Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

[Storm, Selina (DLSLtd,RAL,LSCI)]

Dear Isabel, dear all,

I think that I might not have expressed my thoughts as clearly as I would have 
liked to, therefore
one more mail on the subject:

I never meant to say that developers should stay at home and only expert users 
should go to the
workshops in the future, and I apologize if that was the impression I gave. 
Graeme gave all the reasons
why a mixture would be the best case.

Selina

From: CCP4 bulletin board  on behalf of Isabel Uson 

Sent: Friday, February 7, 2020 5:34 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Macromolecular Crystallography workshop in South America 
2020


I would like to add my thoughts. Best wishes,


Isabel



1-   I appreciate Eddy Snell is raising an issue that is real and I would like 
to thank him for it.

2-   I feel the discussion should be separated from this particular workshop in 
Montevideo. In the recent workshop in Shanghai I was the only female speaker. 
Is it that different? Would it have been different if I had been able to accept 
their invitation to this edition of a workshop I regularly attend? There have 
been quite a few more women in their program in past editions of the South 
American workshops and it would be extremely unfair to pick on them rather than 
valuing their role advancing science and education. I am indebted to Brazil and 
CCP4 for funding my research and for the opportunities their education and 
support constantly open.

3-   As a developer, I appreciate being involved in the decision of who 
represents my methods, I expect my male colleagues will feel the same way, so 
having a parallel detached pool of female tutors is problematic from the onset 
and places such tutors in a vulnerable position, open for criticism. I would 
welcome offers of such cooperation and I am open to work with volunteers.

4-   I have thought for a long time on why it is that we (women) lag back in 
our careers and for me the deepest insight came reading the homework of a 14 
year old girl. School assignment for sports: the composition and strategy of a 
football team for her class. “And myself I would place as a defender because I 
want to play and I will have far better chances taking the ball from my 
opponent than expecting any of the boys in my team to ever pass it to me.” To 
me this is the essence. Anyone who is different from the pre-conceived role 
model has to fight for opportunities, if you conform to what people expect, you 
still need to make the best of your opportunities but they will arrive 
repeatedly.

5-   We need to create (early) opportunities for those who do not conform to 
the norm because they get too few. In the school story, the teacher reacted 
issuing a rule that for two weeks only goals scored by the girls in the teams 
would count. This prompted a change. So, positive discrimination is necessary 
where it will make a difference. It is even a misnomer; there should be a 
mechanism to correct the existing negative discrimination. Some environments 
that do not find suitable women to appoint would find some if pushed by 
funding. As research directions are picked when there are grant opportunities.

6-   Gender is just one aspect of diversity, there are others: nationality, 
accent, education background… having a comprehensive look the statistic is far 
more narrow than male-caucasian. The principle of looking away from the obvious 
expectation is general.

7-   This edition of the school in Montevideo will have a speaker who 10 years 
ago was a student in the course. Would a South American student relate more to 
a role model with the same background or with the same gender? To my former 
student-self Eleanor Dodson was as much of a mythological creature in the Olymp 
as George Sheldrick.

On Fri, Feb 7, 2020 at 1:08 AM CCP4BB automatic digest system 
mailto:lists...@jiscmail.ac.uk>> wrote:
There are 32 messages totaling 42454 lines in this issue.

Topics of the day:

  1. Macromolecular Crystallography workshop in South America 2020 (14)
  2. Representation within tutors at workshops (5)
  3. AW: [EXTERNAL] Re: [ccp4bb] Macromolecular Crystallography workshop in
 South America 2020
  4. refinement of 0.73A data in shelxl (8)
  5. [EXTERNAL] Re: [ccp4bb] Representation within tutors at workshops (2)
  6. Postdoc in Paris, France: Methods development for cryo-electron microscopy
 image analysis
  7. [EXTERNAL] [ccp4bb] Macromolecular Crystallography workshop in South
 America 2020

#

--
ICREA Res. Prof. Isabel Usón
Crystallographic Methods
Department of Structural 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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This e-mail and any attachments may contain confidential, copyright and 

[ccp4bb] Postdoctoral studies in structural biology of fertilization, Karolinska Institutet

[Luca Jovine]

Our research group at Karolinska Institutet 
(http://jovinelab.org) is looking for a postdoctoral 
fellow to investigate the molecular mechanism of egg-sperm interaction at 
fertilization by single-particle cryo-EM.

