Re: [ccp4bb] MX data processing with GPUs??

[Leonarski Filip Karol (PSI)]

Dear Ana,

To benefit from GPU architecture, over CPU, the algorithm needs to do quite 
significant number crunching – i.e. do at least certain number of floating 
point operations (FLOP) per one byte of data. It also needs to be highly 
parallel, preferably without conditional (if/else) statements. Finally, there 
is a variety of GPU architectures on the market and it is not exactly obvious 
that code written for one GPU will be optimal on another one. So if the code is 
based on a general purpose library, it will be easier to make sure that it runs 
efficiently on all GPU hardware.

I believe combination of these factors makes a big difference between imaging 
and MX.

Imaging processing is limited by FFT performance, which needs floating point 
performance. Libraries for FFT on GPUs are standard and provided by hardware 
vendors, so it is easy to implement.

On the other hand MX algorithms for image processing, at least the one I know 
of, do only handful of FLOP per pixel and they will probably not benefit from 
GPU processing significantly, even if ported to such architecture – which would 
be also a non-negligible effort. So while it is not impossible to imagine 
GPU-accelerated MX software and hopefully people are working on this, it is not 
a low hanging fruit, like in case of GPU acceleration for imaging or cryo-EM.

On a side note if one could find a way to use machine learning for data 
processing and implement data processing pipeline in Tensorflow, then GPUs 
would pay off quickly.

Regarding Tim’s Raspberry Pi argument – it should be compared with Nvidia 
Jetson price, which is more or less RPi with GPU, and it won’t be actually that 
significant difference.

Best,
Filip


From: CCP4 bulletin board  on behalf of Ana Carolina de 
Mattos Zeri 
Reply to: Ana Carolina de Mattos Zeri 
Date: Tuesday, 18 February 2020 at 20:58
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] MX data processing with GPUs??

Dear all
we have asked this of a few people, but the question remains:
does any of you have experienced/tried using GPU based software to treat MX 
data? for reducing or subsequent image analysis?
is it a lost battle?
how do you deal with the crescent amount of data we are facing, at Synchrotrons 
and XFELs?
Here at the Manaca beamline at Sirius we will continue to support CPU based 
software, but due to developments in the imaging beam lines, GPU machines are 
looking very attractive.
many thanks in advance for your thoughts,
all the best
Ana


Ana Carolina Zeri, PhD
Manaca Beamline Coordinator (Macromolecular Micro and Nano Crystallography)
Brazilian Synchrotron Light Laboratory (LNLS)
Brazilian Center for Research in Energy and Materials (CNPEM)
Zip Code 13083-970, Campinas, Sao Paulo, Brazil.
(19) 3518-2498
www.lnls.br
ana.z...@lnls.br






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Re: [ccp4bb] [3dem] Which resolution?

[Marin van Heel]

Hi Pawel,

We can indeed agree to disagree upon many basic things in life. We
apparently disagree on the basic assumptions upon which you choose to build
your science!   What I am criticising is the very foundation you use to
construct your science, namely the flawed Frank & Al-Ali (1975) formula
relating SNR and CCC! Agreed, their errors are not of your making and not
your responsibility!  It is, however, your choice and your judgement to
build upon that flawed foundation.  At the end of the day, your construct,
even when based on shaky foundations created by others, will remain your
responsibility!

Sorry,
Marin

On Sun, Feb 16, 2020 at 1:59 PM Penczek, Pawel A <
pawel.a.penc...@uth.tmc.edu> wrote:

> Marin,
>
> The statistics in 2010 review is fine. You may disagree with assumptions,
> but I can assure you the “statistics” (as you call it) is fine. Careful
> reading of the paper would reveal to you this much.
>
> Regards,
> Pawel
>
> On Feb 16, 2020, at 10:38 AM, Marin van Heel 
> wrote:
>
> 
>
> * EXTERNAL EMAIL *
> Dear Pawel and All others 
>
> This 2010 review is - unfortunately - largely based on the flawed
> statistics I mentioned before, namely on the a priori assumption that the
> inner product of a signal vector and a noise vector are ZERO (an
> orthogonality assumption).  The (Frank & Al-Ali 1975) paper we have refuted
> on a number of occasions (for example in 2005, and most recently in our
> BioRxiv paper) but you still take that as the correct relation between SNR
> and FRC (and you never cite the criticism...).
> Sorry
> Marin
>
> On Thu, Feb 13, 2020 at 10:42 AM Penczek, Pawel A <
> pawel.a.penc...@uth.tmc.edu> wrote:
>
>> Dear Teige,
>>
>> I am wondering whether you are familiar with
>>
>> Resolution measures in molecular electron microscopy.
>> Penczek PA. Methods Enzymol. 2010.
>> Citation
>>
>> Methods Enzymol. 2010;482:73-100. doi: 10.1016/S0076-6879(10)82003-8.
>>
>> You will find there answers to all questions you asked and much more.
>>
>> Regards,
>> Pawel Penczek
>>
>>
>> Regards,
>> Pawel
>> ___
>> 3dem mailing list
>> 3...@ncmir.ucsd.edu
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>> 
>>
>



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Re: [ccp4bb] MX data processing with GPUs??

