Re: [ccp4bb] Error in coot post-refine in Phenix

[Susan Lea]

Dear Herman

Thank you - perfect!
Never had to click that before!

Susan

Prof Susan M. Lea
Professor of Microbiology
Wellcome Trust Investigator
Sir William Dunn School of Pathology, Oxford, OX1 3RE
T: +44 1865 275181
Professorial Fellow @ Wadham College, Oxford

On 27 Aug 2020, at 13:34, Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:

Dear Lea,

when doing real space refinement in coot, on has to change the refinement 
weight, otherwise that map gets way to much weight and the coordinates get 
squeezed into to the density with the result you show. The way to do this is to 
click on the R/RC button (in my case in the upper right corner of the coot 
window) and then click on the estimate button behind the refinement weight.

Best regards,
Herman

Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Susan Lea
Gesendet: Donnerstag, 27. August 2020 13:42
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: [EXTERNAL] [ccp4bb] Error in coot post-refine in Phenix


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

Has anyone else run into this problem? Using Phenix (nightly download of  a few 
days ago) for real space refinement of coordinates against a cryoEM map all 
looks good until
I try and fit a small region in coot 0.9EL  when, post-fit, end up with bonds 
being drawn between all clost atoms and chemistry is screwed up (see picture 
below).
Atoms names etc look OK on first glance. Not sure if this is a Coot or Phenix 
problem! Same issue with both .pdb and .cif versions of the coordinates.

Susan


Prof Susan M. Lea
Professor of Microbiology
Wellcome Trust Investigator
Sir William Dunn School of Pathology, Oxford, OX1 3RE
T: +44 1865 275181
Professorial Fellow @ Wadham College, Oxford




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Re: [ccp4bb] Vote for cryoEM

[Susan Lea]

I’d agree, but then I would ;-)
@S_M_Lea

Sent from my iPhone

On 31 Mar 2020, at 20:01, Jurgen Bosch  wrote:

 I personally tweet, and I know a lot of well established scientists that 
tweet too.

Don't pretend Twitter is only junk, there are a lot of serious scientist 
tweeting good and valuable information. True there are enough stupid people 
tweeting BS.

Jürgen

P.S. Follow me on Twitter @Bosch_Lab

On Mar 31, 2020, at 2:01 PM, Gloria Borgstahl 
mailto:gborgst...@gmail.com>> wrote:

I personally don't tweet.


On Tue, Mar 31, 2020 at 12:21 PM Sweet, Robert 
<27e0eb9d20ec-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Real Men (and possibly Women too) Don't Tweet.

Bob


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of James Holton mailto:jmhol...@lbl.gov>>
Sent: Tuesday, March 31, 2020 12:18 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Vote for cryoEM

Allessandro,

The link you provide directs to a website hosted at someting called 
"twitter.com".  My spam filter flagged it as junk.

-James Holton
MAD Scientist

On 3/31/2020 8:41 AM, Alessandro Vannini wrote:
We are head to head with mass-spectrometry in the #JBCMethodsMadness 
CHAMPIONSHIP. This can’t happen!

Get out and VOTE! 15 min to go!

https://twitter.com/jbiolchem/status/1244655631316987905?s=20

[cid:part2.4691618D.6AA0935A@lbl.gov]

Sent from my iPhone



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

[Susan Lea]

Perhaps some of the respondents to this question should real Angela Saini’s 
Inferior before commenting in public
Susan

Sent from my iPhone

On 5 Feb 2020, at 19:18, Robert Nicholls  wrote:


As a Caucasian male I hesitate to post; I know that there are a lot of people 
who are sensitive to this subject, so feel that I'm treading on eggshells in 
responding... Nevertheless I feel obliged to respond, having a certain amount 
of insight into the topic in the context of these workshops.

Personally I don't find posts such as this - which simply incite (positive) 
discrimination - to be very constructive.

From speaking to organisers and being involved in committees over numerous 
years I know that gender bias is always very much at the forefront of the 
organisers' minds when deciding whom to invite. Especially where funding 
requirements and committees are involved, the issue of gender bias is always 
raised with a heavy hand. Consequently, in modern times whenever there is a 
gender bias in our field it is not a result of naivety or discriminative 
cliqueness, but rather necessity due to the availability of appropriate tutors 
(as correctly indicated by Rasmus). And as Andrew points out, organising these 
workshops takes a lot of effort, and as such it is inappropriate to treat the 
organisers with undue disrespect.

Ultimately, the objective is to teach the topics intended to be covered in the 
workshop. For sure, there are a number of very good females who are appropriate 
for teaching on these courses, despite being in the relative minority. I know a 
number of the females who are very able to tutor on such courses, and by 
personal communication I also know why some of them might not be able to attend 
this particular one this year. As Eleanor has pointed out, sometimes life gets 
in the way.

There is a very good gender balance of participants in these workshops, as is 
indicative of the demographic of practicing structural biologists wishing to 
utilise these software tools. But clearly the gender balance of tutors is 
heavily in favour of males - this represents the difference in gender ratios of 
people engaging with practical structural biology versus computational methods 
development.

