[ccp4bb] Stereo graphics systems

[Chris Richardson]

Apologies for revisiting this oft-discussed subject.

nVidia no longer support their 3D Vision system, and appear to have stopped 
manufacturing it.  Does anyone have suggestions for an alternative?  Not all of 
our scientists use it, but those who find it valuable would be sad to lose it.

To clarify, I'm seeking a desktop solution as we don't have the space for 3D 
projectors.

If there is nothing else out there, I may have to start searching eBay for 
second hand IR emitters.

Regards,

Chris
-- 
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
 
 
 


The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
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Re: [ccp4bb] Stereo graphics systems

[Daum, Bertram]

Hi Chris, 

We had the same problem, so ended up ordering the stuff from Amazon and eBay. 
The good news is that the stuff is still available through those channels. 

All the best, 
Bertram 

--
Dr Bertram Daum
Senior Research Fellow
University of Exeter 

+441392727455
www.exeter.ac.uk

Living Systems Institute 
Stocker Road 
Exeter
Devon
EX4 4QD
United Kingdom

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http://www.bristol.ac.uk/wolfson-bioimaging/equipment/cryo-em/ 



> On 13 Sep 2019, at 11:22, Chris Richardson  wrote:
> 
> Apologies for revisiting this oft-discussed subject.
> 
> nVidia no longer support their 3D Vision system, and appear to have stopped 
> manufacturing it.  Does anyone have suggestions for an alternative?  Not all 
> of our scientists use it, but those who find it valuable would be sad to lose 
> it.
> 
> To clarify, I'm seeking a desktop solution as we don't have the space for 3D 
> projectors.
> 
> If there is nothing else out there, I may have to start searching eBay for 
> second hand IR emitters.
> 
> Regards,
> 
> Chris
> -- 
> Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
> 
> 
> 
> 
> 
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
> Limited by Guarantee, Registered in England under Company No. 534147 with its 
> Registered Office at 123 Old Brompton Road, London SW7 3RP.
> 
> This e-mail message is confidential and for use by the addressee only.  If 
> the message is received by anyone other than the addressee, please return the 
> message to the sender by replying to it and then delete the message from your 
> computer and network.
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Secrets of ZYMIT

[mesters]

Besides detergents and I do not know what secret ingredients, the 
mixture includes *two* proteolytic enzymes.


If I were to design the mixture for needle cleaning, to digest different 
types of proteins, I would probably not use a costly enzyme with high 
substrate specificity, I would use proteases as found in washing powders 
such as savinase and neutrase (metalloenzyme) or any other combination 
of two out of six enzymes as offered by Novo Nordisk..



Jeroen


Am 09.09.19 um 00:01 schrieb Jorg Stetefeld:


Hi everyone,


this is Joerg Stetefeld.


I would like to approach the community in a peculiar case of a 
specific proteolytic cleavage during crystallization attempts.


Performing several crystallization screens we figured out that ZYMIT 
(https://www.ipcol.com/cleaners/zymit-low-foam) is the reason for a 
highly specific, but undesireable cleavage of protein components in 
our setups. Most remarkably, the cleavage site of our crystallisation 
target is not described in any protease database, and is highly 
inaccessible.




According to a publication by Naschberger /et al/, 2014 
(doi:10.1107/S2053230X14026053) the authors very nicely describe the 
phenomenon. They also describe a very elegant protease removal 
protocol, which works in our hands very well.


At this point, however, I would like to know what is “behind” ZYMIT? 
Naschberger /et al/ say “Zymit contains an unspecified‘protease 
enzyme’ as a trade secret (http://www.ipcol.com/pdfs/Zymit_msds.pdf)”.



Does anyone has more insight into the secrets of ZYMIT? Our attempts 
to contact several vendors here in Canada/ abroad failed and a further 
characterisation of its nature would help us to understand this 
particular phenomenon of proteolytic cleavage.




Thank you very much in advance- Your advise is appreciated.


js





Jörg Stetefeld


**

https://stetefeldlab.ca/





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--
*Dr.math. et dis. nat.Jeroen R. Mesters*
Deputy, Lecturer, Program Coordinator /Infection Biology
/ 
Visiting 
Professorship (South Bohemian University) in Biophysics

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*University of Lübeck*
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[ccp4bb] Postdoc position at Imperial College London

[Ali, Maruf]

Dear All

A quick reminder of a job opening for a postdoc researcher to join my group at 
Imperial College.  The closing date for applications is 18th Sept 2019.

The research project focuses on determining the structure and mechanism of ER 
chaperone complexes involved in stress signaling/unfolded protein response and 
protein homeostasis.  Methodology will include cryo-electron microscopy (EM) 
and a suite of biophysical, biochemical and cellular assays to determine 
structure and function.