[Chun Hong Yoon]

Dear Ana,

how do you deal with the crescent amount of data we are facing, at
Synchrotrons and XFELs?
At LCLS, we plan to stream data to near-by supercomputing facilities for serial 
crystallography data processing. So we are developing code to fully utilize 
both CPUs and GPUs on these machines.

I agree with Tim that CPUs are more cost effective, but in my opinion GPUs are 
worth it if you plan to incorporate deep neural networks / compression / 
simulation etc in your data processing pipeline.

Best,
Chuck
--
Chunhong Yoon, Ph.D.

Head of LCLS Data Analytics
LCLS / SLAC National Accelerator Laboratory
2575 Sand Hill Road
Menlo Park, CA 94025
Bldg. 901, Rm. 132


On Feb 18, 2020, at 1:44 PM, Tim Gruene 
mailto:tim.gru...@univie.ac.at>> wrote:

Dear Ana,

you may want to check how many single board computers (like the Raspberry Pi
or true open source hardware platform) you can buy for a single GPU high end
graphics card.
It may be cheaper at better performance compared to GPU computing.

XDS (and possibly also DIALS) can distribute its job across ssh, hence you
only need the appropriate network connections.

XDS wouldn't run on Raspberry Pi, although it may not be difficult to port.

Best,
Tim


On Tuesday, February 18, 2020 8:48:17 PM CET Ana Carolina de Mattos Zeri
wrote:
Dear all
we have asked this of a few people, but the question remains:
does any of you have experienced/tried using GPU based software to treat MX
data? for reducing or subsequent image analysis? is it a lost battle?
how do you deal with the crescent amount of data we are facing, at
Synchrotrons and XFELs? Here at the Manaca beamline at Sirius we will
continue to support CPU based software, but due to developments in the
imaging beam lines, GPU machines are looking very attractive. many thanks
in advance for your thoughts,
all the best
Ana



Ana Carolina Zeri, PhD
Manaca Beamline Coordinator (Macromolecular Micro and Nano Crystallography)
Brazilian Synchrotron Light Laboratory (LNLS)
Brazilian Center for Research in Energy and Materials (CNPEM)
Zip Code 13083-970, Campinas, Sao Paulo, Brazil.
(19) 3518-2498
www.lnls.br>
ana.z...@lnls.br








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--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] MX data processing with GPUs??

[Tim Gruene]

Dear Ana,

you may want to check how many single board computers (like the Raspberry Pi 
or true open source hardware platform) you can buy for a single GPU high end 
graphics card. 
It may be cheaper at better performance compared to GPU computing.

XDS (and possibly also DIALS) can distribute its job across ssh, hence you 
only need the appropriate network connections. 

XDS wouldn't run on Raspberry Pi, although it may not be difficult to port.

Best,
Tim


On Tuesday, February 18, 2020 8:48:17 PM CET Ana Carolina de Mattos Zeri 
wrote:
> Dear all
> we have asked this of a few people, but the question remains:
> does any of you have experienced/tried using GPU based software to treat MX
> data? for reducing or subsequent image analysis? is it a lost battle?
> how do you deal with the crescent amount of data we are facing, at
> Synchrotrons and XFELs? Here at the Manaca beamline at Sirius we will
> continue to support CPU based software, but due to developments in the
> imaging beam lines, GPU machines are looking very attractive. many thanks
> in advance for your thoughts,
> all the best
> Ana
> 
> 
> 
> Ana Carolina Zeri, PhD
> Manaca Beamline Coordinator (Macromolecular Micro and Nano Crystallography)
> Brazilian Synchrotron Light Laboratory (LNLS)
> Brazilian Center for Research in Energy and Materials (CNPEM)
> Zip Code 13083-970, Campinas, Sao Paulo, Brazil.
> (19) 3518-2498
> www.lnls.br
> ana.z...@lnls.br
> 
> 
> 
> 
> 
> 
> 
> 
> Aviso Legal: Esta mensagem e seus anexos podem conter informa??es
> confidenciais e/ou de uso restrito. Observe atentamente seu conte?do e
> considere eventual consulta ao remetente antes de copi?-la, divulg?-la ou
> distribu?-la. Se voc? recebeu esta mensagem por engano, por favor avise o
> remetente e apague-a imediatamente.
> 
> Disclaimer: This email and its attachments may contain confidential and/or
> privileged information. Observe its content carefully and consider possible
> querying to the sender before copying, disclosing or distributing it. If
> you have received this email by mistake, please notify the sender and
> delete it immediately.
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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[ccp4bb] MX data processing with GPUs??