I understand the argument that it is good for female tutors to be present as 
role models in such workshops, but it is worth noting that the people attending 
these workshops do not intend to become methods developers - they simply want 
to know how to best use the tools available. Consequently there is a 
qualitative difference between tutors and participants. Therefore, there is 
limited capability for the participants to see the tutors as role models in 
this context.

I feel that the junior vs senior argument isn't at all relevant. More senior 
developers will of course be generally preferred - it is necessary for 
individuals with sufficient experience to be available to help in these 
workshops (again as indicated by Rasmus). But I have seen many junior software 
developers sent to teach at CCP4 workshops (irrespective of gender). Indeed, it 
is necessary for junior developers to gain such experience in order to grow. 
This is very necessary in order to meet the demands of an expanding and 
evolving community.

From a purely statistical point of view it seems reasonable to me for the 
gender bias of tutors in such workshops to realistically reflect the 
demographic of crystallographic software developers. Consequently, I feel that 
the real problem lies in the proportion of females who want to become methods 
developers. My personal experience is that there is absolutely no 
discrimination whatsoever when interviewing or encouraging potential scientists 
to enter the field. Perhaps I have been fortunate enough to not be exposed to 
an environment where there is any such discrimination.

For me, the real problem lies in the proportion of females who are interested 
in a career in computational methods development; I believe this issue stems 
back to the proportion of females who choose theoretical/computational degrees 
at undergraduate level. I do not know how to encourage more females to engage 
with the field at earlier stages in their career - perhaps this is a problem 
for those teaching in universities to attempt to address. Fortunately I have 
seen a rise in the number of females interested in computational methods 
development in recent years (particularly in bioinformatics), which is very 
encouraging - perhaps this represents changing times...

Ultimately, positive discrimination is nevertheless discrimination. And as such 
is unethical, and should not be supported by a conscientious scientific 
community. I would prefer to see a system whereby gender, race and creed are 
not seen as a factor when deciding who should be chosen for a particular role. 
Personal merit should be the only consideration.

If this results in a gender bias then the problem should be addressed at the 
source, not 

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

[Susan Lea]

Dear Tim
I’m already teaching at 3 workshops this year - there are many others who could 
do a better job (and who are also women)
Susan

Sent from my iPhone

On 5 Feb 2020, at 12:21, Roversi, Pietro (Dr.)  wrote:


Dear all,

my twopenny worth - when Helen Walden and I put together the 2013 CCP4 Weekend 
list of speakers,
we were delighted to end up with a not-so-gender-imbalanced list of speakers,
but we did achieve that balance *intentionally*.

As we attempt to redress a de facto longstanding bias against women in the 
workplace,
everybody in charge of this kind of decision is expected to *intentionally* 
look for excellent women scientists.

They will find them if they look - and the event will be better because of 
participation of women as well as
male scientists.

with best wishes,

Pietro




Pietro Roversi

Lecturer (Teaching and Research) https://le.ac.uk/natural-sciences/

LISCB Wellcome Trust ISSF Fellow

<https://bit.ly/2I4Wm5Z>https://le.ac.uk/liscb/research-groups/pietro-roversi


Leicester Institute of Structural and Chemical Biology
Department of Molecular and Cell Biology, University of Leicester
Henry Wellcome Building
Lancaster Road, Leicester, LE1 7HB
England, United Kingdom

Tel. +44 (0)116 2297237



From: CCP4 bulletin board on behalf of Tim Gruene
Sent: Wednesday, 05 February 2020 16:18
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Macromolecular Crystallography workshop in South America 
2020

Dear Susan, dear Silvia,

why don't both of you offer to teach as tutors at this CCP4 workshop?

I do not believe that this 'imbalance' has been done intentionally by any of
the people involved.

Both of you should take a step forward, tutor in South America. In case your
offer is rejected, you may start to argue.

Best regards,
Tim

On Wednesday, February 5, 2020 1:48:32 PM CET Susan Lea wrote:
> ‘Role’ models are not what are needed - just a better representation of our
> community. This is lazy scheduling and in a community where there have
> always been influential women we should do better - CCP4 has let the whole
> community down by allowing their name to be associated with this.
 Perhaps
> we could encourage the speakers to do as many of my colleagues have started
> to do - ask who else is speaking at a meeting and refuse to participate if
> the list does not reflect the community.
> Susan
>
> Sent from my iPhone
>
> On 5 Feb 2020, at 07:38, Silvia Onesti  wrote:
>
>  Maybe CCP4 should explicitely ask for gender balance before sponsoring a
> workshop?

> Silvia
>
> -
> Silvia Onesti - Head of Structural Biology
>
> Elettra - Sincrotrone Trieste S.C.p.A.
> AREA Science Park, 34149 Basovizza, Trieste ITALY
>
> Email: silvia.one...@elettra.eu<mailto:silvia.one...@elettra.eu>
> Tel. +39 040 3758451  Mob +39 366 6878001
>
> http://www.elettra.trieste.it/People/SilviaOnesti
> http://www.elettra.trieste.it/labs/structural-biology
> ---
>
>
> On 5 Feb 2020, at 03:09, Alejandro Buschiazzo
> mailto:ale...@pasteur.edu.uy>> wrote:

> Thank you for your comment, we cannot agree more.
>
> We are aware of this, and still are in the process of inviting a few more
> speakers.
 We shall  thus bring more  women on board, and achieve a
> balanced group!
> Cheers,
> Alejandro (on behalf of the organizers)
>
>
> El 4 feb. 2020, a la(s) 22:02, Edward Snell
> mailto:esn...@hwi.buffalo.edu>> escribió:

>
> ​It is great that this workshop is occurring but I couldn't help but notice
> that there seem to be a lot of male speakers and tutors. I was wondering if
> it might be appropriate to add some female role models. There are some
> great candidates?

