Re: [ccp4bb] Problem in real space - please sign & invite other scientists to sign this letter

[Edwin Pozharski]

Dear Daniel,

with all due respect, I do believe that you are making several mistakes in
your argument.

English is not my native tongue, but I suspect that there is a substantial
difference between "author" and "signatory".  What people are asked to do
here is essentially to sign a petition, not to become a co-author in
traditional sense.  There were 39 signatories to the US Constitution,
certainly not all of them are considered its authors.

Furthermore, most structural biologists are trained scientists and it is
rather routine part of our job to evaluate research we are not exactly
experts in.  I am not a climatologist, but I do take exception to your
assertion that I am therefore automatically too ignorant to understand
basic concepts that pertain to global warming and climate change.  A
climatologist wouldn't instantly know what B-factors are, but is certainly
capable of understanding the concept if you explain it.

Using physical science and its data to arrive at conclusions regarding
religion, politics and economic theory (!) is not at all embarrassing.
(And letter in question hardly does any "preaching", certainly not about
religion)

As for your demand that people stick to structural biology, may I suggest
that your reaction to exactly one entry in ccp4bb that elicited almost zero
follow up (until your comment) feels a bit overblown?  If you strongly
disagree with Dr Ripple and his colleagues, that is fine, but why shouldn't
people at ccp4bb occasionally share somewhat orthogonal information?  None
of us want to see inappropriate content, I am just not sure why you feel
that this specific post is something that needs to be purged.

Just to be clear - your post does create an impression that you might hold
the opinion that, as they say, "global warming is a hoax".  Please, let's
not have further discussion online on the specifics, but I think it might
be helpful if you could confirm or deny this.

Cheers,

Ed.

---
"I disapprove of what you say, but I will defend to the death your right to
say it"
Evelyn Beatrice Hall, "The Friends of Voltaire"

On Tue, Aug 20, 2019 at 9:23 PM Daniel M. Himmel, Ph. D. <
danielmhim...@gmail.com> wrote:

> Dear colleagues,
>
>
>
> Since when does being a structural biologist make us experts in
> climatology,
>
> and isn't it a breach of basic ethical practice and professionalism as
> scientists
>
> to sign on as authors to an article for which we have neither contributed
>
> research nor intellectual content of the manuscript?  Are we now going
> against
>
> the standard to which the editorial policies of leading reputable
> biological
>
> journals normally hold us as authors?  And doesn't it hurt the credibility
>
> of a serious scientific article, its authors, and the journal in which it
> appears
>
> if biologists with no expertise in earth science/astrophysics appear
>
> without humility as authors to such an article?
>
>
>
> Are you not embarrassed to put your name to an article that uses physical
>
> sciences data as a platform for preaching about religion, politics, and
> economic
>
> theory ("...social and economic justice for all...")?
>
>
>
> Does it not upset you when someone unfamiliar with structural biology draws
>
> firm conclusions that heavily depend on the part of a structural model
> that has high
>
> B-factors?  So why are you unconcerned that you may be guilty of an
> analogous
>
> error when, as structural biologists, you put your name to a controversial
> interpretation
>
> of selected earth science data?  See, for example,
>
> https://blogs.agu.org/geospace/2017/02/24/living-warm-peak-ice-ages/
> about the ways
>
> climate data can be misinterpreted by choosing too tight a time interval,
> and lets stick to
>
> structural biology and allied sciences in the CCP4 list, please.
>
>
>
> Respectfully,
>
> Daniel M. Himmel
>
>
>
>>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Problem in real space - please sign & invite other scientists to sign this letter

[Dale Tronrud]

Dear Dr Himmel,

   I certainly agree that a scientist getting into the nitty-gritty of a
field outside of their training can make quite silly mistakes.  The link
you have provided to us makes an excellent example of your point.

   Dr Akasofu is a trained space scientist who studied the aurora
borealis and then spent most of his career in administration. (According
to the blog post)  Since his childhood he has disbelieved most anything
proposed by experts in whatever field.  Now we are expected to take
seriously his vague ramblings about "cycles" in climate?  What evidence
does he present?  Nothing but speculation that the climate "might" be
driven by this or "might" be driven by that.  Dr Akasofu brings nothing
to the table.

Dale Tronrud

On 8/20/2019 6:23 PM, Daniel M. Himmel, Ph. D. wrote:
> Dear colleagues,
> 
>  
> 
> Since when does being a structural biologist make us experts in
> climatology, 
> 
> and isn't it a breach of basic ethical practice and professionalism as
> scientists 
> 
> to sign on as authors to an article for which we have neither contributed
> 
> research nor intellectual content of the manuscript?  Are we now going
> against 
> 
> the standard to which the editorial policies of leading reputable
> biological 
> 
> journals normally hold us as authors?  And doesn't it hurt the credibility 
> 
> of a serious scientific article, its authors, and the journal in which
> it appears 
> 
> if biologists with no expertise in earth science/astrophysics appear 
> 
> without humility as authors to such an article?
> 
>  
> 
> Are you not embarrassed to put your name to an article that uses physical
> 
> sciences data as a platform for preaching about religion, politics, and
> economic
> 
> theory ("...social and economic justice for all...")?
> 
>  
> 
> Does it not upset you when someone unfamiliar with structural biology draws
> 
> firm conclusions that heavily depend on the part of a structural model
> that has high
> 
> B-factors?  So why are you unconcerned that you may be guilty of an
> analogous
> 
> error when, as structural biologists, you put your name to a
> controversial interpretation 
> 
> of selected earth science data?  See, for example,
> 
> https://blogs.agu.org/geospace/2017/02/24/living-warm-peak-ice-ages/
> about the ways 
> 
> climate data can be misinterpreted by choosing too tight a time
> interval, and lets stick to 
> 
> structural biology and allied sciences in the CCP4 list, please.
> 
>  
> 
> Respectfully,
> 
> Daniel M. Himmel
> 
>  
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 



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[ccp4bb] RES: [ccp4bb] Problem in real space - please sign & invite other scientists to sign this letter

[Rafael Marques]

Dear Daniel.

I really understand your point of view and I must say that I agree with it, at 
certain extent. Science is all about evidence and not what we (sometimes) want 
to see or want to believe. You are completely right when you say that, inside 
academia, evidence should be always discussed by those who have deep knowledge 
about the subject. Good science is based on good standards, and good standards 
are exactly what make our science so robust.

