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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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