>
>
> 
> From: CCP4 bulletin board
> mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of
> Alejandro Buschiazzo mailto:ale...@pasteur.edu.uy>>
> Sent: Tuesday, February 4, 2020 7:30 PM
> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: [ccp4bb] Macromolecular Crystallography workshop in South America
> 2020

> Dear colleagues,
>
> We are pleased to announce the 8th South American Macromolecular
> Crystallography School:

> Macromolecular Crystallography School 2020
> "Structural Biology to enhance high impact research in health and disease”
>
> To be held at the Institut Pasteur de Montevideo (Uruguay) - September 9-19,
> 2020

> http://pasteur.uy/novedades/mx2020/
>
> The application deadline is July 9, 2020. For further inquiries :
> mx2...@pasteur.edu.uy<mailto:mx2...@pasteur.edu.uy>

>
> Main Topics:
>
> •   data processing;
>
> •   phasing and structure

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

[Susan Lea]

‘Role’ models are not what are needed - just a better representation of our 
community. This is lazy scheduling and in a community where there have always 
been influential women we should do better - CCP4 has let the whole community 
down by allowing their name to be associated with this.
Perhaps we could encourage the speakers to do as many of my colleagues have 
started to do - ask who else is speaking at a meeting and refuse to participate 
if the list does not reflect the community.

Susan

Sent from my iPhone

On 5 Feb 2020, at 07:38, Silvia Onesti  wrote:

 Maybe CCP4 should explicitely ask for gender balance before sponsoring a 
workshop?

Silvia

-
Silvia Onesti - Head of Structural Biology

Elettra - Sincrotrone Trieste S.C.p.A.
AREA Science Park, 34149 Basovizza, Trieste ITALY

Email: silvia.one...@elettra.eu
Tel. +39 040 3758451  Mob +39 366 6878001

http://www.elettra.trieste.it/People/SilviaOnesti
http://www.elettra.trieste.it/labs/structural-biology
---


On 5 Feb 2020, at 03:09, Alejandro Buschiazzo 
mailto:ale...@pasteur.edu.uy>> wrote:

Thank you for your comment, we cannot agree more.

We are aware of this, and still are in the process of inviting a few more 
speakers.
We shall  thus bring more  women on board, and achieve a balanced group!

Cheers,
Alejandro (on behalf of the organizers)


El 4 feb. 2020, a la(s) 22:02, Edward Snell 
mailto:esn...@hwi.buffalo.edu>> escribió:


​It is great that this workshop is occurring but I couldn't help but notice 
that there seem to be a lot of male speakers and tutors. I was wondering if it 
might be appropriate to add some female role models. There are some great 
candidates?




From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Alejandro Buschiazzo 
mailto:ale...@pasteur.edu.uy>>
Sent: Tuesday, February 4, 2020 7:30 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

Dear colleagues,

We are pleased to announce the 8th South American Macromolecular 
Crystallography School:

Macromolecular Crystallography School 2020
"Structural Biology to enhance high impact research in health and disease”

To be held at the Institut Pasteur de Montevideo (Uruguay) - September 9-19, 
2020

http://pasteur.uy/novedades/mx2020/

The application deadline is July 9, 2020. For further inquiries : 
mx2...@pasteur.edu.uy


Main Topics:

•   data processing;

•   phasing and structure determination;

•   model refinement and validation;

•   introduction to crystallography + cryo-electron microscopy integration

Confirmed speakers and tutors (so far... a few more will join the crew):

Alejandro Buschiazzo (Institut Pasteur de Montevideo, Uruguay)
Paul Emsley (Laboratory of Molecular Biology MRC, Cambridge, UK)
Rafael Junqueira Borges (Instituto de Biociências UNESP, Botucatu, Brazil)
Ronan Keegan (STFC Rutherford Appleton Lab - CCP4, Didcot, UK)
Eugene Krissinel (STFC Rutherford Appleton Lab - CCP4, Didcot, UK)
Joāo Muniz (Instituto de Fisica de São Carlos, Brazil)
Garib Murshudov (Laboratory of Molecular Biology MRC, Cambridge, UK)
Colin Palmer (STFC Rutherford Appleton Lab - CCP-EM, Didcot, UK)
James Parkhurst (Diamond Light Source, Didcot, UK)
Randy Read (University of Cambridge, UK)
Kyle Stevenson (STFC Rutherford Appleton Lab - CCP4, Didcot, UK)
Clemens Vonrhein (Global Phasing Ltd, Cambridge, UK)

Please find the application form and further contact information at 
http://pasteur.uy/novedades/mx2020/
(this www site will be updated regularly, so stay tuned!)

This Workshop is supported by the Collaborative Computational Project Nº4 
(CCP4, UK) & Science and Technology Facilities Council (UK); the Centro de 
Biologia Estructural del Mercosur (CeBEM); and the Programa Iberoamericano de 
Ciencia y Tecnologia para el Desarrollo (CYTED) through de MICROBES consortium.