While I must say that it bothers me when someone who is not an expert in "my" 
field criticizes my job, I recognize that what makes what we do different than 
any religion is exactly the possibility of being criticized, both by those 
related to the field and those who might have  a good point of view.

Also, we know the rules inside the academia, how to analyze data and we know 
too that, in general, the population does not understand at all the meaning and 
the methods inside science. If we try to explain any scientific data to these 
people using our methods and standards it will be a huge failure (I can't even 
change the mind of my nephews, which after a NatGeo show started to believe in 
mermaids). When we deal with a non-academic public, we must emphasize how 
important is to make science, the good things that came from it and, most 
important, we need to be understood.

In fact, there is some discussion if the global warming is only natural or if 
it has been happening because the human activity. However, it is pretty clear 
that mankind is affecting the weather by the increase of carbon dioxide in the 
atmosphere and the large impact caused by cattle. A five minutes search on 
Google can give you back several papers, but I am going to present you only 
this one, concerned in devaluation.

HTTPS://www.scientificamerican.com/article/co2-emissions-reached-an-all-time-high-in-2018/

As scientists, we are the ones who might have no knowledge in the field, but 
the ones able to point out a critical view. When we refuse to talk to the 
population cause we are not experts is that field, someone else takes our 
place. And generally, they attack science and scientists, giving simple answers 
for complex problems. That is because they know what the population wants to 
hear. That is how Trump has become the USA president and Billboards did the 
same here in Brazil.

When we refuse to look for information, refuse to spread it to the general 
population  and hide inside the academia, we must be aware that someone, for 
sure, is taking our place. That is exactly why currently so many people believe 
that the Earth is flat and that vaccines provoke diseases. That is also the 
meaning why Greta Thunders, a sixteen years old teenager activist , is better 
known than the experts in the field. If we want to be believed we must take 
back our place. To hind is not an option.

Regards




Rafael Marques da Silva
Mestrando em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +55 16 99766-0021

   "A sorte acompanha uma mente bem treinada"



De: CCP4 bulletin board  em nome de Daniel M. Himmel, 
Ph. D. 
Enviado: Tuesday, August 20, 2019 10:23:05 PM
Para: CCP4BB@JISCMAIL.AC.UK 
Assunto: Re: [ccp4bb] Problem in real space - please sign & invite other 
scientists to sign this letter

Dear colleagues,

Since when does being a structural biologist make us experts in climatology,
and isn't it a breach of basic ethical practice and professionalism as 
scientists
to sign on as authors to an article for which we have neither contributed
research nor intellectual content of the manuscript?  Are we now going against
the standard to which the editorial policies of leading reputable biological
journals normally hold us as authors?  And doesn't it hurt the credibility
of a serious scientific article, its authors, and the journal in which it 
appears
if biologists with no expertise in earth science/astrophysics appear
without humility as authors to such an article?

Are you not embarrassed to put your name to an article that uses physical
sciences data as a platform for preaching about religion, politics, and economic
theory ("...social and economic justice for all...")?

Does it not upset you when someone unfamiliar with structural biology draws
firm conclusions that heavily depend on the part of a structural model that has 
high
B-factors?  So why are you unconcerned that you may be guilty of an analogous
error when, as structural biologists, you put your name to a controversial 
interpretation
of selected earth science data?  See, for example,
https://blogs.agu.org/geospace/2017/02/24/living-warm-peak-ice-ages/ about the 
ways
climate data can be misinterpreted by choosing too tight a time interval, and 
lets stick to
structural biology and allied sciences in the CCP4 list, please.

Respectfully,
Daniel M. Himmel

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Problem in real space - please sign & invite other scientists to sign this letter

[Edward A. Berry]

Sorry- Richard Muller (How could  I get that wrong?!)



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Problem in real space - please sign & invite other scientists to sign this letter

[Edward A. Berry]

Agreed. I support green new deal and I think we should be doing all we can to 
combat climate change,
not because I have studied it and concluded it is a problem but because some 
very smart people have, and have come to that conclusion. But I would not sign 
a letter saying that I have concluded, AS A SCIENTIST, that it is a problem we 
can do something about. That turns a scientific investigation into a popularity 
contest. I don't want to be one the 97% that Peter Mueller is talking about in 
his response (currently second in the list, I think) to:
https://www.quora.com/It-is-claimed-that-97-of-climate-scientists-state-that-anthropogenic-climate-change-is-real-What-evidence-do-the-3-who-dont-think-so-have-What-are-some-good-counterarguments-to-their-claims

On 08/20/2019 09:23 PM, Daniel M. Himmel, Ph. D. wrote:

Dear colleagues,

Since when does being a structural biologist make us experts in climatology,

and isn't it a breach of basic ethical practice and professionalism as 
scientists

to sign on as authors to an article for which we have neither contributed

research nor intellectual content of the manuscript?  Are we now going against

the standard to which the editorial policies of leading reputable biological

journals normally hold us as authors?  And doesn't it hurt the credibility

of a serious scientific article, its authors, and the journal in which it 
appears

if biologists with no expertise in earth science/astrophysics appear

without humility as authors to such an article?

Are you not embarrassed to put your name to an article that uses physical

sciences data as a platform for preaching about religion, politics, and economic

theory ("...social and economic justice for all...")?

Does it not upset you when someone unfamiliar with structural biology draws

firm conclusions that heavily depend on the part of a structural model that has 
high

B-factors?  So why are you unconcerned that you may be guilty of an analogous

error when, as structural biologists, you put your name to a controversial 
interpretation

of selected earth science data?  See, for example,

https://blogs.agu.org/geospace/2017/02/24/living-warm-peak-ice-ages/ 

 about the ways

climate data can be misinterpreted by choosing too tight a time interval, and 
lets stick to

structural biology and allied sciences in the CCP4 list, please.

Respectfully,

Daniel M. Himmel


--

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Re: [ccp4bb] Problem in real space - please sign & invite other scientists to sign this letter

[Daniel M. Himmel, Ph. D.]

Dear colleagues,



Since when does being a structural biologist make us experts in
climatology,

and isn't it a breach of basic ethical practice and professionalism as
scientists

to sign on as authors to an article for which we have neither contributed

research nor intellectual content of the manuscript?  Are we now going
against

the standard to which the editorial policies of leading reputable
biological

journals normally hold us as authors?  And doesn't it hurt the credibility

of a serious scientific article, its authors, and the journal in which it
appears

if biologists with no expertise in earth science/astrophysics appear

without humility as authors to such an article?



