Re: [ccp4bb] Problem with crystal structure solution

[Phil Jeffrey]

Hello Gargi

I don't think you mean Fc.  Apart from anything else, there's not enough 
room for 4 more domains per Fab.


I think you mean the CL:CH1 domain dimer of the Fab.  Fabs have a 
well-characterized variability in the "elbow angle" between the VL:VH 
domain pair and the CL:CH1 domain pair.  I suspect you've tried 
molecular replacement without trying a range of different elbow angles. 
I see +ve difference map peaks within domains and -ve difference map 
peaks along polypeptide chain, which is refinement's way of saying that 
it doesn't want atoms in the latter location and wants atoms in the 
former location.


There's also some quite serious clashing (chain interdigitation) in 
places, which can't possibly be correct.


The easiest way to do this is to re-do your molecular replacement with 
VL:VH and CL:CH1 models which will inherently allow their correct 
relative placement to be modeled.  If you managed to get TFZ of 42 with 
flawed models, this should be a pretty easy thing to pull off, but if 
not please contact me off list.


Phil Jeffrey
Princeton




On 3/27/23 1:52 PM, Kher, Gargi M wrote:

Hello,

I obtained diffraction data for one of my crystallographic projects. 
Data collection determined the space group to be P1 at a ~2.67Å. I 
solved it using MR (it contains a Fab-Fab complex) and the Phaser 
solution (TFZ of 42.0), which is close to the Matthews coefficient 
prediction, placed 16 Fabs in the unit cell (8 copies of the same 
Fab-Fab complex). The Matthews coefficient was predicted to be 2.44 with 
9 copies in the ASU, but for 8 and 10 copies in the unit cell, the 
Matthews coefficients were 2.75 and 2.20, respectively. I did set up MR 
jobs searching for 9 and 10 Fab-Fab copies in the unit cell, but still, 
only 8 Fabs were placed.


While most of the Fabs fit nicely in the density, 6 Fcs (chains e, 
A, M, Q, U, and c) do not fit within the electron density. I 
have tried re-processing my data, but P1 seems to be the “correct” space 
group, and Xtriage does not indicate any red flags. There is some extra 
positive density visible close to these Fcs. I believe these 6 Fcs might 
be in a different orientation/position than how they’re currently being 
placed, and should fit into the additional positive density I’m seeing. 
However, I have been unable to place them correctly: either by using 
rigid body refinement in Phenix for these 6 Fc domains or doing it 
manually as Fc domains.


Does anyone have ideas as to what might be happening here and what I 
could do to try and fix this? I’ve attached my PDB and MTZ file for your 
reference.


Thank you,

Gargi Kher




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[ccp4bb] Post-doctoral post at ICR with CR-UK Catalyst Grant

[Andrew Turnbull]

Posted on behalf of Prof. Terry Rabbitts:

-

Post-doctoral post at ICR to develop LMO2 Protac compounds for leukaemia 
treatment

The Institute of Cancer Research (ICR), London, is one of the world's most 
influential cancer research institutes, with an outstanding record of 
achievement dating back more than 100 years. Today, the ICR leads the world at 
isolating cancer-related genes and discovering new targeted drugs for 
personalised cancer treatment. Together with our hospital partner The Royal 
Marsden, we are rated in the top four centres for cancer research and treatment 
worldwide. As well as being a world-class institute, we are a college of the 
University of London. The ICR is committed to our mission to make the 
discoveries that defeat cancer.
ICR is split between labs in Chelsea and Sutton and the Division of Cancer 
Therapeutics is located in the new Centre for Cancer Drug Discovery building at 
the Sutton site. It is a multidisciplinary comprising around 200 staff 
dedicated to the discovery and development of novel therapeutics for the 
treatment of cancer. Our Chromosomal Translocation and Intracellular Antibody 
Therapeutics Group is within the Division of Cancer Therapeutics and is focused 
on new strategies using intracellular antibodies, and derivates, for therapy 
aimed at hard-to-drug chromosomal translocation gene products. This work 
includes intracellular antibodies for inhibiting transcription factors and 
protein-protein interactions.