The position, funded by a long-term grant from the Knut and Alice Wallenberg 
foundation, will benefit from a close collaboration with Alexey Amunts 
laboratory at SciLifeLab (https://www.scilifelab.se/researchers/alexey-amunts/) 
as well as easy access to local cryo-EM facilities (Stockholm node of the 
Cryo-EM Swedish National Facility 
(https://www.scilifelab.se/facilities/cryo-em/) and KI 3D-EM 
(https://ki.se/en/research/3d-em)) that together include 3 x Titan Krios with 
K3 detectors, a Talos Arctica with K2 and a Talos L120C with Ceta-D. Joining 
our groups will thus provide a unique opportunity to build upon the strengths 
of two complementary labs and state-of-the-art technology, in order to tackle 
one of the most fundamental questions in biology and understand how life begins.

Candidates must hold (or be about to receive) a Ph.D. degree and have 
significant hands-on experience in structural biology. Although proven 
experience in single-particle cryo-EM and knowledge of helical reconstruction 
will constitute an advantage, excellent candidates with experience in X-ray 
crystallography and a strong interest in learning cryo-EM will also be taken 
into consideration. Additionally, previous experience in mammalian cell 
expression as well as purification and biochemical characterization of 
glycoproteins will be considered an asset. At least one first author paper in a 
high-quality international peer-reviewed journal, fluency in English (both 
written and oral), good team spirit and a very strong personal drive to excel 
in science are required.

For more information about this position and to submit an application through 
the KI MyNetwork recruitment system (deadline 3 March 2020), please visit:

https://ki.varbi.com/se/what:job/jobID:313955

We look forward to receiving your application!

With best wishes,

Luca


Luca Jovine, Ph.D.
Professor of Structural Biology & EMBO Member
Karolinska Institutet
Department of Biosciences and Nutrition
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org




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Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

[Isabel Uson]

I would like to add my thoughts. Best wishes,


Isabel



1-   I appreciate Eddy Snell is raising an issue that is real and I would
like to thank him for it.

2-   I feel the discussion should be separated from this particular
workshop in Montevideo. In the recent workshop in Shanghai I was the only
female speaker. Is it that different? Would it have been different if I had
been able to accept their invitation to this edition of a workshop I
regularly attend? There have been quite a few more women in their program
in past editions of the South American workshops and it would be extremely
unfair to pick on them rather than valuing their role advancing science and
education. I am indebted to Brazil and CCP4 for funding my research and for
the opportunities their education and support constantly open.

3-   As a developer, I appreciate being involved in the decision of who
represents my methods, I expect my male colleagues will feel the same way,
so having a parallel detached pool of female tutors is problematic from the
onset and places such tutors in a vulnerable position, open for criticism.
I would welcome offers of such cooperation and I am open to work with
volunteers.

4-   I have thought for a long time on why it is that we (women) lag back
in our careers and for me the deepest insight came reading the homework of
a 14 year old girl. School assignment for sports: the composition and
strategy of a football team for her class. *“And myself I would place as a
defender because I want to play and I will have far better chances taking
the ball from my opponent than expecting any of the boys in my team to ever
pass it to me.” *To me this is the essence. Anyone who is different from
the pre-conceived role model has to fight for opportunities, if you conform
to what people expect, you still need to make the best of your
opportunities but they will arrive repeatedly.

5-   We need to create (early) opportunities for those who do not conform
to the norm because they get too few. In the school story, the teacher
reacted issuing a rule that for two weeks only goals scored by the girls in
the teams would count. This prompted a change. So, positive discrimination
is necessary where it will make a difference. It is even a misnomer; there
should be a mechanism to correct the existing negative discrimination. Some
environments that do not find suitable women to appoint would find some if
pushed by funding. As research directions are picked when there are grant
opportunities.

6-   Gender is just one aspect of diversity, there are others: nationality,
accent, education background… having a comprehensive look the statistic is
far more narrow than male-caucasian. The principle of looking away from the
obvious expectation is general.