Are you not embarrassed to put your name to an article that uses physical

sciences data as a platform for preaching about religion, politics, and
economic

theory ("...social and economic justice for all...")?



Does it not upset you when someone unfamiliar with structural biology draws

firm conclusions that heavily depend on the part of a structural model that
has high

B-factors?  So why are you unconcerned that you may be guilty of an
analogous

error when, as structural biologists, you put your name to a controversial
interpretation

of selected earth science data?  See, for example,

https://blogs.agu.org/geospace/2017/02/24/living-warm-peak-ice-ages/ about
the ways

climate data can be misinterpreted by choosing too tight a time interval,
and lets stick to

structural biology and allied sciences in the CCP4 list, please.



Respectfully,

Daniel M. Himmel



>



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[ccp4bb] Postdoctoral scientist position at Columbia University

[Lawrence Shapiro]

Postdoctoral scientist position in the Shapiro lab 
Columbia University in New York City

Crystallography, single-particle cryo-EM, and cryo-EM tomography neuronal 
surface proteins.

Our research program, in the new Mind Brain Behavior Institute at Columbia, is 
focused on proteins that mediate cell-cell recognition and their function in 
building the neural networks of the brain.  Our lab is part of the vibrant NYC 
structural biology community, with regular access to beamlines at APS/Argonne 
and NSLS2/Brookhaven, and numerous Titan Krios microscopes at Columbia and the 
nearby New York Structural Biology Center.

Relevant publications include:
Brasch et al, Nature Nature (2019) 569, 280-283. 
Cosmanescu et al, Neuron (2018) 100, 1385-1400.
Dionne et al, Neuron (2018) 99, 480-492.

Candidates should have a PhD in Structural Biology/Biophysics or related 
disciplines, and a track record of research achievements. Knowledge of protein 
purification and experience in structural biology are essential.

Funds for this post are available for 3 years in the 

Informal inquiries may be made to Dr Lawrence Shapiro (l...@columbia.edu).



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Re: [ccp4bb] Problem in .mtz creation

[Eleanor Dodson]

Cannot you use COOT in expert mode, and give the F and Phi you have?
Eleanor

On Tue, 20 Aug 2019 at 15:45, Jonathan Cooper <
0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:

> Sorry, it's mapmask, not extend anymore.
>
> Sent from Yahoo Mail on Android
> 
>
> On Tue, 20 Aug 2019 at 15:28, Jonathan Cooper
> <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
> You should be able to make a map with FFT by assigning F1 to your Fcalc
> and PHI to your Phicalc, if not with the gui, then certainly with the
> command line. You will need to make it cover your coordinates by ticking a
> gui option or running extend in the command line.
>
> Sent from Yahoo Mail on Android
> 
>
> On Tue, 20 Aug 2019 at 15:02, Vijayakumar Rajendran
>  wrote:
> Dear All,
> I have a problem in viewing electron density map by opening .mtz file in
> coot. Actually I have a PDB cordinates of water molecules of my protein
> using Hollow program. I generated the .mtz file using SFall program in
> CCP4i by providing the cryst card. The generated mtz file contains FCalc
> and PhiCalc. When I open this mtz file in coot along with the hollow pdb
> file, I am not getting the electron density.
>  I tried running FFT, but it failed as it doesn't have SIGFP and FOM
> column since its a non experimental co-ordinates.
> Please help me where is the issue.
>
> Thanks in advance.
>
> ---
> Dr. R. Vijayakumar,
> Research Associate,
> Molecular Biophysics Unit,
> Indian Institute of Science,
> Bangalore 560 012
>
> --
>
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>
>
> --
>
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>
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Re: [ccp4bb] need someone officially settle a pdb dispute for a publication

[Jürgen Bosch]

Can’t help you with this, however, I have a couple of PDB deposits that I did 
not publish on and if somebody took them and used my coordinates that’s fine as 
long as they cite the DOI affiliated with the deposition.

Now the question for you, were A and B collaborating on this? If so then 
there’s a different problem and indeed misconduct or at least not good practice 
by B.

Communication is a skill, that some people definitely need to learn.

Jürgen 
 

> On Aug 20, 2019, at 11:45 AM, Flemming Goery  
> wrote:
> 
> Dear All, 
> 
> A and B belong to 2 different institutes. A claimed B has used his pdb for a 
> publication in Journal C. Journal C did not give the retraction, but permit 
> complain related to the journal publication author issue, with the 
> prerequisite journal C did not have the authority on authorship dispute. Then 
> A has e-mailed to the institute head of B with academic misconduct by B as 
> claim, the institute head of B did not give reply.
> 
> In this situation, can A have the journal  authorship  dispute settled by a 
> neutral reviewer (Journal C view: you (A) need to reach out to the 
> institutions that have authority to adjudicate on such matters, as 
> investigation and adjudication on authorship claims falls outside the remit 
> of journal editors. )? Who are qualified as the neutral reviewer so that the 
> review decision can be submitted to Journal C?
> 
> If you believe you are qualified, or you know somebody or some organization 
> qualified, please let me know and I will introduce the issue to you by 
> separate e-mail (it is best not disseminated, am I right?)
> 
> Best regards.
> 
> Flemming
> 
> 
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> 



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[ccp4bb] need someone officially settle a pdb dispute for a publication

[Flemming Goery]

Dear All,

A and B belong to 2 different institutes. A claimed B has used his pdb for a 
publication in Journal C. Journal C did not give the retraction, but permit 
complain related to the journal publication author issue, with the prerequisite 
journal C did not have the authority on authorship dispute. Then A has e-mailed 
to the institute head of B with academic misconduct by B as claim, the 
institute head of B did not give reply.

In this situation, can A have the journal  authorship  dispute settled by a 
neutral reviewer (Journal C view: you (A) need to reach out to the institutions 
that have authority to adjudicate on such matters, as investigation and 
adjudication on authorship claims falls outside the remit of journal editors. 
)? Who are qualified as the neutral reviewer so that the review decision can be 
submitted to Journal C?

If you believe you are qualified, or you know somebody or some organization 
qualified, please let me know and I will introduce the issue to you by separate 
e-mail (it is best not disseminated, am I right?)

Best regards.

Flemming




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[ccp4bb] MX Industrial Liaison Scientist position at Diamond Light Source - closing date September the 1st

[Waterman, Jitka (DLSLtd,RAL,CEO)]

Dear all,

The Industrial Liaison group at Diamond Light Source currently offers an 
exciting opportunity to join our team. We are looking for a passionate and 
experienced structural biologist capable of contributing to the entire 
experiment from crystallisation to data analysis and model building. An 
understanding of structure-guided drug design and experience with protein 
production are also key to being able to consult effectively in this role. As 
this is a client-facing position you will need excellent communication skills 
with the ability to interact at both a technical and business level.

