and selected talks from submitted 
abstracts.

Scientific organisers:
John Briggs (MRC-LMB)
Rebecca Thompson (University of Leeds)

Registration site:
http://www.cvent.com/d/xbqsqk

Registration fees:
PI/Industrial: £225.00
Student/PostDoc: £175.00

We have also ensured reasonably priced accommodation is available from 
Nottingham University (£60/room/night; available on registration).

We hope to see you there!

Best wishes,

Tom, Colin and the rest of the CCP-EM team





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[ccp4bb] CCP-EM Spring Symposium - registration closes this Friday (29th March)

[Tom Burnley - UKRI STFC]

Dear all,

Just a quick reminder that registration for the Spring Symposium will close 
this Friday (29th March).

Full details and talk titles can be found here:

http://www.cvent.com/d/xbqsqk

The Spring Symposium aims to provide a forum to highlight state of the art 
developments in computational cryo-EM and related themes as well as showcasing 
outstanding recent applications. We aim to promote an inclusive, friendly 
atmosphere welcoming both old and new to the community and there is the 
opportunity to present your work via a poster or a selected talk.

Topics include instrument technology, sample preparation, image processing, 
single particle reconstruction, tomography and model building.

The conference will be held 29th April - 1st May at the University of 
Nottingham, UK & the first day (29th April) will include the Biological 
Cryo-imaging User Meeting for eBIC & B24.

Confirmed speakers & talk titles include:

John Rubinstein (University of Toronto) - CryoEM for scarce and unstable 
membrane protein complexes
Sjors Scheres (MRC-LMB) - Developments in RELION-3

David Bhella (University of Glasgow) - The Scottish Centre for Macromolecular 
Imaging - early adopters of the JEOL CryoARM300
Thomas Braun (University of Basel) - TBC
Doryen Bubeck (Imperial College London) - CryoEM of the membrane attack complex 
reveals how proteins cross lipid bilayers
Felix Weis (EMBL) - How to get the maximum out of your cryo-EM data collection 
session
Wanda Kukulski (MRC-LMB) - Cellular membrane architectures studied by 
correlative microscopy and electron cryo-tomography
Stephen Muench (University of Leeds) - New approaches to grid preparation in 
cryo Electron Microscopy
Stefan Pfeffer (University of Heidelberg) - Structural insights into the 
co-translational machinery for protein folding and maturation
Shaun Rawson (Harvard Medical School) - Rapid evaluation of EM datasets
Sonja Welsch (Thermo Fisher Scientific) - News on Thermo Fisher Scientific’s 
2019 developments for cryoTEM
Pamela Williams (Astex Pharmaceuticals) - TBC

Michele Darrow (TTP Labtech) - Chameleon: Next Generation Sample Preparation 
for CryoEM based on Spotiton
Giulia Weissenberger (CryoSol) - VitroJet: Next Generation Sample Preparation 
for cryo-EM

Plus: what's new at CCP-EM, EBI and eBIC, and selected talks from submitted 
abstracts.

Scientific organisers:
John Briggs (MRC-LMB)
Rebecca Thompson (University of Leeds)

Registration site:
http://www.cvent.com/d/xbqsqk

Registration fees:
PI/Industrial: £225.00
Student/PostDoc: £175.00

We have also ensured reasonably priced accommodation is available from 
Nottingham University (£60/room/night; available on registration).

We hope to see you there!

Best wishes,

Tom, Colin and the rest of the CCP-EM team




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Re: [ccp4bb] Some kind of bug, Can't perform invert selection through file menu in subset selection for micrographs

[Tom Burnley - UKRI STFC]

Dear Suchi,


For questions on Relion (and other EM related things) best to try the CCP-EM 
mailing list (and whilst your reposting I'll try and reproduce your bug on my 
mac ):


https://www.jiscmail.ac.uk/CCPEM

Best wishes,


Tom


From: CCP4 bulletin board  on behalf of Suchi Goel 

Sent: 27 March 2019 02:49:24
To: ccp4bb
Subject: [ccp4bb] Some kind of bug, Can't perform invert selection through file 
menu in subset selection for micrographs

[Screen Shot 2019-03-27 at 11.45.21.png]
[Screen Shot 2019-03-27 at 11.42.19.png]Hi Everyone,

I work on imac and I am kind of stuck at the stage where I want to optimize FOM 
for autopicking. I tried to select subset of micrographs as manual suggested 
but the file tab does not show invert selection to only select a few later. I 
can't unselect all the micrographs already ticked for selection. Could someone 
suggest any fix to that. Pics attached above.

Best Regards,
Suchi Goel



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[ccp4bb] Abstract Registration Deadline Today - CCP-EM Spring Symposium: 29 April - 1 May Nottingham University

[Tom Burnley - UKRI STFC]

Dear all,

A quick reminder that today is the last day to register an abstract for the 
selected talks.  If you are interested and haven't registered for the Symposium 
please see here for full details:

http://www.cvent.com/d/xbqsqk

If you have already registered but haven't submitted an abstract yet you can 
update your application via the 'Already Registered' link on the Cvent site 
above.

Best wishes,

Tom, Colin and the rest of the CCP-EM team


---



We are pleased to announce that registration is now open for the fifth annual 
CCP-EM Spring Symposium. Sign up on the event website before 25 January for an 
Early Bird discount:

http://www.cvent.com/d/xbqsqk

The Spring Symposium aims to provide a forum to highlight state of the art 
developments in computational cryo-EM and related themes as well as showcasing 
outstanding recent applications. We aim to promote an inclusive, friendly 
atmosphere welcoming both old and new to the community and there is the 
opportunity to present your work via a poster or a selected talk.

Topics include instrument technology, sample preparation, image processing, 
single particle reconstruction, tomography and model building.

The conference will be held 29th April - 1st May at the University of 
Nottingham, UK. A provisional programme is available on the event website.

Confirmed speakers include:

John Rubinstein (University of Toronto)
Sjors Scheres (MRC-LMB)

David Bhella (University of Glasgow)
Thomas Braun (University of Basel)
Doryen Bubeck (Imperial College London)
Wim Hagen (EMBL)
Wanda Kukulski (MRC-LMB)
Stephen Muench (University of Leeds)
Stefan Pfeffer (University of Heidelberg)
Shaun Rawson (Harvard Medical School)
Sonja Welsch (Thermo Fisher Scientific)
Pamela Williams (Astex Pharmaceuticals)

Michele Darrow (TTP Labtech)
Giulia Weissenberger (CryoSol)

Plus: what's new at CCP-EM, EBI and eBIC

Scientific organisers:

John Briggs (MRC-LMB)
Rebecca Thompson (University of Leeds)

Registration site:
http://www.cvent.com/d/xbqsqk

Registration fees:
PI/Industrial: £225.00 (Early Bird price £175.00 before 25 Jan)
Student/PostDoc: £175.00 (Early Bird price £125.00 before 25 Jan)

We have also ensured reasonably priced accommodation is available from 
Nottingham University (£60/room/night; available on registration).


We hope to see you there!

Best wishes,

Colin, Tom and the rest of the CCP-EM team





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[ccp4bb] CCP-EM Madrid and Icknield High Resolution EM Model Building & Validation Workshops

[Tom Burnley - UKRI STFC]

Dear all,

There are still some places left for our two model building workshops.  Please 
note deadline for applications is tomorrow (14th Feb).

(1) Introduction to model building and refinement using cryo-EM maps.
14-15 March CNIO, Madrid

Introduction to atomic model building using EM data.  This 2 day course with 
provide lectures and tutorials covering the basics of atomic modeling with 
CCP-EM, Coot, Refmac, LocScale, Coot & Scipion.

Speakers/tutors include:
Tom Burnley (STFC), Jose María Carazo (CNB-CSIC), Ana Casañal (MRC-LMB), Paul 
Emsley (MRC-LMB), Wojtek Galej (EMBL), Arjen Jakobi (TU Delft), Rob Nichols 
(MRC-LMB), Colin Palmer (STFC).