[Ana Carolina de Mattos Zeri]

Dear all
we have asked this of a few people, but the question remains:
does any of you have experienced/tried using GPU based software to treat MX 
data? for reducing or subsequent image analysis?
is it a lost battle?
how do you deal with the crescent amount of data we are facing, at Synchrotrons 
and XFELs?
Here at the Manaca beamline at Sirius we will continue to support CPU based 
software, but due to developments in the imaging beam lines, GPU machines are 
looking very attractive.
many thanks in advance for your thoughts,
all the best
Ana



Ana Carolina Zeri, PhD
Manaca Beamline Coordinator (Macromolecular Micro and Nano Crystallography)
Brazilian Synchrotron Light Laboratory (LNLS)
Brazilian Center for Research in Energy and Materials (CNPEM)
Zip Code 13083-970, Campinas, Sao Paulo, Brazil.
(19) 3518-2498
www.lnls.br
ana.z...@lnls.br








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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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Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

[Marin van Heel]

Dear John,

I really like your lecture notes! My Imperial/Leiden lecture notes –
currently being updated – look a lot like yours. The earlier version:

(https://www.single-particles.org/methodology/MvH_Phase_Contrast.pdf)

And you are fully correct: “resolution of cryoEM imaging varies locally”!

That is exactly the point!

The existing cryo-EM dogmas, however,  PREVENT you from doing things right,
which seriously hampers progress (see our BioRxiv paper:
https://www.biorxiv.org/content/10.1101/224402v1 ).

Cheers,

Marin

On Tue, Feb 18, 2020 at 4:36 AM John R Helliwell 
wrote:

> Hi Colin,
> Yes I agree, see eg page 7 of
> https://www2.physics.ox.ac.uk/sites/default/files/2011-06-08/optics_notes_and_slides_part_5_pdf_63907.pdf
>  (and
> there maybe better weblinks).
>
> The resolution of cryoEM imaging varies locally and so the “local scaling
> in a complex way” is what we have to get into in practice..
>
> Greetings,
> John
>
> Emeritus Professor John R Helliwell DSc
>
>
>
> On 17 Feb 2020, at 21:57, Nave, Colin (DLSLtd,RAL,LSCI) <
> colin.n...@diamond.ac.uk> wrote:
>
> 
>
> Hi John
>
> I agree that neutrons have a role to increase the contrast for certain
> atoms. The “water window” for x-ray imaging also fulfils a similar role.
> The “locally scaled in a complex way” is a bit beyond me.
>
>
>
> The relationship between “ diffraction” errors and “imaging” errors is
>  based on Parseval’s theorem applied to the errors for electron densities
> and structure factors.  See for example
> https://www-structmed.cimr.cam.ac.uk/Course/Fourier/Fourier.html and
> scroll down to Parseval’s theorem. Admittedly not a primary reference but I
> think Randy (and Parseval, not to be confused with Wagner’s opera), are
> unlikely to have got it wrong.
>
>
>
> Imaging (with both electrons and x-rays) can be lensless (as in MX, CDI
> and variants) or with an objective lens (electron microscopes have nice
> objective lenses). The physical processes are the same up to any lens but
> MX, CDI etc. use a computer to replace the lens. The computer algorithm
> might be imperfect resulting in visible termination errors. With a decent
> lens, one can also see diffraction ripples (round bright stars in a
> telescope image) due to the restricted lens aperture.
>
>
>
> Good debate though.
>
>
>
> Colin
>
> *From:* John R Helliwell 
> *Sent:* 17 February 2020 16:36
> *To:* Nave, Colin (DLSLtd,RAL,LSCI) 
> *Cc:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?
>
>
>
> Hi Colin,
>
> Neutrons are applied to the uranyl hydrides so as to make their scattering
> lengths much more equal than with X-rays, and so side step ripple effects
> of the uranium in the Xray case, which obscures those nearby hydrogens.
>
> In terms of feature resolvability the email exchange (and there may be
> better ones):-
> http://www.phenix-online.org/pipermail/phenixbb/2017-March/023326.html
>
> refers to “locally scaled in a complex way”. So, is the physics of the
> visibility of features really comparable between the two methods of cryoEM
> and crystal structure analysis?
>
> Greetings,
>
> John
>
> Emeritus Professor John R Helliwell DSc
>
>
>
>
>
>
>
> On 17 Feb 2020, at 13:59, Nave, Colin (DLSLtd,RAL,LSCI) <
> colin.n...@diamond.ac.uk> wrote:
>
> 
>
> Hi John
>
> I agree that if I truncate the data at a high information content
> threshold (e.g. 2 bits)  series termination errors might hide the lighter
> atoms (e.g. the hydrogens in uranium hydride crystal structures). However,
> I think this is purely a limitation of producing electron density maps via
> Fourier transforms (i.e. not the physics). A variety of techniques are
> available for handling series termination including ones which are
> maximally non-committal with respect to the missing data. The issue is
> still there in some fields (see
> https://onlinelibrary.wiley.com/iucr/itc/Ha/ch4o8v0001/ ). For protein
> crystallography perhaps series termination errors have become less
> important as people are discouraged from applying some I/sigI type cut off.
>
>
>
> Cheers
>
> Colin
>
>
>
>
>
>
>
> *From:* John R Helliwell 
> *Sent:* 17 February 2020 12:09
> *To:* Nave, Colin (DLSLtd,RAL,LSCI) 
> *Subject:* Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?
>
>
>
> Hi Colin,
>
> I think the physics of the imaging and the crystal structure analysis,
> respectively without and with Fourier termination ripples, are different.
> For the MX re Fourier series for two types of difference map see our
> contribution:-
>
>
>
> http://scripts.iucr.org/cgi-bin/paper?S0907444903004219
>
>
>
> Greetings,
>
> John
>
>
>
> Emeritus Professor John R Helliwell DSc
>
>
> https://www.crcpress.com/The-Whats-of-a-Scientific-Life/Helliwell/p/book/9780367233020
>
>
>
>
>
>
>
>
> On 17 Feb 2020, at 11:26, "colin.n...@diamond.ac.uk" <
> colin.n...@diamond.ac.uk wrote:
>
> 
>
>
>
> Dear all.
>
> Would it help to separate out the issue of the FSC from the value of the
> threshold? My unders