Further details and information on the application process are available at 
https://vacancies.diamond.ac.uk/vacancy/industrial-liaison-scientist-mx-393043.html
Closing date for applications is Sunday the 1st of September.

Best regards,
Jitka

Dr Jitka Waterman
Industrial Liaison Scientist
www.diamond.ac.uk/industry

Diamond Light Source Ltd.
Harwell Science and Innovation Campus
Didcot, Oxfordshire
OX11 0DE
United Kingdom



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Re: [ccp4bb] Problem in .mtz creation

[Jonathan Cooper]

Sorry, it's mapmask, not extend anymore.

Sent from Yahoo Mail on Android 
 
  On Tue, 20 Aug 2019 at 15:28, Jonathan 
Cooper<0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:   You should be 
able to make a map with FFT by assigning F1 to your Fcalc and PHI to your 
Phicalc, if not with the gui, then certainly with the command line. You will 
need to make it cover your coordinates by ticking a gui option or running 
extend in the command line.

Sent from Yahoo Mail on Android 
 
  On Tue, 20 Aug 2019 at 15:02, Vijayakumar 
Rajendran wrote:   Dear All,I have a problem 
in viewing electron density map by opening .mtz file in coot. Actually I have a 
PDB cordinates of water molecules of my protein using Hollow program. I 
generated the .mtz file using SFall program in CCP4i by providing the cryst 
card. The generated mtz file contains FCalc and PhiCalc. When I open this mtz 
file in coot along with the hollow pdb file, I am not getting the electron 
density. 
 I tried running FFT, but it failed as it doesn't have SIGFP and FOM column 
since its a non experimental co-ordinates.Please help me where is the issue. 

Thanks in advance.
---Dr. R. Vijayakumar,
Research Associate,
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore 560 012

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Re: [ccp4bb] Problem in .mtz creation

[Jonathan Cooper]

You should be able to make a map with FFT by assigning F1 to your Fcalc and PHI 
to your Phicalc, if not with the gui, then certainly with the command line. You 
will need to make it cover your coordinates by ticking a gui option or running 
extend in the command line.

Sent from Yahoo Mail on Android 
 
  On Tue, 20 Aug 2019 at 15:02, Vijayakumar 
Rajendran wrote:   Dear All,I have a problem 
in viewing electron density map by opening .mtz file in coot. Actually I have a 
PDB cordinates of water molecules of my protein using Hollow program. I 
generated the .mtz file using SFall program in CCP4i by providing the cryst 
card. The generated mtz file contains FCalc and PhiCalc. When I open this mtz 
file in coot along with the hollow pdb file, I am not getting the electron 
density. 
 I tried running FFT, but it failed as it doesn't have SIGFP and FOM column 
since its a non experimental co-ordinates.Please help me where is the issue. 

Thanks in advance.
---Dr. R. Vijayakumar,
Research Associate,
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore 560 012

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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Better Beamline suggestion!

[Jürgen Bosch]

Hi Chandra,

If I remember correctly, the SSRL beam lines 12-2 and 14-1  allow kappa offset 
plus you can swing out the detector.
You might have to come up with a special collection strategy, that you collect 
in resolution bins to avoid overlaps.

Jürgen

P.S. my previous messages got blocked, let’s see if this one passes.

> On Aug 20, 2019, at 5:18 AM, colin.n...@diamond.ac.uk 
>  wrote:
> 
> I agree with Ed that focusing on the detector might be better than on the 
> crystal. An alternative is to reduce the beam divergence which might be 
> easier on some beamlines. 
> 
> The idea is to ensure the instrument parameters (e.g. beam size, beam 
> divergence, detector distance) and data collection parameters (e.g. rotation 
> increments) do not degrade the diffraction pattern. This should ensure all 
> spots which are intrinsically separated are properly resolved. I don't really 
> see the need for a multi circle goniometer if this is done. If the spots are 
> naturally smeared due to crystal imperfections then they overlap anyway. In 
> this case, as Ed says, one has to ensure the profiles are adequately sampled 
> so that any deconvolution procedure has a chance of succeeding.
> 
> Colin
> 
> 
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Edward A. Berry
> Sent: 19 August 2019 17:08
> To: ccp4bb 
> Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Better Beamline suggestion!
> 
>  I would respectfully suggest that higher pixel resolution does not generally 
> help much in these situations. If an average spot is 10 or more pixels wide 
> then the profile is defined pretty well. But if the spots overlap, they still 
> overlap with higher pixel density. It may make profile fitting more accurate, 
> allowing more accurate "deconvolution" of the compound spot into its 
> components, but it will not improve the overlap. Smaller or better-focused 
> (on the detector, not the crystal?) beam, and longer camera length can help.
>   It is analogous to chromatography- If two peaks coming off the column 
> overlap, collecting smaller fractions will not help to resolve them. It may 
> allow a better-informed decision on the cut-off points when you pool the 
> fractions, but it won't separate the overlap.
>   On the other hand a multi-circle goniometer is very useful. I remember in 
> one of our last trips at SSRL (2007-8?) we used a (Huber 4-circle?) and it 
> was very easy to have the long axis in the plane of the image throughout the 
> rotation.  In the absence of such you can resort to carefully bending the 
> loop or bending the pin (Jim Holton made a nifty device for bending the pin) 
> while keeping the xtal bathed in the cold stream.
> 
> 
> On 08/19/2019 11:12 AM, graeme.win...@diamond.ac.uk wrote:
>> Chandra
>> 
>> What you are looking for here is a beamline with a detector with many pixels 
>> (so you can resolve the long axis) and a multi-axis goniometer - probably a 
>> SmarGon / kappa and an Eiger 16M would make a good combination for this. 
>> Searching on
>> 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__biosync.sbkb.org_=DwIFAg=ogn2iPkgF7TkVSicOVBfKg=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA=VcmIp54F7yM1JdiEMdBdR0y7xinGb-nsn2-3LI_BHto=5VFyqMBHljO-AEcXr3-pqjF8xFyEejXetVFOxOXLp_Y=
>> 
>> Should allow you to make up a short list
>> 
>> Best wishes Graeme
>> 
>> On 19 Aug 2019, at 16:08, Chandramohan Kattamuri 
>> <1c5b7cb6c764-dmarc-requ...@jiscmail.ac.uk>
>>  wrote:
>> 
>> 
>> Dear All
>> We recently collected a data set at APS, Chicago with unit cell dimensions 
>> of 68.4; 68.4 and 991.6 A. Our diffraction data extends to 3A with the APS 
>> set up, however, the long axis has been problematic, resulting in streaking 
>> of the diffraction data and requires a very specific orientation of the 
>> crystal for usable diffraction. Can anyone recommend beamlines that can give 
>> us higher resolution, or a source with a better goniometer allowing for more 
>> angle manipulation after looping?
>> Thank a lot
>> Chandra K
>> 
>> 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwIFAg=ogn2iPkgF7TkVSicOVBfKg=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA=VcmIp54F7yM1JdiEMdBdR0y7xinGb-nsn2-3LI_BHto=NIk481IQQfkQVGsehEs9ptANwtNDLPRMWSSzJRcFHUY=
>> 
>> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
> -- 
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you are not the intended addressee or an authorised recipient of the 
> addressee please notify us of receipt by returning the 