Organizers:
Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay
Kyle Stevenson, DPhil. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom
Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP, Brazil

Applicants:
25 students will be selected, prioritizing advanced PhD, postdocs and young 
researchers. The Course will provide financial support covering registration 
fees, and for the case of those students coming from abroad, all local expenses 
(lodging, per diem and local transportation). Look in the www site for details 
on application procedures.

The application deadline is July 9, 2020.

Please address further inquiries to: 
mx2...@pasteur.edu.uy

Looking forward to hosting you in Montevideo!



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Re: [ccp4bb] SEC and MALS

[Susan Lea]

What do you mean by mass from SEC? SEC is not a mass determination method

Sent from my iPhone

On 27 Aug 2019, at 06:57, Natesh Ramanathan 
mailto:nat...@iisertvm.ac.in>> wrote:

Dear  Friends,

Can you share your experience with examples of MALS giving lower 
molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg. 
Dimer),  for the same protein sample?

  If you have/know any published paper, can you please point me to that 
reference paper or send me the paper?

Many thanks.
Best regards,
Natesh


--
--
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
--
Dr. Ramanathan Natesh
Assistant Professor,
School of Biology,
Indian Institute of Science Education and Research Thiruvananthapuram 
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

nat...@iisertvm.ac.in
http://www.researcherid.com/rid/C-4488-2008
ORCID: http://orcid.org/-0002-1145-5962
https://publons.com/author/1520837/ramanathan-natesh#profile
http://faculty.iisertvm.ac.in/natesh

Office Ph. 0091- 471-2778087



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Re: [ccp4bb] challenges in structural biology

[Susan Lea]

I'll shut up soon

Other than when asked to review, I consider it best to concern myself most with 
how I use the share of the limited resources I have access to and refrain from 
commenting on work by others in fields I have sufficiently little knowledge of 
that my estimate of worth is likely to be flawed.

I certainly do not agree that a structure determined by EM is a priori more 
biologically true than one determined by crystallography - as always the only 
question is exactly what is the structure of, and how has the sample had to be 
compromised to determine it.

If you feel you can prove that this is a flawed statement across the whole of 
biology - publish an article and we can shut the synchrotrons.

Yours - from a mixed-method structural biologist ;-)

Susan

Prof. Susan M. Lea,  FMedSci  tel: +44 1865 275181
--
Director of the Central Oxford Structural Microscopy and Imaging Centre & 
Professor of Microbiology
Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ 
WadhamCollege


From: r...@mrc-lmb.cam.ac.uk 
Sent: 17 July 2019 10:21:42
To: Susan Lea
Cc: ccp4bb@jiscmail.ac.uk
Subject: Re: [ccp4bb] challenges in structural biology

Hi Susan,

We are not naive if we care about using the limited resources of this planet
responsibly. This has nothing to do with whoever's favourite method. I have
nothing against crystallography, it is a beautiful art and has been a success
historically. I have solved plenty of crystal structures myself and will
probably have to keep doing it for a little while. But it is naive to ignore
that the time to move on has arrived, and that we have to use resources to
develop better technologies which address the real biological questions
instead of keeping dinosaurs on life support.

How many of the structures solved on synchrotrons worldwide and of the
zillions in the PDB are of any use or biological relevance (original
question)? There is an enormous amount of waste, including the nasty chemicals
use to grow crystals and to phase pointless structures, let's be honest.

Best wishes,

Radu



> I think we are naive if we care about the method used to obtain the structure
> - what matters is getting at the structure.  What is great is that the variety
> of ways we can do this has increased meaning more samples become tractable for
> high resolution structure determination. I don’t see the point of ridiculous
> my method is better than your method arguments - for some samples all methods
> are equivalent, for some there is only one method that will yield answers - we
> just need to train students and develop methods that allow the broadest
> access. Everything else is bias-driven posturing. Let’s just solve some
> structures and learn something about biology.
>
>
> Susan
>
> Sent from my iPhone
>
>> On 17 Jul 2019, at 08:43, r...@mrc-lmb.cam.ac.uk 
>> wrote:
>>
>> Hi Both,
>>
>> I am not questioning the PDB stats, the issue was whether (crystal)
>> structures
>> are sufficiently relevant to address biological questions and justify the
>> resources. Fragment screening is one example where investment in protein
>> crystallography can still be justified (for now). But it doesn't really ask
>> or
>> answer biological questions... for these, whether we like it or not,
>> macromolecular crystallography (or NMR, even in cell) cannot be the future.
>> In
>> my opinion :-)
>>
>> Best wishes,
>>
>> Radu
>>
>>
>>> Stating the crystallography is dead might be a bit premature, it is still
>>> king
>>> for depositions.
>>>
>>>
>>>
>>> In 2017 we had a large number of fragment screening experiments deposited.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> From: CCP4 bulletin board  On Behalf Of Nukri
>>> Sanishvili
>>> Sent: 15 July 2019 23:09
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> Subject: Re: [ccp4bb] challenges in structural biology
>>>
>>>
>>>
>>> I know it is going to hijack the original topic but I could not help...
>>>
>>>
>>>
>>> “The reports of death of (macromolecular) crystallography are greatly
>>> exaggerated.
>>>
>>> If we believed the prognosticators, it has been dead since the 80s when
>>> some
>>> folks made the claim that the only relevant structures were those solved
>>> by
>>> NMR.
>>>
>>> I think we've done quite well since then...
>>>
>>> Best,
>>>
>>> Nukri
>>>
>>>
>>