Please see 
https://www.imperial.ac.uk/jobs/description/NAT00509/research-associate/ for 
further information.

all the best
Maruf

Senior Cancer Research UK Fellow
RM 505 Sir Ernst Chain Building
Department of Life Sciences
Imperial College
London SW7 2AZ
Tel: 0207 594 5733




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Re: [ccp4bb] challenges in structural biology

[James Holton]

I would like to thank everyone who took the time to respond to my 
question that started this thread.  It is really good for me to get a 
sense of the community perspective.  Some debates were predictable, 
others not.  Many ideas I agree with, some not so much.  All were 
thought-provoking. I think this is going to be a really good GRC!


Something I did not expect to distill from all the responses is that the 
dominant challenge in structural biology is financial. The most common 
strategy suggested for addressing this challenge was torpedoing other 
scientists in similar fields, perhaps expecting to benefit from the 
flotsam.  Historically, this strategy is often counterproductive and at 
best inefficient. The good news is there is a lot of room for 
improvement. In reality, we are all on the same ship, and the people in 
our funding agencies fighting to get us what we need can be much more 
effective when armed with positive ideas and clear plans.  That is a 
better strategy for overcoming this challenge.


To this end, my first GRC session title is going to be:

"If I had a trillion dollars for structural biology"

I think we can all agree that science in general is vastly under-funded 
relative to the impact it has on the human condition. For example, I 
estimate the value of a general cure for cancer to be at least a 
trillion dollars.  This is based on the lives claimed every year, 
multiplied by how much one person would gladly pay after being diagnosed 
(amortized over the rest of their much longer life). This is only ~1% of 
the Gross World Product, a real bargain if we can come up with a plan 
that will actually work.


Now, obviously not all cancer research is structural biology, but not 
all structural biology is cancer research either. Let us suppose for a 
moment that you (yes, I'm talking to YOU), were given a trillion-dollar 
budget to do your science.  After buying all the tools and hiring all 
the people you wanted: would that solve all of your problems?  I expect 
not. The intellectual and technical challenges that remain are what I 
believe science is really all about, and the 2020 Diffraction Methods 
GRC will focus on the ones facing structural biology.


My goals here are twofold:
1) I believe it would be healthy for this field if we all spent a little 
time "thinking big"
2) I want to remove financial anxiety from the discussion, both here and 
at the GRC.


I ask for one restraint: please confine the discussion to structural 
biology.  I understand it is difficult to think about the 
trillion-dollar level without involving politics, but the CCP4 Bulletin 
Board is not a political discussion forum, and neither is the GRC. 
Assume all the other worthy causes in the world are given their own 
ample budgets. This trillion is yours, and you have to spend it on 
structural biology.  If you can't think of anything, think harder.


To get you started, a few things that could be done for under a trillion 
dollars:
1) re-do all the protein crystallization in the PDB, 500 times (saving 
all information)
2) buy Google and Facebook, get their AI teams to do machine learning 
and structure prediction for us
3) hire every "biological scientist" in the world, and give each $1M to 
work on your projects

4) re-do the NASA Apollo program three times
5) build 1000 XFELs and 100,000 Titan microscopes (yes, that's "and")
6) solve the phase problem by brute force.  (zettaflops-scale computing 
at $0.03/gflop)

7) build half a dozen terapixel detectors (ask Colin Nave what those can do)
8) fund every NIH grant submitted in the last 5 years. Not just the 
awarded ones, all of them.
9) X-prize style competitions for landmark achievements, such as 
predicting crystallization outcomes, or finding a universal way to stop 
protein from denaturing on the air-water interface.


This is not a to-do list, but rather an attempt to convey the scale of 
what can be done.  Oh, and you have a month or so to think about it. The 
meeting is July 26-31 2020, but my speaker list is due Oct 15.


Now, of course, at the GRC I will not actually have billion-dollar 
prizes to pass around, but I do want to set our sights on those lofty 
goals, and then work on the bridge we will need to get there.


So, when I say "challenge" I mean more than something we all agree is 
hard.  Those would make for very short talks.  I am after something more 
like a benchmark.  Useful challenges should have certain properties.  
They should be:
a) possible, because something that doesn't work no matter what you do 
is no fun.

b) hard, because something that is too easy is also not very interesting
c) realistic, as in relevant to a real-world problem we all agree is 
important

d) accessible, as in reasonable download sizes and/or affordable reagents
e) fast, because it if takes forever to try it nobody will have time to 
participate

f) measurable, as in having a clear and broadly acceptable "score"
g) adjustable, as in the level of "diffic