[ccp4bb] Problem in .mtz creation

[Vijayakumar Rajendran]

Dear All,
I have a problem in viewing electron density map by opening .mtz file in
coot. Actually I have a PDB cordinates of water molecules of my protein
using Hollow program. I generated the .mtz file using SFall program in
CCP4i by providing the cryst card. The generated mtz file contains FCalc
and PhiCalc. When I open this mtz file in coot along with the hollow pdb
file, I am not getting the electron density.
 I tried running FFT, but it failed as it doesn't have SIGFP and FOM column
since its a non experimental co-ordinates.
Please help me where is the issue.

Thanks in advance.

---
Dr. R. Vijayakumar,
Research Associate,
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore 560 012



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[ccp4bb] Postdoc position in membrane protein structural biology

[Ashley Pike]

Dear All,

We are seeking a Postdoctoral Scientist with membrane protein structural 
biology and electron microscopy experience to work as part of a collaboration 
between Professor Liz Carpenter's group at the Structural Genomics Consortium 
(SGC) in Oxford and the Structural Research Group of Boehringer Ingelheim in 
Biberach, Germany.

This position is funded by the Boehringer Ingelheim (BI) and will require the 
postholder to work 70% of the time from SGC labs in Oxford, UK and the 
remaining 30% of the time from the BI labs in Biberach, Germany.

This project aims to study the structures of complexes of human ion channels 
and solute carriers involved in genetic disease, using both electron 
cryo-microscopy and X-ray crystallography, combined with biophysical and 
biochemical methods to study function. This project will provide opportunities 
for training in cryo-EM, first hand insights into drug discovery, opportunities 
for international collaboration and high impact publications in the rapidly 
developing field of cryo-EM.

Follow link for more details and how to apply:
https://my.corehr.com/pls/uoxrecruit/erq_jobspec_version_4.display_form?p_company=10_internal_external=E_display_in_irish=N_process_type=_applicant_no=_form_profile_detail=_display_apply_ind=Y_refresh_search=Y_recruitment_id=141757

The closing date for applications is 11th September.

Please feel to contact Liz Carpenter 
(liz.carpen...@sgc.ox.ac.uk) if you have any 
questions about this position.



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[ccp4bb] Vacancy in R Thermo Fisher, Eindhoven The Netherlands

[Kuijper, Maarten]

At Thermo Fisher Scientific, located in Eindhoven The Netherlands, we have a 
new vacancy in our New Product Development (R) team: 'CryoEM Sample Prep - 
Project Manager'.

Our team is pursuing improvements in efficiency, effectiveness and reliability 
of the sample creation process for Cryo-EM.



As project manager for Sample Preparation you will lead multiple projects 
enabling workflow solutions, in your case this will focus around sample 
preparation.



Next to project management skills, the successful candidate should have a 
background in biochemistry and sample preparation protocols of biological 
specimen for structural analysis. Hands on in CryoEM is a plus.



For further particulars and to apply for these posts, please follow



CryoEM Sample Prep - Project Manager: 
https://jobs.thermofisher.com/ShowJob/Id/723744/CryoEM-Sample-Prep-Project-Manager/







Regards,

Maarten Kuijper

Workflow Architect, Research and Development

Thermo Fisher Scientific





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Re: [ccp4bb] Problem in real space - please sign & invite other scientists to sign this letter

[Casadei Cecilia (PSI)]

Dear Wim,

thank you for this very good initiative.

Kind regards,

Cecilia

__
Paul Scherrer Institut
Dr. Cecilia Casadei
Laboratory of Biomolecular Research
OFLC/104
5232 Villigen PSI
Schweiz

E-Mail: cecilia.casa...@psi.ch


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Wim Burmeister 
[wim.burmeis...@ibs.fr]
Sent: Tuesday, August 20, 2019 10:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problem in real space - please sign & invite other scientists 
to sign this letter

Hello,
I transmit this initiative for those who feel that there is also life outside 
reciprocal space and and not only scientist in specialist disciplines have a 
responsibility in real space.
The graphs in the paper mentioned below are sufficiently explicit to understand 
that there is a big problem.
Best wishes
Wim

Dear Colleague,
We are inviting you and all scientists to sign our new in-press BioScience 
paper "World Scientists' Warning of a Climate Emergency" which we want to 
present to world leaders.

The article is short and can be read in fewer than eight minutes. Just go to 
 
 
http://scientistswarning.forestry.oregonstate.edu/ to read and sign the paper 
(you can also read a condensed version of the article below).

Please forward this email to other scientists within your network or use social 
media as suggested below.