Re: [ccp4bb] challenges in structural biology

[Susan Lea]

I think we are naive if we care about the method used to obtain the structure - 
what matters is getting at the structure.  What is great is that the variety of 
ways we can do this has increased meaning more samples become tractable for 
high resolution structure determination. I don’t see the point of ridiculous my 
method is better than your method arguments - for some samples all methods are 
equivalent, for some there is only one method that will yield answers - we just 
need to train students and develop methods that allow the broadest access. 
Everything else is bias-driven posturing. Let’s just solve some structures and 
learn something about biology.


Susan 

Sent from my iPhone

> On 17 Jul 2019, at 08:43, r...@mrc-lmb.cam.ac.uk  
> wrote:
> 
> Hi Both,
> 
> I am not questioning the PDB stats, the issue was whether (crystal) structures
> are sufficiently relevant to address biological questions and justify the
> resources. Fragment screening is one example where investment in protein
> crystallography can still be justified (for now). But it doesn't really ask or
> answer biological questions... for these, whether we like it or not,
> macromolecular crystallography (or NMR, even in cell) cannot be the future. In
> my opinion :-)
> 
> Best wishes,
> 
> Radu
> 
> 
>> Stating the crystallography is dead might be a bit premature, it is still 
>> king
>> for depositions.
>> 
>> 
>> 
>> In 2017 we had a large number of fragment screening experiments deposited.
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> From: CCP4 bulletin board  On Behalf Of Nukri
>> Sanishvili
>> Sent: 15 July 2019 23:09
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] challenges in structural biology
>> 
>> 
>> 
>> I know it is going to hijack the original topic but I could not help...
>> 
>> 
>> 
>> “The reports of death of (macromolecular) crystallography are greatly
>> exaggerated.
>> 
>> If we believed the prognosticators, it has been dead since the 80s when some
>> folks made the claim that the only relevant structures were those solved by
>> NMR.
>> 
>> I think we've done quite well since then...
>> 
>> Best,
>> 
>> Nukri
>> 
>> 
>> 
>> On Mon, Jul 15, 2019 at 3:45 PM >  > wrote:
>> 
>> Hi Tassos, Tim,
>> 
>> I wonder why would you or anyone on this list worry whether biological
>> questions that can be asked and answered with structures are relevant to
>> justify the resources? I think there is abundant evidence that this is the
>> case. Unless your point is that crystallography is now dead for all practical
>> purposes... then yes, I fully agree :-) It would however be wrong to erase 
>> its
>> historical contribution to understanding biology.
>> 
>> Best wishes,
>> 
>> Radu
>> 
>> 
>>> I would wonder more if the biological questions you can *ask* with a
>>> (crystal)
>>> structure are sufficiently relevant to justify the resources.
>>> 
>>> Sent from my iPhone
>>> 
 On 15 Jul 2019, at 22:08, Tim Grüne >>>  > wrote:
 
 Dear James,
 
 10) are the biological questions that you can answer with a (crystal)
 structure sufficiently relevant to justify the resources?
 
 Best,
 Tim
 
 
 
 Am 15.07.2019 21:44, schrieb Holton, James M:
> Hello folks,
> I have the distinct honor of chairing the next Gordon Research
> Conference on Diffraction Methods in Structural Biology (July 26-31
> 2020).  This meeting will focus on the biggest challenges currently
> faced by structural biologists, and I mean actual real-world
> challenges.  As much as possible, these challenges will take the form of
> friendly competitions with defined parameters, data, a scoring system,
> and "winners", to be established along with other unpublished results
> only at the meeting, as is tradition at GRCs.
> But what are the principle challenges in biological structure
> determination today?  I of course have my own ideas, but I feel like I'm
> forgetting something.  Obvious choices are:
> 1) getting crystals to diffract better
> 2) building models into low-resolution maps (after failing at #1)
> 3) telling if a ligand is really there or not
> 4) the phase problem (dealing with weak signal, twinning and
> pseudotranslation)
> 5) what does "resolution" really mean?
> 6) why are macromolecular R factors so much higher than small-molecule
> ones?
> 7) what is the best way to process serial crystallography data?
> 8) how should one deal with non-isomorphism in multi-crystal methods?
> 9) what is the "structure" of something that won't sit still?
> What am I missing?  Is industry facing different problems than
> academics?  Are there specific challenges facing electron-based
> techniques?  If so, could the combined strength of all the world's
> methods developers solve them?  I'm interested in hearing the voice of
> this community.  On or off-list is 

Re: [ccp4bb] VERY old mtz file..

[Susan Lea]

bring back the lcf format reflection file ;-)

Prof. Susan M. Lea,  FMedSci  tel: +44 1865 275181
--
Director of the Central Oxford Structural Microscopy and Imaging Centre & 
Professor of Microbiology
Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ 
WadhamCollege


From: CCP4 bulletin board  on behalf of Ian Tickle 

Sent: 09 November 2018 19:32:50
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] VERY old mtz file..