The approach so far has resulted in compounds that bind to the chromosomal 
translocation LMO2 transcription factor and that effect T cell leukaemia cell 
growth. The aim is to develop these compounds into drugs for refractory T-cell 
acute leukaemias. All the scientific expertise is in place to make this 
possible and our approach is multi-disciplinary, integrating molecular biology, 
cell biology, antibody design, structural biology, and chemical biology. The 
post is part of a CR-UK funded Therapeutic Catalyst Award in collaboration with 
Professor Angela Russell (University of Oxford, Dept of Chemistry). We aim to 
develop our LMO2 binding compounds to pre-clinical efficacy using 
structure-based drug evolution. These will be the first compounds to be derived 
from an intracellular antibody binding site that have progressed towards phase 
I clinical trials. The post should lead to further work in the group to drug 
using our intracellular antibody approach.

If you are interested in developing antibody derived compounds using 
recombinant protein expression and structural biology for cancer drug 
development, apply for the postdoctoral position (ID575) available in Professor 
Terry Rabbitts's group within the Division. You should have a PhD in structural 
biology and have experience in working with recombinant proteins, in particular 
antibodies and transcription factors. You must have worked with protein 
engineering and as well as  in methods such as X-ray crystallography. 
Experience with cell-based models, such as 3-D cultures would be an advantage. 
The post-doc will be involved in the structure determination of LMO2-binding 
compounds as protein/small molecule complexes by X-ray crystallography. The 
post holder will be responsible for protein production and purification, 
protein crystallisation, structure determination by X-ray crystallography and 
subsequent structural analysis. We benefit from excellent access to Diamond 
Light Source synchrotron at the Harwell Science and Innovation campus, Didcot, 
UK, for X-ray data collection.

The starting salary will be in the range £40,107 to £42,402 p.a. inclusive 
(based on previous postdoctoral experience). The post is offered on a fixed 
term contract of 1.5 years. Informal enquiries to 
terry.rabbi...@icr.ac.uk

Please DO NOT send your application to Professor Rabbitts but apply via the 
e-recruitment system on our website 
www.icr.ac.uk.

For more details see the following link:
Postdoctoral Training Fellow CR-UK Therapeutic Catalyst Grant (Prof T Rabbitts) 
(ID575) in Sutton (Greater London) - The Institute of Cancer Research 
(icr.ac.uk)

Closing date:  23 April 2023

Prof. Terry Rabbitts FRS  FMedSci
Institute of Cancer Research
Division of Cancer Therapeutics
15 Cotswold Road
Sutton, London, SM2 5NG, UK

Email: terry.rabbi...@icr.ac.uk






NOTICE AND DISCLAIMER This 

Re: [ccp4bb] Alexey Vagin

[Stefan Arold]

Dear Eugene

Thanks for sharing the sad news. Alexey was a wonderful person and huge
help for setting up our MorDA-powered Contaminer server.
a big loss for the community!

Stefan


Stefan T Arold,

Professor of Bioscience

Associate Dean, Division of Biological and Environmental Sciences and
Engineering

Computational Bioscience Research Center (CBRC)
King Abdullah University of Science and Technology (KAUST)

Bldg 2, Level 4, Room 4274

Thuwal 23955-6900
Saudi Arabia



On Sun, 26 Mar 2023 at 21:29, Eugene Krissinel - STFC UKRI <
6fcecdb9c847-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear All,
>
> It is with a great sadness that I share with you that Alexey Vagin passed
> away this Saturday in the Radcliffe Hospital in Oxford after suffering from
> a heart attack with subsequent complications. He was 78 years old.
>
> Alexey made many developments in methods and software for macromolecular
> crystallography, to which he devoted his whole life. He is known for his
> BLANC Suite for structure solution done at the Moscow Institute of
> Crystallography in the 1980s, as well as for his contributions to Refmac
> and Monomer Library. Many thousands of researchers have benefited from his
> work on Molrep and Balbes software for Molecular Replacement. After his
> retirement in 2010, Alexey developed and actively maintained the MorDA
> software for MR, which became a monument to his efforts.
>
> Alexey's work will continue to serve generations of researchers through
> his contributions to CCP4, where we will take the best care of his
> distinguished legacy.
>
> With sympathy to everyone who knew Alexey personally and for whom this is
> very sad news,
>
> Eugene
>
>
> --
>
> 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] Alexey Vagin

[Fei Long]

Very sad news to me indeed. Alexei is a great scientist from whom I have 
leant a lot. There are so many cherishing memories of working with him.


May his soul rest in peace.

Fei

On 2023-03-26 19:29, Eugene Krissinel - STFC UKRI wrote:

Dear All,

 It is with a great sadness that I share with you that Alexey Vagin
passed away this Saturday in the Radcliffe Hospital in Oxford after
suffering from a heart attack with subsequent complications. He was 78
years old.