Thanks, Bill

William J. Ripple, Distinguished Professor of Ecology, Oregon State University

To promote the initiative on social media (Facebook and Twitter), please 
consider using the following text:

The 
#ScientistsWarningToHumanity
 is speaking out about the climate emergency. If you are a scientist you can 
support this new initiative by sharing this and adding your signature here: 
 
http://scientistswarning.forestry.oregonstate.edu/

Or

Scientists can support the 
#ScientistsWarningToHumanity
 climate emergency initiative by sharing this and adding your signature here: 
 
 
http://scientistswarning.forestry.oregonstate.edu/

Or

I just signed the 
#ScientistsWarningToHumanity
 climate emergency initiative. If you are a scientist you can support this new 
initiative by sharing this and adding your signature here: 
 
http://scientistswarning.forestry.oregonstate.edu/

World Scientists’ Warning of a Climate Emergency (Condensed Version)
William J. Ripple, Christopher Wolf, Thomas M. Newsome,  scientist 
signatories from xxx countries
We scientists have a moral obligation to clearly warn humanity of any great 
existential threat. In this paper, we present a suite of graphical vital signs 
of climate change over the last 40 years. Results show greenhouse gas emissions 
are still rising, with increasingly damaging effects. With few exceptions, we 
are largely failing to address this predicament. The climate crisis has arrived 
and is accelerating faster than many scientists expected. It is more severe 
than anticipated, threatening natural ecosystems and the fate of humanity. We 
suggest six critical and interrelated steps that governments and the rest of 
humanity can take to lessen the worst effects of climate change, covering 1) 
Energy, 2) Short-lived pollutants, 3) Nature, 4) Food, 5) Economy, and 6) 
Population. Mitigating and adapting to climate change entails transformations 
in the ways we govern, manage, feed, and fulfill material and energy 
requirements. We are encouraged by a recent global surge of concern. 
Governmental bodies are making climate emergency declarations. The Pope issued 
an encyclical on climate change. Schoolchildren are striking. Ecocide lawsuits 
are proceeding in the courts. Grassroots citizen movements are demanding 
change. As scientists, we urge widespread use of our vital signs and anticipate 
that graphical indicators will better allow policymakers and the public to 
understand the magnitude of this crisis, track progress, and realign priorities 
to alleviate climate change. The good news is that such transformative change, 
with social and ecological justice, promises greater human wellbeing in the 
long-run than business as usual. We believe that prospects will be greatest if 
policy makers and the rest of humanity promptly respond to our warning and 
declaration of a climate emergency, and act to sustain life on planet Earth, 
our only home.

William J. Ripple email: 
scientistswarn...@oregonstate.edu







To 

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2019

[Manfred S. Weiss]

Dear all,

the next MX-proposal application deadline: March 01, 2019 is approaching
https://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html

As usual, all proposals will be handled with the new version of GATE,
GATE2.0, https://www.helmholtz-berlin.de/pubbin/hzbgate

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(02/2020-08/2020).

In order to apply for beamtime, please register at the HZB on-line
access tool "GATE" (https://www.helmholtz-berlin.de/pubbin/hzbgate)
and submit a new beam time application proposal.

With the new GATE version, the proposal categories have been improved.
We now expect from each research group only ONE proposal, which can
contain up to 20 individual projects.

HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations in
Germany with nearly 3000 PDB depositions in total. Beamtime is granted
based on the reviewed proposals and on reports from previous research
activities. Please make sure to include them if available.

Experimental setup:

BL14.1:
- Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A)
- Photon flux: 1.8x10¹¹ Phot/sec x 100 mA at sample position
 (0.1-1 sec exposure time per frame)
- PILATUS 6M detector, 141 mm-680 mm max. distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer
- Automatic sample changer (CATS), 90 sample storage capacity
 (SPINE-Pin & EMBL sample magazine compatibility)
- User defined beam shaping from 50 µm-100 µm diameter possible
- In situ crystal-screening using 96-well plates
- 32-core XEON-CPU server, with 10GB uplink to Pilatus 6M
- Data collection control via MXCuBE2
- Common MX-software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out UV-RIP experiments at BL14.1. For further information,
please visit:
https://www.helmholtz-berlin.de/forschung/oe/np/gmx/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A)
- Photon flux: 1.6x10¹¹ Phot/sec x 100 mA at sample position
 (0.05-1 sec exposure time per frame)
- PILATUS 3S-2M detector with 1000 µm Si sensor thickness,
 85 mm - 800 mm distance from the sample (a special mode with
 55 mm distance is also available upon request)
- Nanodiffractometer with fast air-bearing axis and on-axis sample
 microscope
- User defined beam shaping from 30 µm-150 µm diameter possible
- Data collection control via MXCuBE2
- G-ROB sample changer for SPINE and UNIPUCK support
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Common MX-software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- AMPTEK-XRF detector and XFEPLOT software available
- UV-Microsprectrophotometer offline setup available

If you need atomic resolution or better, BL14.2 is the beamline
of choice for you!!

BL14.3:
- Fixed photon energy: 13.8 keV (wavelength: 0.89 A)
- Photon flux: 1.6x10exp10 Phot/sec x 100mA at sample position
 (3-20 sec exposure time per frame)
- Rayonix MX-225 X-ray detector, 54 mm-450 mm distance from the
 sample
- MD2S microdiffractometer with mini-kappa goniometer
- In situ crystal-screening using 96-well plates
- RT data collection
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Data collection control via MXCuBE2
- Common MX software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- REX rapid nozzle exchanger
- HC-Lab dehydration device installed (please specify HC-Lab-beamtime
 in your proposal if needed)
- AMPTEK-XRF detector and XFEPLOT software available

Other facilities:
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpix CCD-camera
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)

S1-biolab facilities (separate registration required):
- Protein production and purification (AEKTA)
- nL 96-well crystallization plate formulation and storage at
 5°C and 20°C
- Biophysical characterization with real time PCR (thermofluor assay)
- Contactless compound pipetting using ATS

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please see
https://www.helmholtz-berlin.de/forschung/oe/np/gmx/fragment-screening/index_en.html
or contact mswe...@helmholtz-berlin.de.

Please visit 

[ccp4bb] Call open for beamtime at DESY beamline P11, PETRA III, Deadline: 02.09.2019

[Anja Burkhardt]

Dear all,

Hereby I would like to invite the submission of regular proposals for DESY 
beamline P11 at the PETRA III synchrotron in Hamburg.

The call is open until Monday, 2 September 2019 (inclusive; UTC+1) and is for 
experiments to be performed in the first half of 2020 (2.3.20 – 5.7.20).

Please note that in in the frame of the proposal harmonization efforts between 
European lightsources we have modified our proposal templates!
Preparation guidelines for the proposals and new templates can be found here: 
https://photon-science.desy.de/users_area/user_guide/write_a_proposal/

Beamline P11 is dedicated to structural investigations of biological samples 
and currently provides two experimental endstations: an X-ray microscope (under 
construction) and a crystallography experiment which is in user operation since 
2013.