Full details and registration:
http://www.cvent.com/d/p6qmqf

(2) Icknield Model Building Workshop
15-18 April RAL/Diamond Light Source, Oxfordshire, UK

This is a comprehensive course for EM model building covering advanced use of 
ARP/wARP Buccaneer, CCP-EM, Coot, FlexEM, ISOLDE, LocScale, MolProbity, Refmac. 
 The course is designed such that applicants bring their own 'live' high 
resolution datasets to work on with the developers during the workshop.

Tutors and topics include:

Tristan Croll (Cambridge)
ISOLDE: Interactive model building/real-space refinement based on interactive 
Molecular Dynamics

Grzegorz Chojnowski (Lamzin group, EMBL)
ARP/wARP: Automated model building of protein structures

Kevin Cowtan (York)
Buccaneer: Automated model building

Paul Emsley (MRC-LMB Cambridge)
Judit Debreczeni (AstraZeneca)
Coot: Macromolecular model building, model completion and validation

Arjen Jakobi (TU Delft)
LocScale: reference-based density scaling for local sharpening of cryo-EM maps

Jane Richardson (Duke)
MolProbity: All-atom structure validation

Garib Murshudov (MRC-LMB Cambridge)
Rangana Warshamanage (MRC-LMB)
Refmac: Refinement of high-resolution EM structures

Osman Salih (EBI)
EMBD: Deposition in EMBD

Agnel Joseph (CCP-EM, STFC) & Sony Malhotra (Topf Group, Birkbeck)
FlexEM: Fitting and refinement of atomic structures guided by cryoEM density

Full details and registration:
http://www.cvent.com/d/46qmq3

Please apply to course you think most relevant to you (email 
tom.burn...@stfc.ac.uk if unsure).  Each course has a maximum of 40 places to 
register interest.  We will select the most suitable 20 for each course and the 
course fees will be requested if your application is accepted.

Registration for each workshop will close either when all registration places 
are taken or by 14th Feb.  Successful applications will be informed shortly 
afterwards.  Any project details provided will be treated with strict 
confidence.

All the best,

Tom, Colin and Rafa




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[ccp4bb] CCP-EM RELION 3 Image Processing Workshops 18th & 19th February 2019

[Tom Burnley - UKRI STFC]

For EM curious crystallographers we are running an introduction to Relion for 
EM image processing...


Dear all,


We are pleased to announce two one-day workshops introducing the basics of 
RELION 3 led by developer and structural biologist Rafael Fernandez-Leiro 
(Spanish National Cancer Centre, Madrid) and assisted by Joshua Lobo 
(eBIC/Diamond) and the CCP-EM team. It is organised by CCP-EM and hosted at 
Diamond Light Source on the Rutherford Appleton Laboratory campus (directions).

The workshops will involve a hands-on tutorial of RELION 3 for cryo-EM 
single-particle analysis (http://www2.mrc-lmb.cam.ac.uk/relion). It will 
encompassing all stages of the pipeline encompassing micrograph inspection, CTF 
estimation, (automated) particle picking, 2D and 3D classification, 3D 
high-resolution refinement, movie-processing and map sharpening (see e.g. A 
pipeline approach to single-particle processing in RELION, R Fernandez-Leiro & 
S Scheres, doi: 10.1107/S2059798316019276).

Note that this is a one day course and we will repeat the contents on each day.

Registration of interest closes on the 22nd January and places will be 
confirmed shortly afterwards.

Registration site:
http://www.cvent.com/d/sbqy1j

All the best,

Tom, Colin and the rest of the CCP-EM team





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[ccp4bb] Job Opening - Computational Scientist - STFC / CCP-EM

[Tom Burnley - UKRI STFC]

Dear all,

We are seeking a computational scientist, focusing on the application of 
machine learning to cryoEM.

This permintant position will be embedded in a new team in the Scientific 
Computing Department of STFC and based at the Rutherford Appleton Laboratory in 
Oxfordshire, UK, home to the Diamond Light Source, the ISIS Neutron and Muon 
Source and the Central Laser Facility.  The team will consistent of several 
developers who will apply machine learning to scientific data across multiple 
domains.  The EM specific role will be guided by CCP-EM and will work closely 
with the national EM facility (eBIC / DLS).  For informal enquiries please 
contact myself: Tom Burnley (tom.burn...@stfc.ac.uk) or Martyn Winn 
(martyn.w...@stfc.ac.uk).

All the best,

Tom

Job description:

This opening is a great opportunity that combines two of the most exciting 
subjects in life science: Machine Learning (ML) and cryo-electron microscopy 
(cryoEM).  Following recent progress in electron cryo-microscopy (cryo-EM), as 
recognised by the 2017 Nobel Prize in Chemistry, it is now possible to 
determine structures of biological macromolecules in atomic detail from images 
of molecules in frozen solution. This revolution has led to major investments 
in cryoEM, including at the Electron Bio-Imaging Centre (eBIC) at Diamond on 
the Harwell campus. Such facilities are generating large amounts of data daily, 
and the bottleneck has moved to data processing. At the same time, AI and 
machine learning techniques are coming of age, and promising fast and reliable 
data-driven analysis of data.

STFC have created the Scientific Machine Learning (SciML) group to focus 
efforts on applying the latest AI and machine learning techniques to large 
experimental datasets. This role, one of several being created in the SciML 
group, will develop and apply advanced data analytical techniques to cryoEM 
datasets, in close collaboration with eBIC.

Further details and application:

https://www.nature.com/naturejobs/science/jobs/650553-computational-scientist

http://www.topcareer.jobs/Vacancy/irc245954_8504.aspx



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[ccp4bb] CCP-EM Spring Symposium - Live Stream

[Tom Burnley - UKRI STFC]

Dear all,

If you are interested in cryoEM The CCP-EM Spring Symposium is now live.  The 
meeting is similar in style and content to the CCP4 Study Weekend.

You can watch talks live using:

https://livestream.com/accounts/9771311/events/8144974

The full schedule is here:

http://www.ccpem.ac.uk/downloads/symposium/schedule_2018.pdf

Speakers include:
Mark Basham (Diamond)
Sacha de Carlo (Dectris)
Ana Casanal (MRC-LMB)
Peter Cherepanov (Crick Institute)
Paul Emsley (MRC-LMB)
Hans-Werner Fink (Zurich University)
Tim Gruene (Paul Scherrer Institut)
Nicola Guerrini (STFC)
Ben Himes (Janelia)
Arjen Jakobi (TU Delft)
Corinne Smith (University of Warwick)
Carlos Oscar Sanchez Sorzano (CSIC Madrid)
Chris Russo (MRC-LMB)
Beata Turonova (EMBL)
Giulia Zanetti (Birkbeck)
Kai Zhang (MRC-LMB)
Xiaodong Zhang (Imperial)

Best wishes,

CCP-EM team

[ccp4bb] CCP-EM: Instruct Workshop for High Resolution Model Building and Refinement (4th Icknield)

[Tom Burnley]

Dear all,

Further to lasts week message...:

1) Mea culpa... to my shame I forget to include 'Instruct' in the title of
the workshop.  They are kindly supporting this workshop.

2) Places to register interest are filling up rapidly so if you would like
to come please register soon:

cvent.com/d/btq6g6

This course is aimed at structural biologists with high resolution EM maps
ready for / in the process of model building and refinement. This four day
course (1st-4th May) will host some of the leading software developers and
provide ample contact time to allow delegates to discuss their data in
detail alongside traditional lectures and tutorials. It will cover all
aspects of model building including: map optimisation, docking, automated
model building, medium resolution refinement, high resolution refinement,
interactive refinement, validation and deposition.

The course will be held at the RAL / Diamond Campus, Harwell, UK, site of
the eBIC national facility. Registration is free and we will provide food
and three nights accommodation at the Bear Hotel in nearby Wantage (nights
of 1st, 2nd and 3rd May). Please note that during the application process
you will be asked if you would like to make an accommodation request - if
you would like accommodation provided for you free of charge please select
yes and let us know which nights you would like. If you do not want
accommodation provided for you please select no. Delegates are asked to
meet their own travel costs. Please see the agenda for full course times.