 Alexey made many developments in methods and software for
macromolecular crystallography, to which he devoted his whole life. He
is known for his BLANC Suite for structure solution done at the Moscow
Institute of Crystallography in the 1980s, as well as for his
contributions to Refmac and Monomer Library. Many thousands of
researchers have benefited from his work on Molrep and Balbes software
for Molecular Replacement. After his retirement in 2010, Alexey
developed and actively maintained the MorDA software for MR, which
became a monument to his efforts.

 Alexey's work will continue to serve generations of researchers
through his contributions to CCP4, where we will take the best care of
his distinguished legacy.

 With sympathy to everyone who knew Alexey personally and for whom
this is very sad news,

 Eugene


--
Dr. Fei Long
Structural Studies Division
UKRI Laboratory of Molecular Biology
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge
CB2 0QH UK
Email:fl...@mrc-lmb.cam.ac.uk



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[ccp4bb] wwPDB NEWS: Access Depositions Using ORCiD

[Deborah Harrus]

Dear all,

We are pleased to announce that contact authors can now useORCiDs 
to authenticate OneDep access. This authentication 
method allows each contact author to login to OneDep without the need 
for password sharing to view and access all their depositions.


OneDep login using a deposition ID and password is still possible, but 
will only provide access to the specific deposition.


Using ORCiD with OneDep returns a summary table of the entries in which 
the ORCiD has been provided for the contact author. Users can further 
access each of their entries’ deposition interfaces without the need to 
login again using a deposition ID or password.


The ORCiD sign-in button is located below the existing login 
fields./The ORCiD sign-in button is located below the existing login 
fields./
After using the ORCiD login, this OneDep panel will displaying all 
available depositions. 
/After using the 
ORCiD login, this OneDep panel will displaying all available depositions./












First-time OneDep contact authors will need to verify their email 
address before being able to create new depositions, similar to creating 
a new deposition without being logged-in with ORCiD.


Please be aware that adding a contact author ORCiD in the “Admin > 
Contact information” OneDep page will grant this author access to the 
current deposition.


Providing ORCiDs for OneDep contact authorshas been mandatory since 2018 
.



Read this news online: 
https://www.wwpdb.org/news/news?year=2023#641872ffe0a2cc03bf315460



Kind regards,

Deborah Harrus

PDBe

--
---
Deborah Harrus, Ph.D.
Lead Annotator
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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[ccp4bb] Alexey Vagin

[Carter, Charlie]

I never met Alexei Vagin and it has been some time since I’ve done much 
crystallography. Nonetheless, this news saddens me because of the oversize 
reputation I knew he had built. His name became legendary even to me quite 
early on. I appreciate knowing that his personality was as generous as his 
reputation was robust as a scientist.

Charlie



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Re: [ccp4bb] Alexey Vagin

[Jon Agirre]

I met Alexey at an EMBO course in Gif-sur-Yvette in 2005. I thought he
was impressive and had an incredible sense of humour: from his
friendly competition with Jorge Navaza, to his remarks about making
MOLREP properly automated so he could have 'more time to smoke'.
Back then, his York website was full of hilarious crystallography
memes, long before the explosion of social media. A brilliant guy who
helped make crystallography both fun and interesting.

My condolences,
Jon


On Sun, 26 Mar 2023 at 19:41, James Foadi
<09daa8ec3774-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> I am very sad to hear this! Alexey was one of my favourites when I was in 
> York, and I have had many lovely conversations with him. You are right, 
> Eugene, his contributions have helped and will keep helping many 
> crystallographers and methods developers.
>
> May his soul rest in peace!
>
> James
>
>
> Sent from Yahoo Mail for iPhone
>
> On Sunday, March 26, 2023, 7:29 pm, Eugene Krissinel - STFC UKRI 
> <6fcecdb9c847-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Dear All,
>
> It is with a great sadness that I share with you that Alexey Vagin passed 
> away this Saturday in the Radcliffe Hospital in Oxford after suffering from a 
> heart attack with subsequent complications. He was 78 years old.
>
> Alexey made many developments in methods and software for macromolecular 
> crystallography, to which he devoted his whole life. He is known for his 
> BLANC Suite for structure solution done at the Moscow Institute of 
> Crystallography in the 1980s, as well as for his contributions to Refmac and 
> Monomer Library. Many thousands of researchers have benefited from his work 
> on Molrep and Balbes software for Molecular Replacement. After his retirement 
> in 2010, Alexey developed and actively maintained the MorDA software for MR, 
> which became a monument to his efforts.
>
> Alexey's work will continue to serve generations of researchers through his 
> contributions to CCP4, where we will take the best care of his distinguished 
> legacy.
>
> With sympathy to everyone who knew Alexey personally and for whom this is 
> very sad news,
>
> Eugene
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