PS if you're interested in software archaeology and you have the CCP4 library 
source code handy, check out these routines that I wrote for VAX/VMS.  Yes, we 
kept it in the source distribution all these years!

ccp4-7.0-src/checkout/libccp4/fortran/vmsdiskio.for

Subroutines QFIEEE & QTIEEE illustrate the horrible data mangling you had to do 
just to convert between Vax floating-point and IEEE (on top of the 
byte-swapping!).

Those were the days!

Cheers

-- Ian


On Fri, 9 Nov 2018 at 19:17, Ian Tickle 
mailto:ianj...@gmail.com>> wrote:

All MTZ (and map) files from the very beginning had an architecture-dependent 
'machine-stamp' in the header which *should* cause the read routines to do the 
necessary conversions if needed (i.e. where the writing & reading machine 
formats differ).  This was absolutely necessary in the days when we had a 
goodly mix of formats (VAX, Convex, Cray, SGI, IBM mainframe, IBM PC, Mac ...). 
 Now pretty well everything is Intel or compatible, i.e. little-endian IEEE 
format, so this functionality hasn't been real-world tested for aeons and it's 
possible in the meantime that it's fallen into disrepair.

Cheers

-- Ian


On Fri, 9 Nov 2018 at 18:57, Ethan A Merritt 
mailto:merr...@u.washington.edu>> wrote:
On Friday, November 9, 2018 9:12:36 AM PST Robert Esnouf wrote:
>
> Without checking further, there is a "dd" option for swapping big-endian to 
> little-endian... swab. This may simply be the issue...

DEC computers used a different floating point format.
Swapping endian-ness would be sufficient, although it might be required in 
addition.

Ethan


>
> The output of od -x may help decode the header of the file...
>
> Regards,
> Robert
>
> --
>
> Dr Robert Esnouf
>
> University Research Lecturer,
> Director of Research Computing BDI,
> Head of Research Computing Core WHG,
> NDM Research Computing Strategy Officer
>
> Main office:
> Room 10/028, Wellcome Centre for Human Genetics,
> Old Road Campus, Roosevelt Drive, Oxford OX3 7BN, UK
>
> Emails:
> rob...@strubi.ox.ac.uk / 
> rob...@well.ox.ac.uk / 
> robert.esn...@bdi.ox.ac.uk
>
> Tel:   (+44)-1865-287783 (WHG); (+44)-1865-743689 (BDI)
>
>
> -Original Message-
> From: "Pavel Afonine" mailto:pafon...@gmail.com>>
> To: CCP4BB@JISCMAIL.AC.UK
> Date: 09/11/18 13:54
> Subject: Re: [ccp4bb] VERY old mtz file..
>
> Now I see the value of storing data in plain text files even more (mind Shelx 
> or X-plor formats, for example) -;)
>
>
>  readable files.>
>
> On Fri, Nov 9, 2018 at 9:47 PM Clemens Vonrhein 
> mailto:vonrh...@globalphasing.com>> wrote:
>
> Hi Eleanor,
>
> You could try running the oldest MTZ2VARIOUS binary you can find -
> e.g.
>
>   wget ftp://ftp.ccp4.ac.uk/ccp4/4.2/binaries/ccp4-4.2_Linux.tar.gz
>   tar -xvf ccp4-4.2_Linux.tar.gz bin/mtz2various
>
>   bin/mtz2various hklin ...
>
> Any older binaries (ftp://ftp.ccp4.ac.uk/ccp4/4.0.1/) will require an
> SGI or Dec/Alpha machine ;-)
>
> If that doesn't help I would first check that it is actually a correct
> MTZ file: does the ASCII header (trailer) show up with
>
>   strings your.mtz
>
> towards the end?
>
> Cheers
>
> Clemens
>
> On Fri, Nov 09, 2018 at 12:47:09PM +, Eleanor Dodson wrote:
> > Anyone any idea what to do about this?? Created in 1992!!
> > Seems unreadable..
> >
> > No CTYP lines input for file:  1
> > Indices output even if all data items flagged "missing"
> >  Warning, NOT all LABOUT data lines given
> > Warning: Machine stamp corrupted? Assuming native format.
> > >> CCP4 library signal library_file:End of File (Error)
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> --
>
> *--
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK   
> www.globalphasing.com
> *--
>
> 
>
> To unsubscribe from the CCP4BB list, click the 

[ccp4bb] Two Postdoctoral Research Posts in Oxford

[Susan Lea]

https://www.path.ox.ac.uk/content/postdoctoral-research-assistant-structural-biologyprotein-chemistry-2-posts

POSTDOCTORAL RESEARCH ASSISTANT IN STRUCTURAL BIOLOGY/PROTEIN CHEMISTRY (2 
POSTS)

Closing date: Friday, 11 May 2018 - 12pm
Grade 7: £31,604 - £38,833 p.a.

We are seeking to appoint two talented Postdoctoral Research Assistants under 
the supervision of Professor Susan Lea 
(https://www.path.ox.ac.uk/content/susan-lea). This project aims to dissect 
innate immune system regulatory pathways and how these are manipulated by 
bacterial and parasite pathogens. These posts will build on recent work 
identifying inhibitors of complement in tick saliva that allow dissection of 
regulatory pathways in human complement.