7-   This edition of the school in Montevideo will have a speaker who 10
years ago was a student in the course. Would a South American student
relate more to a role model with the same background or with the same
gender? To my former student-self Eleanor Dodson was as much of a
mythological creature in the Olymp as George Sheldrick.

On Fri, Feb 7, 2020 at 1:08 AM CCP4BB automatic digest system <
lists...@jiscmail.ac.uk> wrote:

> There are 32 messages totaling 42454 lines in this issue.
>
> Topics of the day:
>
>   1. Macromolecular Crystallography workshop in South America 2020 (14)
>   2. Representation within tutors at workshops (5)
>   3. AW: [EXTERNAL] Re: [ccp4bb] Macromolecular Crystallography workshop in
>  South America 2020
>   4. refinement of 0.73A data in shelxl (8)
>   5. [EXTERNAL] Re: [ccp4bb] Representation within tutors at workshops (2)
>   6. Postdoc in Paris, France: Methods development for cryo-electron
> microscopy
>  image analysis
>   7. [EXTERNAL] [ccp4bb] Macromolecular Crystallography workshop in South
>  America 2020
>
> #


-- 
ICREA Res. Prof. Isabel Usón
Crystallographic Methods
Department of Structural 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] Macromolecular Crystallography workshop in South America 2020

[Peter Keller]

On 06/02/2020 10:16, Goldman, Adrian wrote:


The overall bias in society is a fact but one that, maybe, that 
neither CCP4bb nor this workshop is equipped to handle or affect? The 
bias that Bärbel refers to starts very young indeed - in the early 
interactions that young children experience - clothing colours,


On the particular issue of gendered colour choices, the Wikipedia page 
makes interesting reading: 
. 
Among other things, the "Commentary" section describes an industry-led 
drive to standardise on colour choices for birth announcement stationery 
in the USA. Make of that what you will


Regards,

Peter.

--
Peter Keller Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom




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Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

[John R Helliwell]

Dear Tassos, Dear Colleagues,
Just to mention that in the UK we are guided by the Equality Challenge Unit’s 
Athena SWAN initiative https://www.ecu.ac.uk/equality-charters/athena-swan/ 
(SWAN is Science Women’s Academic Network, founded originally at Imperial 
College). 
In particular, I mention that affirmative action (eg providing special 
initiatives for training purposes) to move away from there being under 
represented groups is allowed in the UK whereas positive discrimination in 
recruitment is not. In other countries the law is different.
In the particular case under discussion in this thread there is guidance such 
as here https://ecm31.ecanews.org/en/statement-on-gender-balance.php 
Best wishes,
John 
Emeritus Professor John R Helliwell DSc
Gender Equality Champion, School of Chemistry, University of Manchester 
2009-2011.