Specific features of the P11 crystallography endstation:
    • High photon flux (1.3 × 10^13 ph/s at 12 keV) at the sample position
    • Broad energy range from 5.5 - 26 keV
    • Full SAD/MAD capability
    • High-precision single axis goniostat
    • Fast data collection via Pilatus 6M detector (25 Hz frame rate, 154 – 
2000 mm sample-to-detector distance)
    • Fast automatic sample changer (20 s) with uni-puck compatibility and 368 
sample storage capacity
    • Cryo-shutter for crystal annealing
    • Beam size tunability from 4 × 9 µm² to 300 × 300 µm² within a minute
    • Microbeam capability (4 × 9 µm² focal spot with 1.3 × 10^13 ph/s photon 
flux and 1 × 1 µm² with 2 × 10^11 ph/s)
    • Serial synchrotron crystallography using a tape-drive setup for liquid 
sample delivery and Si-chips for fixed targets
    • Parallel beam option for large unit cell systems
    • Data collection via Python-based GUI
    • Automated data processing with XDSAPP
    • 40 core workgroup server for fast data processing


For detailed information about our experimental setup please visit our homepage 
http://photon-science.desy.de/facilities/petra_iii/beamlines/p11_bio_imaging_and_diffraction

Looking forward to meeting you at P11.

On behalf of the P11 team,
Anja Burkhardt



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[ccp4bb] Senior lecturer position at Uppsala University – extended application time

[Stefan Knight]

Dear colleagues,

The application deadline for this position has been extended until September 20.

A senior lecturer position in experimental structural biology is available in 
the Structural Biology program at the Department of Cell and Molecular Biology 
(ICM), Uppsala University. 

The Department of Cell and Molecular Biology (http://icm.uu.se 
) is one of the most international, broad and distinguished 
bimolecular departments in Europe. Research interests range all the way from 
genetics to the biophysics of single molecules.

The advertised position is within the Structural Biology program 
(http://www.icm.uu.se/structural-biology 
) at ICM, where current research 
covers structural and functional studies of a wide range of fundamental 
biological processes ranging from protein synthesis, metal homeostasis, enzyme 
catalysis, and protein evolution to chaperone directed assembly of spider silk 
and other complex structures, and antibiotic resistance. We are now looking for 
a lecturer to complement and broaden both the expertise and research scope 
within the program.

We are primarily seeking persons with expertise in structure determination 
using single particle cryo-EM. For further details and instructions on how to 
apply, please visit http://www.uu.se/jobb/detaljsida/?positionId=279114 
. 

If you have any questions related to the position, don’t hesitate to contact me 
(contact info below) or Maria Selmer (phone: +46-(0)18-471 4177, email: 
maria.sel...@icm.uu.se ).


Stefan D Knight, PhD
Professor of Biology, especially Structural Biology
Program Head, Structural Biology
Department of Cell and Molecular Biology, Uppsala University
Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala
Sweden

Voice: +46 (0)18 471 45 54
Fax: +46 (0)18 53 03 96
E-mail: ste...@xray.bmc.uu.se 


"We trained very hard, but it seemed that every time we were beginning to 
form into teams, we would be reorganised.  I was to learn later in life that 
we tend to meet any new situation by reorganising - and a wonderful method 
it can be for creating the illusion of progress while producing confusion, 
inefficiency and demoralisation."

– Commonly attributed to Gaius Petronius Arbiter (d. AD 66). However, there is 
no solid 
evidence for this attribution, and the real origin of the quote appears to be 
Charlton Ogburn, 
"Merrill's Marauders”, Harpers Magazine, January 1957 (see e.g. 
http://quoteinvestigator.com/2013/11/12/reorganizing/ 
).









Stefan D Knight, PhD
Professor of Biology, especially Structural Biology
Program Head, Structural Biology
Department of Cell and Molecular Biology, Uppsala University
Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala
Sweden

Voice: +46 (0)18 471 45 54
Fax: +46 (0)18 53 03 96
E-mail: ste...@xray.bmc.uu.se 


"We trained very hard, but it seemed that every time we were beginning to 
form into teams, we would be reorganised.  I was to learn later in life that 
we tend to meet any new situation by reorganising - and a wonderful method 
it can be for creating the illusion of progress while producing confusion, 
inefficiency and demoralisation."

– Commonly attributed to Gaius Petronius Arbiter (d. AD 66). However, there is 
no solid 
evidence for this attribution, and the real origin of the quote appears to be 
Charlton Ogburn, 
"Merrill's Marauders”, Harpers Magazine, January 1957 (see e.g. 
http://quoteinvestigator.com/2013/11/12/reorganizing/ 
).



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 



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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Better Beamline suggestion!

[colin.n...@diamond.ac.uk]

I agree with Ed that focusing on the detector might be better than on the 
crystal. An alternative is to reduce the beam divergence which might be easier 
on some beamlines. 

The idea is to ensure the instrument parameters (e.g. beam size, beam 
divergence, detector distance) and data collection parameters (e.g. rotation 
increments) do not degrade the diffraction pattern. This should ensure all 
spots which are intrinsically separated are properly resolved. I don't really 
see the need for a multi circle goniometer if this is done. If the spots are 
naturally smeared due to crystal imperfections then they overlap anyway. In 
this case, as Ed says, one has to ensure the profiles are adequately sampled so 
that any deconvolution procedure has a chance of succeeding.

Colin


-Original Message-
From: CCP4 bulletin board  On Behalf Of Edward A. Berry
Sent: 19 August 2019 17:08
To: ccp4bb 
Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Better Beamline suggestion!

  I would respectfully suggest that higher pixel resolution does not generally 
help much in these situations. If an average spot is 10 or more pixels wide 
then the profile is defined pretty well. But if the spots overlap, they still 
overlap with higher pixel density. It may make profile fitting more accurate, 
allowing more accurate "deconvolution" of the compound spot into its 
components, but it will not improve the overlap. Smaller or better-focused (on 
the detector, not the crystal?) beam, and longer camera length can help.
   It is analogous to chromatography- If two peaks coming off the column 
overlap, collecting smaller fractions will not help to resolve them. It may 
allow a better-informed decision on the cut-off points when you pool the 
fractions, but it won't separate the overlap.
   On the other hand a multi-circle goniometer is very useful. I remember in 
one of our last trips at SSRL (2007-8?) we used a (Huber 4-circle?) and it was 
very easy to have the long axis in the plane of the image throughout the 
rotation.  In the absence of such you can resort to carefully bending the loop 
or bending the pin (Jim Holton made a nifty device for bending the pin) while 
keeping the xtal bathed in the cold stream.