The postholder will manage his/her own academic research and administrative 
activities, test hypotheses and analyse scientific data from a variety of 
sources as well as assist with the design and implementation of experiments. 
You will collaborate in the preparation of scientific reports and journal 
articles and the presentation of papers and posters at conferences and also 
represent the research group at external meetings/seminars.

Applicants should have a PhD or equivalent experience/qualification. You should 
have experience in expression and purification of proteins from heterologous 
expression systems and analysis of these proteins using biophysical and 
biochemical techniques is essential together as is an interest in using 
structures to understand biological questions. The postholders must be 
meticulous in their approach to record keeping and highly organised and have 
excellent communication skills. Previous laboratory experience is essential and 
should include a high level of competence in molecular biology techniques (e.g. 
DNA purification, plasmid manipulation).

Both posts are fixed-term appointments available for 2 years. If you are 
interested in this role, and have the skills and experience we are looking for, 
please apply online. You will be required to upload a CV and supporting 
statement as part of your online application.

The closing date for applications is 12.00 midday on Friday 11 May 2018. 
Interviews will be held as soon as possible thereafter.



Susan

Prof. Susan M. Lea,  FMedSci  tel: +44 1865 275181
--
Director of the Central Oxford Structural Microscopy and Imaging Centre & 
Professor of Microbiology
Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ 
WadhamCollege

[ccp4bb] Final Call for Oxford Workshop

[Susan Lea]

A few places left - closing deadline 1st December 2017

Workshop on real-time cryo-EM image processing with SIMPLE

Oxford, 9-10th January 2018
(designed to allow attendance at the CCP4 workshop immediately after)

http://simplecryoem.com/Oxford/workshop2018.html

Course overview:
SIMPLE (Single-particle IMage Processing Linux Engine) is a program package for 
cryo-EM image processing, featuring algorithms for all aspects of 
single-particle image analysis. A recent focus of the SIMPLE development team 
has been the establishment of a streaming pipeline, allowing real-time image 
processing of data directly from the microscope with a minimal computing setup.

This workshop is aimed at facility personnel, postdocs and students using 
single-particle reconstruction as their primary research tool. Processing 
through 2D, ab initio 3D, heterogeneity analysis, to high resolution refinement 
 will be introduced by each participant independently working through all 
stages.
The new SIMPLE GUI will also be introduced allowing all stages of processing 
through web browsers on any device.

40 attendees can be accommodated.

Venue:
The workshop will be the first based at the Central Oxford Structural 
Microscopy Imaging Centre. This new facility, consisting of a suite of direct 
electron detector equipped microscopes at 200 and 300kV, brings the cryo-em 
revolution to scientists based in the Oxford Science Area. A central computing 
facility associated with the cryo-EM Centre has driven development of the 
automated real time processing of single particle data to facilitate informed 
sample selection.

Fees:
The workshop will cost £150 to include registration, lunch (on both days), 
coffee breaks. Attendees will need to arrange overnight accommodation in 
Oxford. Please register interest using the link at top.
 
The organizing committee
Susan Lea
Dominika Elmlund
Hans Elmlund

Prof. Susan M. Lea,  FMedSci  tel: +44 1865 275181
--
Director of the Central Oxford Structural Microscopy and Imaging Centre & 
Professor of Microbiology
Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ 
WadhamCollege

[ccp4bb] Oxford workshop on real-time cryo-EM image processing with SIMPLE

[Susan Lea]

Workshop on real-time cryo-EM image processing with SIMPLE

Oxford, 9-10th January 2018
(designed to allow attendance at the CCP4 workshop immediately after)

http://simplecryoem.com/Oxford/workshop2018.html

Course overview:
SIMPLE (Single-particle IMage Processing Linux Engine) is a program package for 
cryo-EM image processing, featuring algorithms for all aspects of 
single-particle image analysis. A recent focus of the SIMPLE development team 
has been the establishment of a streaming pipeline, allowing real-time image 
processing of data directly from the microscope with a minimal computing setup.

This workshop is aimed at facility personnel, postdocs and students using 
single-particle reconstruction as their primary research tool. Processing 
through 2D, ab initio 3D, heterogeneity analysis, to high resolution refinement 
 will be introduced by each participant independently working through all 
stages.
The new SIMPLE GUI will also be introduced allowing all stages of processing 
through web browsers on any device.

40 attendees can be accommodated.

Venue:
The workshop will be the first based at the Central Oxford Structural 
Microscopy Imaging Centre. This new facility, consisting of a suite of direct 
electron detector equipped microscopes at 200 and 300kV, brings the cryo-em 
revolution to scientists based in the Oxford Science Area. A central computing 
facility associated with the cryo-EM Centre has driven development of the 
automated real time processing of single particle data to facilitate informed 
sample selection.

Fees:
The workshop will cost £150 to include registration, lunch (on both days), 
coffee breaks. Attendees will need to arrange overnight accommodation in 
Oxford. Please register interest using the link at top.
 