-- 
Dr Jon Agirre
Royal Society University Research Fellow (assistant professor)
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
Office: B/K065 Phone: +44 (0) 1904 32 8252



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[ccp4bb] PostDoc Positions in FIB-SEM/cryo-ET in Dortmund

[Stefan Raunser]

Dear colleagues!

I would like to draw your attention to the following job opportunities. 
Deadline April 7!

Best,
Stefan
 
PostDoc Positions (m/f/d) in Electron Cryo-Tomography (cryo-ET)

There are exciting immediate Postdoctoral positions in the lab of Stefan 
Raunser in the Department of Structural Biochemistry at the Max Planck 
Institute for Molecular Physiology in Dortmund, Germany. This is a unique 
opportunity to become a part of a world-renowned research institute with a 
diverse faculty with backgrounds in chemistry, biology and physics, and to 
perform interdisciplinary science in a lively and supportive environment!

We seek highly motivated, self-driven and creative thinkers who are prepared to 
take risks in defining and addressing important scientific problems, and who 
use quantitative experimental, computational and/or technical approaches in 
their work. The positions are available immediately in the Department of 
Structural Biochemistry (Director: Stefan Raunser) and are initially limited to 
3 years.

Summary:

Research projects in the Raunser lab focus on important biological questions 
concerning the structural organization of muscles, cytoskeletal proteins and 
bacterial toxin complexes. Our ultimate goal is to understand the mechanisms 
and structure-function relationship underlying these processes in health and 
disease in molecular detail. To this end, we employ single particle electron 
cryo-microscopy (cryo-EM), cryogenic focused ion beam milling (cryo-FIB), 
electron cryo-tomography (cryo-ET), X-ray crystallography, biochemical and 
biophysical methods and cell biology.

There are several projects available in our lab for talented and outstanding 
young researchers who are eager to apply cryo-FIB and cryo-ET to look deeper 
into cells and tissues in order to visualize and understand cellular components 
that have never been seen before.

Requirements:

Ideal candidates should hold an excellent PhD in structural biology, 
biophysics, physics or in an equivalent area with previous experience in single 
particle cryo-EM or cryo-ET.

Strong written and oral communication skills in English are required. 

Why join us?

Being a part of the community at the Max Planck Institute is more than just a 
job. Our dynamic research environment, distinct culture, and diverse community 
foster collaboration and excellence in every corner of science. We offer an 
extensive range of benefits and resources such as:

•   access to state-of-the-art research facilities

•   opportunities to collaborate on cutting-edge research

•   an international and exciting working atmosphere

•   an integrated training program that includes lectures, advanced 
scientific workshops, complementary skill courses and opportunities for career 
development

•   a mentoring program to guide and promote young scientists

Salary:

Payment depends on personal conditions and qualification according to the 
directive of the TVöD. Social benefits correspond to those of the public 
service.

How to Apply:

Applicants should submit a CV, a motivation letter outlining research 
experiences and interests and two reference letters by April 7th, 2023 to 
Stefan Raunser at raunser-jobsea...@mpi-dortmund.mpg.de 

 
Additional Information:

The Max Planck Society (Max Planck Gesellschaft – MPG) is committed to 
increasing the number of individuals with disabilities in its workforce and 
therefore encourages applications from such qualified individuals. The MPG 
seeks to increase the number of women in those areas where they are 
underrepresented and therefore explicitly encourages women to apply. 
Furthermore, the MPG strives to foster an inclusive culture and diversity 
within its workforce. Therefore, all qualified applicants are encouraged to 
apply and will receive consideration for employment without regard to race, 
religion, color, national origin, age, sex, sexual orientation, disability 
status, or any other characteristic protected by applicable law.