> On 7 Feb 2020, at 09:32, Anastassis Perrakis  wrote:
> 
>  Dear all,
> 
> Andrea made the statement: "There is dicrimination in crystallography, just 
> like in most other academic fields.”
> 
> And I do agree with her. There was discrimination, and there still is.
> 
> However, this discrimination changed from negative (against women) to 
> positive (promoting women in science).
> 
> There is positive discrimination for women, in every committee I have been, 
> be it for fellowships, grants or meetings, there is full awareness that we 
> need more women in science. I do strongly argue this is a positive and much 
> needed development which I fully support, as we need to achieve balance in 
> gender representation in academia.
> 
> However, I think that often we miss the long term goal: the long-term goal, 
> in my opinion, is to have gender-blind procedures for all decisions. Right 
> now, I wholeheartedly agree we need to make decisions with a positive 
> gender-bias for women, but that does not mean that the KPI for success is 
> achieving 50-50% representation in every single academic discipline. The long 
> term goal is to make sure that anyone regardless of gender can have an 
> opportunity to do whatever they like to do in academia and in life in general.
> 
> Before the flame wars begin, I recommend to read these articles:
> 
> https://www.ncbi.nlm.nih.gov/pubmed/19824299 
> https://journals.sagepub.com/doi/10.1177/0956797617741719
> 
> Best regards,
> 
> Tassos
> 
> 
>> On Feb 6, 2020, at 17:18, Andrea Thorn  wrote:
>> 
>> Dear all,
>> 
>> here are some numbers. There are definitly fewer females than males in 
>> crystallography: 
>> attendees of IUCr congresses - 36% female; keynote speakers - 28-17% female
>> (Source: 
>> https://blogs.iucr.org/crystallites/2018/03/07/women-in-crystallography-we%e2%80%99re-not-just-historical/)
>> There are even fewer women in methods development. In the years 2013-2019, 
>> CCP4 Developers' meeting (supposedly the largest developer-only meeting in 
>> crystallography in Europe) had 50-60 attendees, of which 5-10 were female. I 
>> also think that not every woman may have the confidence to self-describe as 
>> computational methods developer even if she codes.
>> 
>> We may not be many, but we are around! I can think about a few dozen female 
>> computational methods developers from the top of my head, and I am very 
>> willing to make a list if any organizer would be interested.
>> 
>> There is dicrimination in crystallography, just like in most other academic 
>> fields. There are quite a few high-profile examples of this, for example 
>> Isabella Karle not getting a Nobel Price or Jane Richardson only becoming a 
>> professor after decades of leading the lab with Dave and inventing the 
>> ribbon diagram. So I think there is some room for improvement even in our 
>> discipline. Why not go for it?
>> 
>> Best wishes,
>> 
>> 
>> 
>> Andrea.
>> 
>> PS. If you are a coding crystallographer (m/f/d) looking for a PhD thesis or 
>> postdoc, send me an email - we are recruiting!
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>>> Am 06.02.2020 um 11:26 schrieb Bärbel Blaum:
>>> Gosh Emmanual, your email is one amazing example of what the problem is, 
>>> every single paragraph - thanks for putting that one out!
>>>  
>>> My last email for this subject, I promise. Thanks a lot for the off-list 
>>> feedbacks!
>>>  
>>> Bärbel
>>>  
>>> -- 
>>> Bärbel Blaum, PhD
>>> Inthera Bioscience AG
>>> Einsiedlerstrasse 34
>>> CH-8820 Waedenswil
>>> Switzerland
>>> E-Mail: baerbel.bl...@intherabio.com
>>> Phone: +41 43 477 94 72--
>>>  
>>>  
>>>  
>>> Von: CCP4 bulletin board  im Auftrag von Emmanuel 
>>> Saridakis 
>>> Antworten an: Emmanuel Saridakis 
>>> Datum: Donnerstag, 6. Februar 2020 um 11:16
>>> An: 
>>> Betreff: Re: [ccp4bb] Macromolecular Crystallography workshop in South 
>>> America 2020
>>>  
>>>  
>>> Dear All,
>>>  
>>> To strike a more positive note, crystallography (esp. macromolecular) has 
>>> always had a very high representation of women at top levels: Kathleen 
>>> Lonsdale, Dorothy Crowfoot Hodgkin, Rosalind Franklin and Ada 

Re: [ccp4bb] refinement of 0.73A data in shelxl

[Tim Gruene]

Hi Phil,

yes, you are right. I mixed up the occupancy number with the part number.

I find these things easier in front of the res-file.

Thanks a lot for correcting this.