The organizing committee
Susan Lea
Dominika Elmlund
Hans Elmlund


Prof. Susan M. Lea,  FMedSci  tel: +44 1865 275181
--
Director of the Central Oxford Structural Microscopy and Imaging Centre & 
Professor of Microbiology
Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ 
WadhamCollege

[ccp4bb] Four PostDoc positions in Oxford

[Susan Lea]

In addition to the posts working on Tat secretion we also have two posts 
looking at Notch signalling in Oxford.
I'm reposting the link for the Tat positions as I failed to post that correctly 
last week :-)

Notch signalling - With Susan Lea  Penny Handford http://tinyurl.com/pcv5xlq 
Tat protein secretion - With Susan Lea  Ben Berks http://tinyurl.com/nervhmz

Please apply via the online application form as applications cannot be accepted 
in other ways

Best
Susan


Prof. Susan M. Lea  tel: +44 1865 275181

Professor of Microbiology
Sir William Dunn School of Pathology, Oxford OX1 3RE UK

Professorial Fellow @ Wadham College, 

[ccp4bb] Two Postdoctoral Research Assistants in Oxford

[Susan Lea]

We seek to appoint two Research Associates to undertake structural studies of 
the Tat protein transporter. The Tat system is a highly unusual protein 
transport pathway that moves folded proteins across the bacterial cytoplasmic 
membrane [Nature Rev.Microbiol. (2012) 10: 483]. The Tat system is required for 
the virulence of many bacterial pathogens. We have recently determined the 
structure of the core Tat transporter component TatC by X-ray crystallography 
[Nature (2012) 492: 210]. This project aims to build upon this success by 
determining high resolution structures of TatC in complex with other Tat 
components and with substrate targeting peptides. The project will also 
encompass related biochemical analysis of Tat complexes. 

Applicants must have an interest in structural biology and should possess, or 
expect to shortly obtain, a PhD in Biochemistry or Structural Biology or a 
related discipline. Applicants must have expertise in protein purification and 
characterisation as well as expertise in at least one of the following: X-ray 
crystallography or other high resolution structural method; working with 
membrane proteins; biochemical and biophysical analysis of protein-protein 
interactions; biochemistry of protein transport. 

These full-time posts are available immediately, working jointly with Professor 
Ben Berks in the Department of Biochemistry and Professor Susan Lea in the Sir 
William Dunn School of Pathology, South Parks Road, Oxford. The positions are 
funded by the Medical Research Council (MRC) for up to 48 months in the first 
instance. 

https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.display_form



Prof. Susan M. Lea  tel: +44 1865 275181

Professor of Chemical Pathology  
Sir William Dunn School of Pathology, Oxford OX1 3RE UK

Tutorial Fellow @ Brasenose College, Oxford OX1 4AJ

Re: [ccp4bb] raw data deposition

[Susan Lea]

I think the key is that the questions asks is a waste of money.
In a straightened funding time it may just be that storing the raw images in 
addition to the processed
data doesn't float to the top of the list of things that must be done whatever 
else happens in science.


Something can be desirable but just not come above a funding barrier.




Susan



Prof. Susan M. Lea  tel: +44 1865 275181

Professor of Chemical Pathology   Co-Director of the James Martin Vaccine 
Design Institute
Sir William Dunn School of Pathology, Oxford OX1 3RE UK

Tutorial Fellow @ Brasenose College, Oxford OX1 4AJ


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller 
[j-kell...@fsm.northwestern.edu]
Sent: 27 October 2011 17:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] raw data deposition

One thing that the poll is useful for is something I find surprising:
~40% when I checked found storing images a waste of time. So, I guess
this might be useful for finding the silent [significant] minority.
Why not have those folks chime in about why they think this is
useless, even to store images of solved datasets?

JPK

On Thu, Oct 27, 2011 at 11:25 AM, Gerard Bricogne
g...@globalphasing.com wrote:
 Dear Ed,

 I am really puzzled by this initiative. It assumes that there is a
 pre-formed collective opinion out there, independent from and unaffected
 by the exchanges of views that have taken place on this BB, that would be
 worth more than the conclusions we might reach by pursuing these exchanges.

 The thread you are obviously deciding to dissociate yourself from was
 initiated in response to a suggestion that views on this topic would
 usefully be aired publicly on this BB rather than posted off-list to Tom
 Terwilliger, who immediately agreed that this was a good idea and has been
 very supportive of this discussion.

 Shouldn't we continue to try and put our heads together to reach a
 consensus, rather than collect opinions that may be little more than prior
 prejudices?

 What shall we gain by such a vote? I may be misunderstanding what you
 have in mind, of course :-) .


 With best wishes,

  Gerard.

 --
 On Thu, Oct 27, 2011 at 12:08:24PM -0400, Ed Pozharski wrote:
 I am curious as to what the collective opinion on the raw data
 deposition actually is across the cross-section of the macromolecular
 crystallography community subscribed to the bb.  So, if you have a
 second and a formed opinion on the idea of the depositions of the raw
 data, please vote here

 http://tinyurl.com/3qlwwsh

 I'll post the results as soon as they look settled.

 Cheers,

 Ed.

 --
 Hurry up before we all come back to our senses!
Julian, King of Lemurs

 --

 ===
 * *
 * Gerard Bricogne g...@globalphasing.com  *
 * *
 * Global Phasing Ltd. *
 * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
 * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
 * *
 ===




--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***