The course is limited to 20 delegates who will be selected from all
applicants.  A maximum of 50 applicants can register interest.

Applications will close on ***Wednesday 28th March*** and the 20 successful
applicants will be informed the following day. Please note the short
registration time as we would like to strongly encourage applicants to work
on 'live' datasets.

* Registration site
cvent.com/d/btq6g6

* Confirmed tutors / topics:

Tristan Croll (Cambridge)
ISOLDE: Interactive model building/real-space refinement based on
interactive molecular dynamics

Kevin Cowtan (York)
Buccaneer: automated model building

Paul Emsley (MRC-LMB Cambridge)
Coot: macromolecular model building, model completion and validation

Arjen Jakobi (Delft)
LocScale: scaling tool using prior model information to improve map
contrast

Oleg Kovalevskiy (Murshudov group, MRC-LMB Cambridge)
Refmac: refinement of high-resolution EM structures

Ardan Patwardhan (EBI)
EMBD: deposition in EMBD

Joerg Schaarschmidt (Bonvin Group, Utrecht)
Powerfit: Fast and sensitive rigid-body fitting into cryo-EM density maps

Maya Topf (Birkbeck)
FlexEM: fitting and refinement of atomic structures guided by cryoEM density


Best wishes,

Tom



-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em <https://twitter.com/ccp_em>* | *www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] Subject: CCP-EM Icknield Workshop for High Resolution Model Building and Refinement - Registration Open

[Tom Burnley]

Dear all,

We are proud to announce the 2018 Icknield Workshop kindly supported by
Instruct. This course is aimed at structural biologists with high
resolution EM maps ready for / in the process of model building and
refinement. This four day course (1st-4th May) will host some of the
leading software developers and provide ample contact time to allow
delegates to discuss their data in detail alongside traditional lectures
and tutorials. It will cover all aspects of model building including: map
optimisation, docking, automated model building, medium resolution
refinement, high resolution refinement, interactive refinement, validation
and deposition.

The course will be held at the RAL / Diamond Campus, Harwell, UK, site of
the eBIC national facility. Registration is free, thanks to generous
funding from Instruct, and we will provide food and three nights
accommodation at the Bear Hotel in nearby Wantage (nights of 1st, 2nd and
3rd May). Please note that during the application process you will be asked
if you would like to make an accommodation request - if you would like
accommodation provided for you free of charge please select yes and let us
know which nights you would like. If you do not want accommodation provided
for you please select no. Delegates are asked to meet their own travel
costs. Please see the agenda for full course times.

The course is limited to 20 delegates who will be selected from all
applicants.  A maximum of 50 applicants can register interest.

Applications will close on ***Wednesday 28th March*** and the 20 successful
applicants will be informed the following day. Please note the short
registration time as we would like to strongly encourage applicants to work
on 'live' datasets.

* Registration site:
cvent.com/d/btq6g6

* Confirmed tutors / topics:

Tristan Croll (Cambridge)
ISOLDE: Interactive model building/real-space refinement based on
interactive molecular dynamics

Kevin Cowtan (York)
Buccaneer: automated model building

Paul Emsley (MRC-LMB Cambridge)
Coot: macromolecular model building, model completion and validation

Arjen Jakobi (Delft)
LocScale: scaling tool using prior model information to improve map
contrast

Oleg Kovalevskiy (Murshudov group, MRC-LMB Cambridge)
Refmac: refinement of high-resolution EM structures

Ardan Patwardhan (EBI)
EMBD: deposition in EMBD

Joerg Schaarschmidt (Bonvin Group, Utrecht)
Powerfit: Fast and sensitive rigid-body fitting into cryo-EM density maps

Maya Topf (Birkbeck)
FlexEM: fitting and refinement of atomic structures guided by cryoEM density


Best wishes,

Tom and the CCP-EM team


-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em <https://twitter.com/ccp_em>* | *www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] CCP-EM Spring Symposium IV: 11-12th April 2018 - Registration now closes Wed 7th March

[Tom Burnley]

Dear all,

Due to the recent bad weather we have extended the registration period for
the Spring Symposium: it will now close this Wednesday (7th March).  Please
do register by then if you would to attend:

http://www.cvent.com/d/9tq4ln

This conference aims to provide a forum to highlight state of the art
developments in computational cryoEM and related themes as well as
showcasing outstanding recent applications. We promote an inclusive,
friendly atmosphere welcoming both old and new to the community. Topics
range from detector developments, image processing, single particle
reconstruction, high resolution model building & validation, machine
learning, tomography and electron diffraction.

The conference will be held 11-12th April at Keele University 2018
conference centre. Confirmed speakers include:

Mark Basham (Diamond)
SuRVoS: software for volume segmentation.
https://diamondlightsource.github.io/SuRVoS/

Sacha de Carlo (Dectris)
Detector technologies for high-resolution TEMs.

Ana Casanal (MRC-LMB)
Architecture of eukaryotic mRNA 3′-end processing machinery.
http://science.sciencemag.org/content/358/6366/1056.full

Peter Cherepanov (Crick Institute)
A supramolecular assembly mediates lentiviral DNA integration.
http://science.sciencemag.org/content/355/6320/93.long

Paul Emsley (MRC-LMB)
Coot model-building.
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

Hans-Werner Fink (Zurich University)
“Holography with Low-Energy Electrons: a Tool for Single Molecule
Structural Biology.”
http://www.pnas.org/content/114/7/1474

Achilleas Frangakis (Goethe University Frankfurt)
“Image reconstruction and reliability algorithms for electron tomography.”

Tim Gruene (Paul Scherrer Institut)
"Collecting Diffraction Data with an Electron Microscope."

Nicola Guerrini (STFC)
Direct electron detector development at STFC from the Falcon and beyond.

Ben Himes (Janelia)
emClarity: software for sub-tomogram alignment and classification for
hetrogeneous specimens.
https://www.biorxiv.org/content/early/2017/12/08/231605

Arjen Jakobi (TU Delft)
“Improving density interpretation by local sharpening of cryo-EM density
maps.”
https://git.embl.de/jakobi/LocScale https://elifesciences
.org/articles/27131

Corinne Smith (University of Warwick)
"Defining clathrin cage interactions using high resolution cryoEM."

Carlos Oscar Sanchez Sorzano (CSIC Madrid)
"Complex Image Processing Workflows and High resolution reconstructions
using Scipion."
http://scipion.i2pc.es/

Chris Russo (MRC-LMB)
Ewald sphere correction using a single side-band image processing
algorithm.
https://www.sciencedirect.com/science/article/pii/S030439911730431X
Charge accumulation in electron cryomicroscopy.
https://www.sciencedirect.com/science/article/pii/S0304399117304291
Microscopic charge fluctuations cause minimal contrast loss in cryoEM.
https://www.sciencedirect.com/science/article/pii/S0304399117304308

Beata Turonova (EMBL)
Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF
improves subtomogram averaging resolution to 3.4 Å.
https://doi.org/10.1016/j.jsb.2017.07.007

Giulia Zanetti (Birkbeck)
"Coat protein complexes studied by cryo-tomography and sub-tomogram
averaging."

Kai Zhang (MRC-LMB)
Gctf: real-time CTF determination and correction.
https://dx.doi.org/10.1016%2Fj.jsb.2015.11.003

Xiaodong Zhang (Imperial)
"High resolution complexes determined by SPR EM." [Final title to be
confirmed.]

Plus what's new at CCP-EM, EBI and eBIC

Registrations close Friday 2nd March.

Registration site:
http://www.cvent.com/d/9tq4ln

Registration fees:
PI/Industrial: £175.00
Student/PostDoc: £100.00

We have also ensured reasonably priced accommodation is available from Keele
University (£70/room/night; available on registration).