Best,
Tim

On Thursday, February 6, 2020 10:26:51 PM CET Phil Jeffrey wrote:
> That doesn't sound right re: PART numbers
> 
> classically:
> 
> PART 1
> majority disordered atoms with FVAR/occupancy of e.g. "21." instead
> of usual "11."
> PART 2
> minority disordered atoms with FVAR/occupancy of e.g. "-21."
> PART 0
> The 21.000/-21.000 pairs makes the sum of occupancies add to 1.0, but
> the actual value of each group is defined by the second free variable.
> 
> See: http://shelx.uni-goettingen.de/shelxl_html.php#PART
> The "PART 1" atoms would not interact with the "PART 2" atoms.
> There's even an example for a disordered SER in the documentation.
> 
> PART -n is used for disorders that overlap on themselves on symmetry
> axes.  "If n is negative, the generation of special position constraints
> is suppressed and bonds to symmetry generated atoms with the same or a
> different non-zero PART number are excluded; this is suitable for a
> solvent molecule disordered on a special position of higher symmetry
> than the molecule can take".
> 
> I use PART 1/PART 2/PART 0 all the time in "small molecule world" but
> I've used PART -1 precisely once.
> 
> Phil Jeffrey
> Princeton
> 
> On 2/6/20 4:15 PM, Tim Gruene wrote:
> > Dear Matthias,
> > 
> > 
> > some developers introduce new features of their refinement programs with
> > the words " ... which has been there in SHELXL since the beginning of
> > time".
> > 
> > If you are only looking for two conformations, you are looking for the
> > combination of free variable number N with part N and part -N. In case you
> > deal with more than two conformations, take a look at SUMP (as Jon
> > suggested).
> > 
> > The use of free variables is easier to explain right at the computer, so
> > please ask a colleague near you office, who is familiar with SHELXL for
> > the
> > details.
> > 
> > Best,
> > Tim
> > 
> > On Thursday, February 6, 2020 8:10:01 PM CET Barone, Matthias wrote:
> >> Sorry if the mail was not clear. I figured that out now yes. As I wrote
> >> in
> >> the update, I found this stupid error I made and now everything looks
> >> good.
> >> 
> >> Now that I got the feeling of how shelxl works, I miss one of it's
> >> features
> >> in the pdb format, namely the possibility to link occupancies of a double
> >> confirmation to another moiety, say a water or a double confirmation of
> >> the
> >> ligand. It's there a way to use something similar like FVAR in a pdb
> >> file?
> >> 
> >> 
> >> 
> >> 
> >> Dr. Matthias Barone
> >> 
> >> AG Kuehne, Rational Drug Design
> >> 
> >> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> >> Robert-Rössle-Strasse 10
> >> 13125 Berlin
> >> 
> >> Germany
> >> Phone: +49 (0)30 94793-284
> >> 
> >> 
> >> From: bogba...@yahoo.co.uk 
> >> Sent: Thursday, February 6, 2020 5:01:14 PM
> >> To: Barone, Matthias
> >> Cc: CCP4BB@JISCMAIL.AC.UK
> >> Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl
> >> 
> >> 
> >> Hello, hope I can help.
> >> 
> >> 
> >> OK, so here is the disp table...
> >> 
> >> SFAC  C H CL N O
> >> 
> >> DISP $C 0.005100.00239 15.73708
> >> 
> >> DISP $H-0.20.0  0.66954
> >> 
> >> DISP $CL0.188450.21747   1035.16450
> >> 
> >> DISP $N 0.009540.00480 28.16118
> >> 
> >> DISP $O 0.016050.00875 47.79242
> >> 
> >> 
> >> If we take these coordinates...
> >> 
> >> N 30.414964   -0.1476350.11689611.00.19533
> >> 0.44341 =
> >> 
> >> H0A   20.427823   -0.1386560.12325611.0   -1.5
> >> 
> >> C 10.348035   -0.1607760.11097911.00.20723
> >> 0.28451 =
> >> 
> >> O 40.363785   -0.1741540.10290611.00.21226
> >> 0.22954 =
> >> 
> >> SG50.1773030.1012670.04057210.040000.06849
> >> 0.03024 =
> >> 
> >> O 40.2413040.0717350.03856710.960000.14982
> >> 0.12755 =
> >> 
> >> ... the first N (followed by 3) is being assigned the scattering factors
> >> of
> >> chlorine because this element is 3rd in the SFAC list. The SG (followed
> >> by
> >> 5) is being assigned the scattering factors of O because the latter is
> >> 5th
> >> in the SFAC list.
> >> 
> >> I think you need to check these  assignments and the chlorine occupancy
> >> are
> >> Ok.
> >> 
> >> Jon Cooper
> >> 
> >> On 6 Feb 2020 11:13, "Barone, Matthias"  wrote:
> >> 
> >> Dear community
> >> here is an update of my shelxl problem. I solved it after an epiphany
> >> last
> >> night in bed... I tried countless things to get the postive density on
> >> the
> >> Cl under control. Markus suggested that the density came from a
> >> radiolysed
> >> chloride, so I tried to superimpose chlorinated and radiolysed ligands.
> >> However that did not