Re: [ccp4bb] disulfides in coot

[Robbie Joosten]

Hi Sam,

Once a disulfide bridge is made Coot will restrain the sulfur atoms to bind. 
The way out is deleting one of the side chains and adding it back while making 
sure the sulfurs do not get too close.

HTH,
Robbie

On 18 Feb 2020 11:24, Sam Tang  wrote:
Dear all

A very technical question which I believe a few simple mouse clicks would 
solve. Is there a way I can ask Coot not to build the disulfide linkage 
automatically (which lies within a strong red density)?

My WinCoot is version 0.8.9.2

Many thanks!

Regards

Sam



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[ccp4bb] disulfides in coot

[Sam Tang]

Dear all

A very technical question which I believe a few simple mouse clicks would
solve. Is there a way I can ask Coot not to build the disulfide linkage
automatically (which lies within a strong red density)?

My WinCoot is version 0.8.9.2

Many thanks!

Regards

Sam



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[ccp4bb] Cryo-EM sample preparation workshop at the ESRF / 9th to 11th of June 2020

[David FLOT]

Dear All,

We are pleased to announce our 2.5-day practical workshop on sample 
preparation for single particle cryo-EM from *June**9^th to 11^th2020*. 
This is the fourth of a series of practical hands-on workshops and is 
aimed at PhDs, PostDocs and scientists new to the field of single 
particle cryo-EM. During the course, participants will learn theoretical 
and practical aspects of sample preparation for single particle cryo-EM 
including prior quality control by negative staining.


There is*no registration fee*and meals and accommodation during the 
workshop will be provided free of charge. However, participants are 
expected to arrange and pay for their own travel to/from Grenoble. A 
maximum of 12 participants will be selected and we will accept a limited 
number of participants’ samples to be tested during the workshop. In the 
case that you plan to bring your own sample(s), please clearly mention 
this in your cover letter, also indicating the importance of the project.


Application for the workshop isopen 
and 
the*deadline for application is March 29^th , 2020*. Successful 
candidates will be informed during the first week after the deadline. 
For more information, please consult http://www.esrf.fr/cryo-em1-2020


Best regards,

David FLOT.

(On behalf of the organizers)


--

 
Dr David FLOT

Beam-Line Operation Manager Tel : (+33) 4 76 88 17 63
Structural Biology GroupFax : (+33) 4 76 88 26 24
ESRF
e-mail : david.f...@esrf.fr http://www.esrf.eu
Room: 30.1.13

Physical addressPostal address
ESRF-The European Synchrotron   ESRF-The European Synchrotron
71, Avenue des Martyrs  CS40220
Grenoble, France38043 Grenoble Cedex 9
France




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