Best wishes,

Tom, Helen, Colin & Martyn


-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em <https://twitter.com/ccp_em>* | *www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] CCP-EM Spring Symposium IV: 11-12th April 2018 - Registration closes this week

[Tom Burnley]

Dear all,

Reminder for CCP-EM Spring Symposium... registration closes this Friday
(2nd March).

This conference aims to provide a forum to highlight state of the art
developments in computational cryoEM and related themes as well as
showcasing outstanding recent applications. We promote an inclusive,
friendly atmosphere welcoming both old and new to the community. Topics
range from detector developments, image processing, single particle
reconstruction, high resolution model building & validation, machine
learning, tomography and electron diffraction.

The conference will be held 11-12th April at Keele University 2018
conference centre. Confirmed speakers include:

Mark Basham (Diamond)
SuRVoS: software for volume segmentation.
https://diamondlightsource.github.io/SuRVoS/

Sacha de Carlo (Dectris)
Detector technologies for high-resolution TEMs.

Ana Casanal (MRC-LMB)
Architecture of eukaryotic mRNA 3′-end processing machinery.
http://science.sciencemag.org/content/358/6366/1056.full

Peter Cherepanov (Crick Institute)
A supramolecular assembly mediates lentiviral DNA integration.
http://science.sciencemag.org/content/355/6320/93.long

Paul Emsley (MRC-LMB)
Coot model-building.
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

Hans-Werner Fink (Zurich University)
“Holography with Low-Energy Electrons: a Tool for Single Molecule
Structural Biology.”
http://www.pnas.org/content/114/7/1474

Achilleas Frangakis (Goethe University Frankfurt)
“Image reconstruction and reliability algorithms for electron tomography.”

Tim Gruene (Paul Scherrer Institut)
"Collecting Diffraction Data with an Electron Microscope."

Nicola Guerrini (STFC)
Direct electron detector development at STFC from the Falcon and beyond.

Ben Himes (Janelia)
emClarity: software for sub-tomogram alignment and classification for
hetrogeneous specimens.
https://www.biorxiv.org/content/early/2017/12/08/231605

Arjen Jakobi (TU Delft)
“Improving density interpretation by local sharpening of cryo-EM density
maps.”
https://git.embl.de/jakobi/LocScale https://elifesciences
.org/articles/27131

Corinne Smith (University of Warwick)
"Defining clathrin cage interactions using high resolution cryoEM."

Carlos Oscar Sanchez Sorzano (CSIC Madrid)
"Complex Image Processing Workflows and High resolution reconstructions
using Scipion."
http://scipion.i2pc.es/

Chris Russo (MRC-LMB)
Ewald sphere correction using a single side-band image processing
algorithm.
https://www.sciencedirect.com/science/article/pii/S030439911730431X
Charge accumulation in electron cryomicroscopy.
https://www.sciencedirect.com/science/article/pii/S0304399117304291
Microscopic charge fluctuations cause minimal contrast loss in cryoEM.
https://www.sciencedirect.com/science/article/pii/S0304399117304308

Beata Turonova (EMBL)
Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF
improves subtomogram averaging resolution to 3.4 Å.
https://doi.org/10.1016/j.jsb.2017.07.007

Giulia Zanetti (Birkbeck)
"Coat protein complexes studied by cryo-tomography and sub-tomogram
averaging."

Kai Zhang (MRC-LMB)
Gctf: real-time CTF determination and correction.
https://dx.doi.org/10.1016%2Fj.jsb.2015.11.003

Xiaodong Zhang (Imperial)
"High resolution complexes determined by SPR EM." [Final title to be
confirmed.]

Plus what's new at CCP-EM, EBI and eBIC

Registrations close Friday 2nd March.

Registration site:
http://www.cvent.com/d/9tq4ln

Registration fees:
PI/Industrial: £175.00
Student/PostDoc: £100.00

We have also ensured reasonably priced accommodation is available from Keele
University (£70/room/night; available on registration).

Best wishes,

Tom, Helen, Colin & Martyn


-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em <https://twitter.com/ccp_em>* | *www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] CCP-EM Spring Symposium IV: 11-12th April 2018 Keele University

[Tom Burnley]

Dear all,

Reminder for CCP-EM Spring Symposium.  Similar to CCP4 Study Weekend
this conference
aims to provide a forum to highlight state of the art developments in
computational cryoEM and related themes as well as showcasing outstanding
recent applications. We promote an inclusive, friendly atmosphere welcoming
both old and new to the community. Topics range from detector developments,
image processing, single particle reconstruction, high resolution model
building & validation, machine learning, tomography and electron
diffraction.

The conference will be held 11-12th April at Keele University 2018
conference centre. Confirmed speakers include:

Mark Basham (Diamond)
SuRVoS: software for volume segmentation.
https://diamondlightsource.github.io/SuRVoS/

Sacha de Carlo (Dectris)
Detector technologies for high-resolution TEMs.

Ana Casanal (MRC-LMB)
Architecture of eukaryotic mRNA 3′-end processing machinery.
http://science.sciencemag.org/content/358/6366/1056.full

Peter Cherepanov (Crick Institute)
A supramolecular assembly mediates lentiviral DNA integration.
http://science.sciencemag.org/content/355/6320/93.long

Paul Emsley (MRC-LMB)
Coot model-building for cryoEM.
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

Hans-Werner Fink (Zurich University)
“Holography with Low-Energy Electrons: a Tool for Single Molecule
Structural Biology.”
http://www.pnas.org/content/114/7/1474

Achilleas Frangakis (Goethe University Frankfurt)
“Image reconstruction and reliability algorithms for electron tomography.”

Tim Gruene (Paul Scherrer Institut)
"Collecting Diffraction Data with an Electron Microscope."

Nicola Guerrini (STFC)
Direct electron detector development at STFC from the Falcon and beyond.

Ben Himes (Janelia)
emClarity: software for sub-tomogram alignment and classification for
hetrogeneous specimens.
https://www.biorxiv.org/content/early/2017/12/08/231605

Arjen Jakobi (TU Delft)
“Improving density interpretation by local sharpening of cryo-EM density
maps.”
https://git.embl.de/jakobi/LocScale https://elifesciences.org/articles/27131


Corinne Smith (University of Warwick)
High resolution cryo-electron microscopy of clathrin cage networks.

Carlos Oscar Sanchez Sorzano (CSIC Madrid)
"Complex Image Processing Workflows and High resolution reconstructions
using Scipion."
http://scipion.i2pc.es/

Chris Russo (MRC-LMB)
Ewald sphere correction using a single side-band image processing
algorithm.
https://www.sciencedirect.com/science/article/pii/S030439911730431X
Charge accumulation in electron cryomicroscopy.
https://www.sciencedirect.com/science/article/pii/S0304399117304291
Microscopic charge fluctuations cause minimal contrast loss in cryoEM.
https://www.sciencedirect.com/science/article/pii/S0304399117304308

Beata Turonova (EMBL)
Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF
improves subtomogram averaging resolution to 3.4 Å.
https://doi.org/10.1016/j.jsb.2017.07.007

Giulia Zanetti (Birkbeck)
Cryo-EM Structure of a Relaxase Reveals the Molecular Basis of DNA
Unwinding during Bacterial Conjugation.
http://www.cell.com/cell/abstract/S0092-8674(17)30423-3

Kai Zhang (MRC-LMB)
Gctf: real-time CTF determination and correction.
https://dx.doi.org/10.1016%2Fj.jsb.2015.11.003

Xiaodong Zhang (Imperial)
Cryo-EM structures of the human INO80 chromatin-remodeling complex.
doi:10.1038/s41594-017-0003-7

Registration site:

http://www.cvent.com/d/9tq4ln
Registration fees:
PI/Industrial: £175.00
Student/PostDoc: £100.00

We have also ensured reasonably priced accomodation is available from Keele
University (£70/room/night; available on registration).