---
Prof. Dr. Stefan Raunser | Director | Dep. Structural Biochemistry | Max Planck 
Institute of Molecular Physiology | Otto-Hahn-Straße 11, 44227 Dortmund, 
Germany | +49 231 133 2300

___
3dem mailing list
3...@ncmir.ucsd.edu 
https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem 




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smime.p7s
Description: S/MIME cryptographic signature

Re: [ccp4bb] [i2dev] Alexey Vagin

[Isabel Uson]

Sad news, I have many fond memories of Alexey, starting from the tour he
gave me of his BLANC suite in York back in 1997 and then his clever humor
and discussions at many workshops and conferences. May his heaven have a
piece of Barcelona, which he loved ("almost as good as home").

Isabel


On Sun, Mar 26, 2023 at 8:29 PM 'Eugene Krissinel - STFC UKRI' via
ysbl-ccp4i2dev  wrote:

> Dear All,
>
> It is with a great sadness that I share with you that Alexey Vagin passed
> away this Saturday in the Radcliffe Hospital in Oxford after suffering from
> a heart attack with subsequent complications. He was 78 years old.
>
> Alexey made many developments in methods and software for macromolecular
> crystallography, to which he devoted his whole life. He is known for his
> BLANC Suite for structure solution done at the Moscow Institute of
> Crystallography in the 1980s, as well as for his contributions to Refmac
> and Monomer Library. Many thousands of researchers have benefited from his
> work on Molrep and Balbes software for Molecular Replacement. After his
> retirement in 2010, Alexey developed and actively maintained the MorDA
> software for MR, which became a monument to his efforts.
>
> Alexey's work will continue to serve generations of researchers through
> his contributions to CCP4, where we will take the best care of his
> distinguished legacy.
>
> With sympathy to everyone who knew Alexey personally and for whom this is
> very sad news,
>
> Eugene
>
> --
> CCP4i2 development & testing
> --
> Bug reports - core:
> https://fg.oisin.rc-harwell.ac.uk/tracker/?atid=169_id=92=browse
> Bug reports - interfaces:
> https://fg.oisin.rc-harwell.ac.uk/tracker/?atid=170_id=92=browse
> Find archived messages:
> https://groups.google.com/a/york.ac.uk/d/forum/ysbl-ccp4i2dev-group
> ---
> To unsubscribe from this group and stop receiving emails from it, send an
> email to ysbl-ccp4i2dev-group+unsubscr...@york.ac.uk.
>


-- 
ICREA Res. Prof. Isabel Usón
Crystallographic Methods
Department of Structural and Molecular Biology,
Molecular Biology Institute of Barcelona, Spanish Research Council;
Barcelona Science Park, Helix Building, 08028 Barcelona (Spain)
http://chango.ibmb.csic.es/ARCIMBOLDO



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Re: [ccp4bb] Alexey Vagin

[Jan Dohnalek]

So sad.

Alexei was a great scientist and a good friend.

I will have only good memories of him.

Jan


On Mon, Mar 27, 2023 at 5:20 AM Nukri Sanishvili  wrote:

> Sad news indeed for so many of us, those who knew Alexei personally and
> those who benefited professionally from his selfless dedication to
> computational crystallography.
> A wise man once said something along the lines of anyone successful today
> standing on the shoulders of giants of the past. Unfortunately, Alexei has
> just become one such giant.
> I am so blessed to have known him professionally from my time at IKAN and
> to have him as a friend. And I am sure this sentiment is shared by all his
> colleagues and anyone who knew him personally.
> Writing this with a very heavy heart, on behalf of my wife as well.
> Nukri
>
>
>
> On Sun, Mar 26, 2023 at 1:29 PM Eugene Krissinel - STFC UKRI <
> 6fcecdb9c847-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Dear All,
>>
>> It is with a great sadness that I share with you that Alexey Vagin passed
>> away this Saturday in the Radcliffe Hospital in Oxford after suffering from
>> a heart attack with subsequent complications. He was 78 years old.
>>
>> Alexey made many developments in methods and software for macromolecular
>> crystallography, to which he devoted his whole life. He is known for his
>> BLANC Suite for structure solution done at the Moscow Institute of
>> Crystallography in the 1980s, as well as for his contributions to Refmac
>> and Monomer Library. Many thousands of researchers have benefited from his
>> work on Molrep and Balbes software for Molecular Replacement. After his
>> retirement in 2010, Alexey developed and actively maintained the MorDA
>> software for MR, which became a monument to his efforts.
>>
>> Alexey's work will continue to serve generations of researchers through
>> his contributions to CCP4, where we will take the best care of his
>> distinguished legacy.
>>
>> With sympathy to everyone who knew Alexey personally and for whom this is
>> very sad news,
>>
>> Eugene
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>


-- 
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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