On 08/19/2019 11:12 AM, graeme.win...@diamond.ac.uk wrote:
> Chandra
>
> What you are looking for here is a beamline with a detector with many pixels 
> (so you can resolve the long axis) and a multi-axis goniometer - probably a 
> SmarGon / kappa and an Eiger 16M would make a good combination for this. 
> Searching on
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__biosync.sbkb.org_=DwIFAg=ogn2iPkgF7TkVSicOVBfKg=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA=VcmIp54F7yM1JdiEMdBdR0y7xinGb-nsn2-3LI_BHto=5VFyqMBHljO-AEcXr3-pqjF8xFyEejXetVFOxOXLp_Y=
>
> Should allow you to make up a short list
>
> Best wishes Graeme
>
> On 19 Aug 2019, at 16:08, Chandramohan Kattamuri 
> <1c5b7cb6c764-dmarc-requ...@jiscmail.ac.uk>
>  wrote:
>
>
> Dear All
> We recently collected a data set at APS, Chicago with unit cell dimensions of 
> 68.4; 68.4 and 991.6 A. Our diffraction data extends to 3A with the APS set 
> up, however, the long axis has been problematic, resulting in streaking of 
> the diffraction data and requires a very specific orientation of the crystal 
> for usable diffraction. Can anyone recommend beamlines that can give us 
> higher resolution, or a source with a better goniometer allowing for more 
> angle manipulation after looping?
> Thank a lot
> Chandra K
>
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
>



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[ccp4bb] Problem in real space - please sign & invite other scientists to sign this letter

[Wim Burmeister]

  
  

  Hello,
  I transmit this initiative for those who feel that there is
  also life outside reciprocal space and and not only scientist
  in specialist disciplines have a responsibility in real space.
  
  The graphs in the paper mentioned below are sufficiently
  explicit to understand that there is a big problem.
  Best wishes
  Wim
   
  Dear Colleague,
We are inviting you and all scientists to sign our new in-press
BioScience  paper "World Scientists' Warning of a
  Climate Emergency" which we want to present to world
leaders.

The article is short and can be read in fewer than eight
minutes. Just go to  http://scientistswarning.forestry.oregonstate.edu/
to read and sign the paper (you can also read a condensed
version of the article below).

Please forward this email to other scientists within your
network or use social media as suggested below. 
    
Thanks, Bill  
  
  
William J. Ripple, Distinguished Professor of Ecology, Oregon
State University

To promote the initiative on social media (Facebook and
  Twitter), please consider using the following text:

The #ScientistsWarningToHumanity is
speaking out about the climate emergency. If you are a scientist
you can support this new initiative by sharing this and adding
your signature here: http://scientistswarning.forestry.oregonstate.edu/


Or

Scientists can support the #ScientistsWarningToHumanity
climate emergency initiative by sharing this and adding your
signature here:  http://scientistswarning.forestry.oregonstate.edu/

Or

I just signed the #ScientistsWarningToHumanity climate emergency initiative. If you are
a scientist you can support this new initiative by sharing this
and adding your signature here: http://scientistswarning.forestry.oregonstate.edu/
   
   World

Scientists’ Warning of a Climate Emergency (Condensed

  Version) 
   William J. Ripple, Christopher
  Wolf, Thomas M. Newsome,  scientist signatories from xxx
  countries 
  We

  scientists have a moral obligation to clearly warn humanity of
  any great existential threat. In this paper, we present a
  suite of graphical vital signs of climate change over the last
  40 years. Results show greenhouse gas emissions are still
  rising, with increasingly damaging effects. With few
  exceptions, we are largely failing to address this
  predicament. The climate crisis has arrived and is
  accelerating faster than many scientists expected. It is more
  severe than anticipated, threatening natural ecosystems and
  the fate of humanity. We suggest six critical and interrelated
  steps that governments and the rest of humanity can take to
  lessen the worst effects of climate change, covering 1)
  Energy, 2) Short-lived pollutants, 3) Nature, 4) Food, 5)
  Economy, and 6) Population. Mitigating and adapting to climate
  change entails transformations in the ways we govern, manage,
  feed, and fulfill material and energy requirements. We are
  encouraged by a recent global surge of concern. Governmental
  bodies are making climate emergency declarations. The Pope
  issued an encyclical on climate change. Schoolchildren are
  striking. Ecocide lawsuits are proceeding in the courts.
  Grassroots citizen movements are demanding change. As
  scientists, we urge widespread use of our vital signs and
  anticipate that graphical indicators will better allow
  policymakers and the public to understand the magnitude of
  this crisis, track progress, and realign priorities to
  alleviate climate change. The good news is that such
  transformative change, with social and ecological justice,
  promises greater human wellbeing in the long-run than business
  as usual. We believe that prospects will be greatest if policy
  makers and the rest of humanity promptly respond to our
  warning and declaration of a climate emergency, and act to
  sustain life on planet Earth, our only home.
   
  William J. Ripple email:
  scientistswarn...@oregonstate.edu
   
   
   
   

  



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Re: [ccp4bb] Better Beamline suggestion!

[Wim Burmeister]

  
  
Hello,
the problem can rather be due to mechanical deformations of the
crystal upon mounting and freezing (bent needle, for example). If
the crystals are needle shaped, aligning the long axis with the
spindle axis and using a beamline with a very small beamsize
"microfocus" and a helical scan in order to expose a sufficient
volume will help.
Best
Wim

On 19/08/2019 17:08, Chandramohan
  Kattamuri wrote:


  
  
  
  Dear All
  

  




We recently collected a data set at
  APS, Chicago with unit
  cell dimensions of 68.4; 68.4 and 991.6 A. Our diffraction
  data extends to 3A
  with the APS set up, however, the long axis has been
  problematic, resulting in
  streaking of the diffraction data and requires a very
  specific orientation of
  the crystal for usable diffraction. Can anyone recommend
  beamlines that can
  give us higher resolution, or a source with a better
  goniometer allowing for
  more angle manipulation after looping?
Thank a lot
Chandra K


  

  
  
  
  
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following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
  


-- 
  
  
  Wim
Burmeister
  

  

  

  

  

  

   Professeur
  Institut


de Biologie Structurale (IBS) CIBB
  71
avenue des Martyrs / CS 20192
  
   38044 Grenoble Cedex 9,
  FRANCE
  E-mail: wim.burmeis...@ibs.fr
Tel:    +33 (0) 457 42 87 41  
Fax: +33 (0) 476 20 94 00
  website 
                                   
map
  
  
  Changement
climatique : «Les autres combats n’ont
aucun sens si celui-là est perdu» (Aurélien
  Barrau)   
  
  
  

  

  

  

  

  

  

  



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