Best wishes,

Tom, Helen, Colin & Martyn

-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em <https://twitter.com/ccp_em>* | *www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] CCP-EM Spring Symposium IV: 11-12th April 2018 Keele University

[Tom Burnley]

Dear all,

We are very pleased to announce the fourth annual 'CCP-EM Spring
Symposium'.

The conference aims to provide a forum to highlight state of the art
developments in computational cryoEM and related themes as well as
showcasing outstanding recent applications. We promote an inclusive,
friendly atmosphere welcoming both old and new to the community. Topics
range from detector developments, image processing, single particle
reconstruction, high resolution model building & validation, machine
learning, tomography and electron diffraction.

The conference will be held 11-12th April at Keele University 2018
conference centre. Confirmed speakers include:

Mark Basham (Diamond)
Sacha de Carlo (Dectris)
Ana Casanal (MRC-LMB)
Peter Cherepanov (Crick Institute)
Paul Emsley (MRC-LMB)
Hans-Werner Fink (Zurich University)
Achilleas Frangakis (Goethe University Frankfurt)
Tim Gruene (Paul Scherrer Institut)
Nicola Guerrini (STFC)
Ben Himes (Janelia)
Arjen Jakobi (TU Delft)
Corinne Smith (University of Warwick)
Carlos Oscar Sanchez Sorzano (CSIC Madrid)
Chris Russo (MRC-LMB)
Beata Turonova (EMBL)
Giulia Zanetti (Birkbeck)
Kai Zhang (MRC-LMB)
Xiaodong Zhang (Imperial)

Registration site:

http://www.cvent.com/d/9tq4ln

Registration fees:
PI/Industrial: £175.00
Student/PostDoc: £100.00

We have also ensured reasonably priced accomodation is available from Keele
University (£70/room/night; available on registration).

Best wishes,

Tom, Helen, Colin & Martyn


-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em <https://twitter.com/ccp_em>* | *www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] Wellcome Trust postdoctoral fellowships available at the University of Oxford

[Tom Burnley]

Dear all,


Posted on behalf of Peijun Zhang...



THREE Wellcome Trust funded postdoctoral fellowships are available in
Peijun Zhang lab at the University of Oxford (https://www.ndm.ox.ac.uk/prin
cipal-investigators/researcher/peijun-zhang
<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ndm.ox.ac.uk%2Fprincipal-investigators%2Fresearcher%2Fpeijun-zhang=01%7C01%7Cpez7%40pitt.edu%7Cb5bf8d1aa6c348f9127008d4d0742b70%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1=ULgsh5XjsMz4y5LImz3X0EN89enjgb7ds1DVDtHaGMg%3D=0>
):



1) Structural mechanisms of HIV-1 restriction by capsid-sensing host
proteins;

2) Correlative cryo super-resolution fluorescence microscopy and cryoET of
HIV-1 and host interactions;

3) Structural mechanism of HIV-1 inhibition by SERINCs;



Zhang lab combines structural methodologies, in particular cryoEM and
cryoET, with biochemistry and functional studies, in conjunction with
molecular-dynamics simulations, to gain new insights into the mechanisms of
HIV-1 inhibition by host cell factors. The Division of Structural Biology
in Oxford has excellent facilities for molecular and cellular cryoEM/ET and
state-of-the-art cryo-fluorescence microscopy and high performance
computing. We are also closely connected to the UK national cryoEM center,
eBIC at the Diamond Light Source (http://www.diamond.ac.uk/Scie
nce/Integrated-facilities/eBIC.html
<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.diamond.ac.uk%2FScience%2FIntegrated-facilities%2FeBIC.html=01%7C01%7Cpez7%40pitt.edu%7Cb5bf8d1aa6c348f9127008d4d0742b70%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1=sYj49Dkc12YQQvPH1zoNhPnjOgOhAyniq5EUVLBk3E8%3D=0>
).



You must be highly motivated, hold a PhD in biophysics/structural biology
or equivalent, and have a demonstrated track record in conducting high
quality original research. Knowledge in cryoEM/ET and protein biochemistry,
and experience in structural biology (posts 1&3), or live-cell fluorescence
microscopy (posts 2&3) are essential.



Online applications are open (*closing date: 07-Aug-2017*)



Postdoctoral Research Fellow in HIV-host interactions

https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec
_version_4.jobspec?p_id=129294
<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.recruit.ox.ac.uk%2Fpls%2Fhrisliverecruit%2Ferq_jobspec_version_4.jobspec%3Fp_id%3D129294=01%7C01%7Cpez7%40pitt.edu%7Cb5bf8d1aa6c348f9127008d4d0742b70%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1=sT4JJOiSDVex7gGX9EnLvjXpZ2U7vF%2B%2Fcbmnyyg%2FjQY%3D=0>



Postdoctoral Research Fellow in Correlative Microscopy

https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec
_version_4.jobspec?p_id=129296
<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.recruit.ox.ac.uk%2Fpls%2Fhrisliverecruit%2Ferq_jobspec_version_4.jobspec%3Fp_id%3D129296=01%7C01%7Cpez7%40pitt.edu%7Cb5bf8d1aa6c348f9127008d4d0742b70%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1=gfvHXZVpgGsNkIJB8iQCI4lwhLPzFlQgNnqzvy6EhnM%3D=0>



Postdoctoral Research Scientist  in STRUBI

https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec
_version_4.jobspec?p_id=129709
<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.recruit.ox.ac.uk%2Fpls%2Fhrisliverecruit%2Ferq_jobspec_version_4.jobspec%3Fp_id%3D129709=01%7C01%7Cpez7%40pitt.edu%7Cb5bf8d1aa6c348f9127008d4d0742b70%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1=4eVdI5%2B%2Fpg%2F1ronNHYaLpyyP5ytOd5o7OuWFC5e2ivc%3D=0>



For details, please contact Peijun Zhang at pei...@strubi.ox.ac.uk



Best wishes,

Peijun

--

Peijun Zhang, PhD

Wellcome Trust Investigator

Division of Structural Biology

Wellcome Trust Centre for Human Genetics

University of Oxford

Roosevelt Drive Oxford OX3 7BN, UK

pei...@strubi.ox.ac.uk

http://www.ndm.ox.ac.uk/principal-investigators/researcher/peijun-zhang
<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ndm.ox.ac.uk%2Fprincipal-investigators%2Fresearcher%2Fpeijun-zhang=01%7C01%7Cpez7%40pitt.edu%7Cb5bf8d1aa6c348f9127008d4d0742b70%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1=owLm4ypxAZwVQdDEzm48lRRQa1%2BeG%2FD8V4U%2BJz3l4Gw%3D=0>



eBIC Director,

Diamond Light Source, UK

http://www.diamond.ac.uk/Science/Integrated-facilities/eBIC.html
<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.diamond.ac.uk%2FScience%2FIntegrated-facilities%2FeBIC.html=01%7C01%7Cpez7%40pitt.edu%7Cb5bf8d1aa6c348f9127008d4d0742b70%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1=sYj49Dkc12YQQvPH1zoNhPnjOgOhAyniq5EUVLBk3E8%3D=0>



-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em <https://twitter.com/ccp_em>* | *www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] position available: Centre Coordinator at eBIC, Diamond Light Source

[Tom Burnley]

Posted on behalf of Peijun Zhang...

Dear all,

I would like to draw your attention to the Centre Co-ordinator position
available at the UK National CryoEM Center (eBIC), Diamond Light Source.
Please see the following links for detail.

http://www.diamond.ac.uk/Careers/Vacancies/All/061-17-CH.html
https://www.nature.com/naturejobs/science/jobs/619081-senior-support-scientist-centre-co-ordinator

Best regards,

Peijun


-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em <https://twitter.com/ccp_em>* | *www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

Re: [ccp4bb] ccp4i2 crashes on start

[Tom Burnley]

One possible source of the problem that we've come across before... ensure
the follow environment variable isn't set:

QT_PLUGIN_PATH

Best wishes,

Tom

On 4 July 2017 at 14:55, Stuart McNicholas <stuart.mcnicho...@york.ac.uk>
wrote:

> Dear Johannes,
>Many apologies, this behaviour should certainly not be expected. The
> cause could be quite difficult to determine, I shall start by installing a
> Ubuntu virtualbox myself.
>
> Best wishes,
> Stuart
>
> On 4 July 2017 at 13:46, Johannes Cramer <johannes.cra...@gmail.com>
> wrote:
>
>> Dear CCP4 bb,
>>
>> I would like to use ccp4i2, but every time I try to start it via command
>> line, I get the following error message:
>>
>> Running CCP4i2 browser from: /home/cramejo/programs/ccp4-7.0/share/ccp4i2
>>> Python 2.7.10 (default, Aug 28 2015, 12:10:46)
>>> [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
>>> Qt version 4.8.7
>>>
>>> 440 367
>>> Segmentation fault (core dumped)
>>
>>
>> Has anyone experienced this behavior? How (where) can I get a more
>> detailed log file? ccp4i (old GUI) works perfectly fine, but the session
>> log that is accessible via the interface is only valid for the current
>> session.
>> I am running 64 bit Kubuntu 10.16 on a windows host virtualbox.
>>
>> Cheers,
>> Johannes
>>
>
>


-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em <https://twitter.com/ccp_em>* | *www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] Joint CCP-EM & CCP-BioSim Workshop on EM & MD @University of Leeds

[Tom Burnley]

Just a reminder that there are still places available...

We are proud to announce a pair of workshops held at the University of
Leeds exploring the crossover between EM and MD.

http://www.ccpem.ac.uk/training/leeds_em_md_2017/leeds_em_md.php

(1) Computation for Biomolecular Cryo-Electron Microscopy and Tomography
Sarah Harris (CCP-BioSim/Physics, Leeds), Albert Solernou (Physics/Leeds)
and Ste Muench (Biological Sciences, Leeds), Tom Burnley (CCP-EM/STFC)

CCPBioSim-EM Workshop (14th July): Structural characterisation of proteins
and protein complexes by cryo-EM and cryo-ET is now providing access to a
wide range of macromolecular assemblies that were inaccessible by X-ray
crystallography or NMR. Although EM analysis can provide information on
different conformational states, it is still an averaging technique and
therefore highly dynamic regions can be difficult to resolve. This
workshop will
explore the emerging computational techniques for achieving biological
understanding from cryo-EM/ET images, and discuss areas most in need of
further development.  Confirmed speakers include:

Christiane Berger-Schaffitzel, University of Bristol
Christian Blau (Lindahl Group, Stockholm University)
Max Bonomi (Vendruscolo Group), Univeristy of Cambridge
Tom Burnley, CCP-EM / STFC
Jose-Maria Carazo, National Center for Biotechnology, Spain
Tristan Croll, Univeristy of Cambridge
Sarah Harris, University of Leeds
Agnel Joseph (Topf Group), Birkbeck
Elena Orlova, Birkbeck

Registration:
https://eventbooking.stfc.ac.uk/news-events/computation-for-biomolecular-
cryo-electron-microscopy-and-tomography-workshop-380

(2) FFEA Workshop (13th July): This will be a hands-on workshop on the new
software tool Fluctuating Finite Element Analysis (FFEA), which calculates
dynamic trajectories for flexible biomolecules directly from cryo-EM/ET
density maps. FFEA aims to provide an equivalent simulation tool for the
EMDB as atomistic MD simulations have for the PDB. This approach uniquely
uses volumetric meshes rather than atomistic co-ordinates as input such
that it can model protein dynamics, protein-protein interactions,
conformational switching between known configurational states and can be
mapped back to atomistic co-ordinates, where these are available. This
workshop is ideal for biomolecular simulators who would like to make full
use of cryo-EM data in their modelling, or for experimentalists who would
like to gain new theoretical insight into the dynamic behaviour of the
structures they observe.

Registration:
https://eventbooking.stfc.ac.uk/news-events/ffea-practical-workshop-381

Best wishes,

Tom

[ccp4bb] Two postdoc positions available at eBIC

[Tom Burnley]

Posted on behalf of Peijun Zhang...

Dear All,

Two postdoc positions are open at eBIC, the UK national cryoEM center at
Diamond Light Source. For further information about these positions, please
contact: Peijun Zhang Tel: +44 (0) 1235 77 8878 (office), E-mail:
peijun.zh...@diamond.ac.uk.

 1. Cryo super-resolution Correlative Microscopy

We are seeking a highly motivated PDRA to carry out his/her own innovative
research by developing and applying an integrative correlative microscopy
workflow to address biological questions. The post holder will use cryo-SIM
at B24 beamline (and further develop other means of) cryo super-resolution
optical microscopy, with a Scios cryoFIB/SEM instrument and Titan Krios
microscopes at Diamond, and set up novel experiments to push the boundaries
of correlative microscopy. Important studies will be the investigation of
pathogen and host cell interactions. In addition, the successful candidate
will play an active role to assist users with their experiments in eBIC.

The post holder should have a PhD degree in structural biology or
biophysics and have a demonstrated record of accomplishment in conducting
high quality original research. Knowledge at postgraduate level in
cryoEM/ET is essential and experience in fluorescence microscopy and live
cell imaging is desirable.

For further information and to apply, please click ‘apply’ below or follow
this link:

http://www.diamond.ac.uk/Careers/Vacancies/All/062_17_CH.html



2. CryoEM Method Development

We are seeking a highly motivated PDRA to develop and apply new cryoEM
sample preparation methods. This position will allow using picolitre volume
dispenser to make cryoEM specimen fast and reliably. Obtaining suitable
cryoEM samples for high-resolution structural determination is currently
one of the main bottlenecks in cryoEM. In addition, the successful
candidate will play an active role in assisting users with their
experiments at eBIC.

The post holder should have a PhD degree in physics/biophysics or
engineering and have a demonstrated record of accomplishment in conducting
high quality original research.

For further information and to apply, please click ‘apply’ below or follow
this link:

http://www.diamond.ac.uk/Careers/Vacancies/All/063_17_CH.html

eBIC (electron Bio-Imaging Centre) at Diamond Light Source provides
scientists with state-of-the-art experimental equipment and expertise in
the field of cryo-electron microscopy, for single particle analysis and
cryo-tomography. Funded by the Wellcome Trust with the UK Medical Research
and Biotechnology and Biology Research Councils, eBIC is a UK National
Centre for cryo-electron microscopy in the life sciences and is currently
the largest centre of its kind worldwide, hosting four Titan Krios, a Talos
Arctica and a Scios instruments.  (
http://www.diamond.ac.uk/Science/Integrated-facilities/eBIC.html).
--
Peijun Zhang, PhD
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive Oxford OX3 7BN, UK
pei...@strubi.ox.ac.uk
http://www.ndm.ox.ac.uk/principal-investigators/researcher/peijun-zhang

eBIC Director,
Diamond Light Source, UK
http://www.diamond.ac.uk/Science/Integrated-facilities/eBIC.html

-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em | www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

Re: [ccp4bb] Using Coot and CCP4 program for cryoEM data

[Tom Burnley]

Hi,

CCP-EM (CCP4 sister project for cryoEM) can help you here.  We have a EM
specific interface for several CCP4 programs as well as some others and
will handle map to mtz conversions for you.

You can download the suite here:
http://www.ccpem.ac.uk/download.php

We recently ran a workshop on high resolution modelling building and the
course material may be useful for you:
http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

Finally we also have an EM mailing list:
https://www.jiscmail.ac.uk/ccpem

All the best,

Tom

On 17 May 2017 at 17:24, MyeongSeon Lee <
0e01bd27cd0f-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi, all.
>
> I have collected cryoEM data and want to use Coot and CCP4 program to
> build model and to refine it.
>
> 1. What is the steps to do this?
> 2. How do I convert cryoEM map file to MTZ file?
> 3. Can I also use Phenix for this purpose?
>
> Thanks to all for your help in advance.
>

[ccp4bb] Joint CCP-EM & CCP-BioSim Workshop on EM & MD @University of Leeds

[Tom Burnley]

We are proud to announce a pair of workshops held at the University of
Leeds exploring the crossover between EM and MD.

http://www.ccpem.ac.uk/training/leeds_em_md_2017/leeds_em_md.php

(1) Computation for Biomolecular Cryo-Electron Microscopy and Tomography
Sarah Harris (CCP-BioSim/Physics, Leeds), Albert Solernou (Physics/Leeds)
and Ste Muench (Biological Sciences, Leeds), Tom Burnley (CCP-EM/STFC)

CCPBioSim-EM Workshop (14th July): Structural characterisation of proteins
and protein complexes by cryo-EM and cryo-ET is now providing access to a
wide range of macromolecular assemblies that were inaccessible by X-ray
crystallography or NMR. Although EM analysis can provide information on
different conformational states, it is still an averaging technique and
therefore highly dynamic regions can be difficult to resolve. This workshop
will explore the emerging computational techniques for achieving biological
understanding from cryo-EM/ET images, and discuss areas most in need of
further development.  Confirmed speakers include:

Christiane Berger-Schaffitzel, University of Bristol
Christian Blau (Lindahl Group, Stockholm University)
Max Bonomi (Vendruscolo Group), Univeristy of Cambridge
Tom Burnley, CCP-EM / STFC
Jose-Maria Carazo, National Center for Biotechnology, Spain
Tristan Croll, Univeristy of Cambridge
Sarah Harris, University of Leeds
Agnel Joseph (Topf Group), Birkbeck
Elena Orlova, Birkbeck

Registration:
https://eventbooking.stfc.ac.uk/news-events/computation-for-biomolecular-cryo-electron-microscopy-and-tomography-workshop-380

(2) FFEA Workshop (13th July): This will be a hands-on workshop on the new
software tool Fluctuating Finite Element Analysis (FFEA), which calculates
dynamic trajectories for flexible biomolecules directly from cryo-EM/ET
density maps. FFEA aims to provide an equivalent simulation tool for the
EMDB as atomistic MD simulations have for the PDB. This approach uniquely
uses volumetric meshes rather than atomistic co-ordinates as input such
that it can model protein dynamics, protein-protein interactions,
conformational switching between known configurational states and can be
mapped back to atomistic co-ordinates, where these are available. This
workshop is ideal for biomolecular simulators who would like to make full
use of cryo-EM data in their modelling, or for experimentalists who would
like to gain new theoretical insight into the dynamic behaviour of the
structures they observe.

Registration:
https://eventbooking.stfc.ac.uk/news-events/ffea-practical-workshop-381

Best wishes,

Tom

-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em | www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] PhD studentship on cryoEM data analysis

[Tom Burnley]

Posted on behalf of Peijun and Kevin:

Dear All,

A joint PhD studentship between Diamond Light Source and University of York
is available to Develop tools to automatically assess the quality and
resolution of cryoEM reconstructions. Please see the link below for
detailed information and how to apply.

http://www.diamond.ac.uk/Careers/Studentships/untitled0.html

Informal enquiries may be addressed to either supervisor:

Peijun Zhang, peijun.zh...@diamond.ac.uk, Diamond Light Source
Kevin Cowtan, kevin.cow...@york.ac.uk, University of York

-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em | www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] CCP-EM Icknield Workshop for High Resolution Model Building - 2017

[Tom Burnley]

Dear all,

We are proud to announce the 2017 Icknield Workshop.  This course is aimed
at structural biologists with high resolution EM maps ready for / in the
process of modelling building and refinement.  This three day course will
host some of the leading software developers and provide ample contact time
to allow delegates to discuss their data in detail alongside traditional
lectures and tutorials.

The course will be held at the RAL / Diamond campus, Harwell, UK.
Registration is free and we will provide food and two nights accommodation
at the Bear Hotel in nearby Wantage (5th & 6th April).  Delegates are asked
to meet their own travel costs.

The course is limited to 20 delegates which will be selected from all
applicants.  A maximum of 40 applicants can register interest.

Applications will close on Sunday 12th March and the 20 successful
applicants will be by Tuesday 14th March.  (Please note the short
registration time as we would like to work on 'live' datasets).

* Confirmed tutors:
Kevin Cowtan (Buccaneer, York)
Paul Emsley (Coot, MRC-LMB Cambridge)
Garib Murshudov (Refmac5, MRC-LMB Cambridge)
Maya Topf (FlexEM, Birkbeck)
Ardan Patwardhan (EMBD, EBI)

* Registration:
https://eventbooking.stfc.ac.uk/news-events/icknield-workshop-376

Best wishes,

Tom

-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em <https://twitter.com/ccp_em>* | *www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] eBIC and CCP-EM Spring Symposia

[Tom Burnley]

Dear all,

eBIC and CCP-EM are proud to announce the inaugural symposium of eBIC, the
UK national cryoEM centre at Diamond Light Source, and the third CCP-EM
Spring Symposium on April 24–26, 2017. This three day conference will be
held at the Diamond/RAL Campus, Harwell, Oxfordshire.

The eBIC opening symposium will be on the first day, highlighting the
advances of cryoEM and feature presentations with an emphasis on emerging
and challenging technologies, followed by CCP-EM featuring of
state-of-the-art presentations related to cryo-EM methods and applications.
Confirmed speakers include:

eBIC Speakers:
Yifan Cheng, UCSF School of Medicine
John Briggs, MRC Laboratory of Molecular Biology
Lori Passmore, MRC Laboratory of Molecular Biology
Radostin Danev Max Planck Institute of Biochemistry
Greg McMullan, MRC Laboratory of Molecular Biology
Sharon Wolf, Weizmann Institute of Science

CCP-EM Speakers:
Piet Gros, Utrecht University
Maya Topf, Birkbeck / UCL
David Waterman, STFC
Tanmay Bharat,  MRC Laboratory of Molecular Biology / University of Oxford
Paul Adams, Lawrence Berkeley National Laboratory
Tristan Croll, University of Cambridge
Erik Lindahl, SciLifeLab
Kay Grunewald, STRUBI
Carolyn Moores, Birkbeck / UCL
Morgan Beeby, Imperial College London
Rob Nicholls,  MRC Laboratory of Molecular Biology
Ausra Domanska, University of Helsinki
Becky Thompson, University of Leeds

Full details and registration for the conference is provided here:

http://www.ccpem.ac.uk/training/spring_symposium_2017/spring_symposium.php
http://www.diamond.ac.uk/Home/Events/2017/eBIC-CCP-EM-Symposium.html

Places are limited and registration will be on a first come first serve
basis.

We look forward to seeing you in April,

Peijun, Tom & Colin and the rest of the eBIC and CCP-EM teams

http://www.diamond.ac.uk/Science/Integrated-facilities/eBIC.html
http://www.ccpem.ac.uk/


-- 


Dr Tom Burnley, PhD
CCP-EM | @ccp_em | www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

Re: [ccp4bb] Cryo-EM

[Tom Burnley]

Hi Faisal,

* This is a good introduction for a non-microscopist:
Cryo-electron microscopy--a primer for the non-microscopist.
Milne JL1, Borgnia MJ, Bartesaghi A, Tran EE, Earl LA, Schauder DM, Lengyel
J, Pierson J, Patwardhan A, Subramaniam S.
http://www.ncbi.nlm.nih.gov/pubmed/23181775

* A recent review:
How cryo-EM is revolutionizing structural biology
Xiao-chen Bai, Greg McMullan, Sjors H.W Scheres
http://www.sciencedirect.com/science/article/pii/S096800041400187X

* For background theory this is good place to start:
Structural Analysis of Macromolecular Assemblies by Electron Microscopy
E. V. Orlova and H. R. Saibil
http://people.cryst.bbk.ac.uk/~ubcg16z/chemrevsmallfigs.pdf

* And for tools for high-resolution modelling building:
Tools for macromolecular model building and refinement into electron
cryo-microscopy
reconstructions
Alan Brown, Fei Long, Robert A. Nicholls, Jaan Toots, Paul Emsley and Garib
Murshudov
http://www.ncbi.nlm.nih.gov/pubmed/25615868

Folmer beat me to it (thanks!).  Please have a look at http://www.ccpem.ac.
uk/ and subscribe to our mailing list:
https://www.jiscmail.ac.uk/ccpem

All the best,

Tom

On 19 May 2015 at 08:04, Folmer Fredslund folm...@gmail.com wrote:

 Hi Faisal,

 I guess a start for you would be to go here:
 http://www.ccpem.ac.uk/
 and subscribe to that mailing list :-)

 Best regards,
 Folmer

 2015-05-19 9:01 GMT+02:00 Faisal Tarique faisaltari...@gmail.com:

 Hi everyone

 A bit off topic..but..I request you to please suggest me some good
 readings related to Cryo-EM..

 Thanx in advance

 --
 Regards

 Faisal
 School of Life Sciences
 JNU




 --
 Folmer Fredslund




-- 
Dr Tom Burnley, PhD
CCP-EM
Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] CCP-EM Spring Symposium

[Tom Burnley]

CCP-EM are proud to announce the inaugural 'CCP-EM Spring Symposium'. This
two day conference will be held at the site of the new National UK Electron
Bio-Imaging Facility on the Harwell Campus, Oxfordshire on the 28-29th May
2015. The theme of the conference is a celebration of the upcoming
facility, the initial alpha release of the CCP-EM software suite (see
http://www.ccpem.ac.uk/ for further information), as well as the exciting
developments in electron microscopy and tomography. Confirmed speakers
include:

John Briggs (EMBL)
Richard Henderson (MRC-LMB)
Juha Huiskonen (STRUBI)
Lori Passmore (MRC-LMB)
Pavel Plevka (CEITEC)
Neil Ranson (University of Leeds)
Alan Roseman (University of Manchester)
Helen Saibil (Birkbeck)
Martyn Winn (STFC)

For more information and registration details please see:

https://eventbooking.stfc.ac.uk/news-events/ccpem-symposium-266

Best wishes,

Tom and the rest of the CCP-EM team.

-- 
Dr Tom Burnley, PhD
CCP-EM
Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] INSTRUCT course on Computational Tools Combining Atomic and Volume Data

[Tom Burnley]

Instruct with CCP-EM is proud to announce the following workshop:

'INSTRUCT course on Computational Tools Combining Atomic and Volume Data'

* Event Details
There is increasing overlap between structural biology disciplines, a
common example being the interpretation of volume data from electron
cryo-microscopy (cryoEM) in terms of atomic models from crystallography
(MX) and nuclear magnetic resonance spectroscopy (NMR). A wide variety of
tools exist to perform rigid-body or flexible fitting. If docking of models
is successful, then one can obtain atomistic detail of large
multi-component complexes, leading to a better understanding of cellular
machinery.

However, because of the limited resolution of cryoEM volumes, fitting of
atomic models is not straightforward, and there is a strong danger of
overfitting. The course will give an overview of the issues involved, an
introduction to selected tools from the cryoEM, MX and NMR fields, and a
discussion of validation. There will be a mixture of lectures and hands-on
practicals. The course will highlight software available from CCISB
partners.

The course is aimed at both electron microscopists wishing to interpret
their volume models, and scientists from MX/NMR looking to understand the
increasing amount of cryoEM data available. The course is open to
investigators at all levels, but participants should have collected, or be
close to collecting, relevant structural data. We will work with examples
from the PDB and EMDB, but participants can bring their own data to look at
if they wish.

The course is limited to 20 delegates which will be selected from all
applicants.  A maximum of 60 applicants can register interest.

Applications will close on Friday 20th February and the 20 successful
applicants will be notified by 2nd March.

* For more information:

https://www.structuralbiology.eu/support/whats-on/calendar-events/computational-tools-combining-atomic-and-volume-data

* For registration:

https://eventbooking.stfc.ac.uk/news-events/instruct-course--on-computational-tools-combining-atomic-and-volume-data-263

* Confirmed tutors:

Maya Topf (Birkbeck)
Alan Roseman (Manchester)
Garib Murshudov (MRC-LMB Cambridge)
Paul Emsley (MRC-LMB Cambridge)
Agnel Praveen Joseph (STFC)
Ardan Patwardhan (EBI)
Stuart McNicholas (York)

Best wishes,

Tom

-- 
Dr Tom Burnley, PhD
Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] RELION Workshop @ Diamond, 16th October 2014

[Tom Burnley]

Dear all,

For those also interested in EM:

We are pleased to announce a one day RELION workshop led by its
developer Sjors Scheres and hosted by CCP-EM on 16th October 2014.

RELION (for REgularised LIkelihood OptimisatioN, pronounced rely-on)
is a stand-alone computer program that employs an empirical Bayesian
approach to refinement of (multiple) 3D reconstructions or 2D class
averages in electron cryo-microscopy (cryo-EM).

The workshop will be held at Diamond House, Harwell, Oxfordshire, UK.

Full details can be found here:

https://eventbooking.stfc.ac.uk/news-events/relion-workshop-224

Bursaries are available for travel within the UK. Registration closes
on Friday 5th September and places will be confirmed by 12th
September.

We look forward to seeing you in October,

Kind regards,

Tom and the rest of the CCP-EM team

-- 
Dr Tom Burnley, PhD
Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

Re: [ccp4bb] Characterization of Protein Conformational Changes

[Tom Burnley]

This sounds like a job for a DDM (difference-distance matrix).  This method
can detect very subtle conformational changes between a pair of protein
structures without performing a structural alignment.  Once the areas of
change have been identified a traditional alignment can be performed using
the conformationally inert regions as a target.

The program ESCET can do this and full details can be found here:

http://schneider.group.ifom-ieo-campus.it/escet/index.html

Alternatively DDMP could be used:

http://www.csb.yale.edu/userguides/datamanip/ddmp/ddmp_descrip.html

Hope that helps,

Tom

On Wed, Jan 7, 2009 at 2:18 PM, Nathaniel Echols nathaniel.ech...@gmail.com
 wrote:

 On Wed, Jan 7, 2009 at 1:54 PM, Jacob Keller 
 j-kell...@md.northwestern.edu wrote:
  I am sure that most here have dealt with the issue, when making
 superpositions of conformationally-different structures,  of which
 regions to align as references and which to call mobile. Conformational
 changes can range from very local (e.g.,
  unwinding of a helix) to very diffuse (e.g., subtle but significant rigid
 body shifts between two domains.) In the first case,
  it would probably make sense to do a global least-squares fitting, but in
 the latter, one would do better to fix one of the
  domains, and show the shift in the other domain. These cases, however,
 presuppose that one knows which type of case
  one is dealing with. This could be done by guesswork and trial-and-error,
 but does anybody know of an approach (e.g., a
  program) to define the most reasonable way to think about a given
 conformational change? Variable-size sliding-window
  least-squares superpositions with comparisons of local versus global
 rmsd's come to mind, but I do not know whether
  this has been implemented anywhere, and would not know readily how to set
 the parameters thereof either.

 DynDom may do this, but I'm not familiar with the program.  (It's in CCP4
 now, I think)

 If you're just trying to get a reasonable superposition and don't care very
 much about the resulting statistics, you can usually use a much simpler
 method called a sieve-fit, described in these references:

 http://www.ncbi.nlm.nih.gov/pubmed/2067013
 http://www.ncbi.nlm.nih.gov/pubmed/10734184

 In practice, the procedure described in the second paper generally worked
 very well for the intended purpose of visualizing any arbitrary
 conformational change in the PDB clearly.  The code that actually performs
 this isn't distributed as far as I know; however, it should be relatively
 trivial to re-implement using CCTBX or something equivalent.

 PyMOL's align command also does some kind of iterative optimization by
 throwing away outliers, but it's much less aggressive and appears to try for
 the best global fit, excluding loops etc.

 -Nat