Re: [ccp4bb] beryllium chloride

[CRAIG A BINGMAN]

Bob,

Yes, Be salts are wildly toxic. They are also useful in structural studies on 
enzymes that perform phosphoryl transfers, almost always as beryllium fluoride 
complexes. The PDB contains about 200 such structures.

Craig

On Apr 1, 2019, at 9:37 PM, Sweet, Robert 
<27e0eb9d20ec-dmarc-requ...@jiscmail.ac.uk>
 wrote:

With all respect, this conversation make my skin crawl a little. I've been 
taught that beryllium salts are EXTREMELY toxic.  Please study this: 
https://pubchem.ncbi.nlm.nih.gov/compound/beryllium_chloride




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Re: [ccp4bb] beryllium chloride

[Sweet, Robert]

With all respect, this conversation make my skin crawl a little. I've been 
taught that beryllium salts are EXTREMELY toxic.  Please study this: 
https://pubchem.ncbi.nlm.nih.gov/compound/beryllium_chloride


Hopefully,


Bob



  Robert M. Sweet   E-Dress:  sw...@bnl.gov
  Deputy Director, LSBR: The Life Science and
   Biomedical Technology Research Center at NSLS-II
  Photon Sciences and Biology Dept
  Brookhaven Nat'l Lab.
  Upton, NY  11973 U.S.A.
  Phones:631 344 3401  (Office)
 631 338 7302  (Mobile)



From: CCP4 bulletin board  on behalf of Diana Tomchick 

Sent: Monday, April 1, 2019 7:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] beryllium chloride

No, that should read

[cid:2D6B8E73-AD29-4B8C-972A-06201D871588]

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Apr 1, 2019, at 5:54 PM, Keller, Jacob 
mailto:kell...@janelia.hhmi.org>> wrote:

Is that 4+ an April fools’ joke? Pretty crazy if not…can’t think of another ion 
with such a charge, well except things like DNA and proteins, but not single 
atoms.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Aaron Finke
Sent: Monday, April 1, 2019 6:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] beryllium chloride

American Elements sells BeCl2 but you’d have to check with them on what scale 
they sell it at. They tend to do custom manufacturing.

https://www.americanelements.com/beryllium-chloride-7787-47-5

BeCl2 dissociates in aqueous solution to form Be(H2O)4+ 2Cl-.


Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu

On Apr 1, 2019, at 17:07, Alexandra Deaconescu 
mailto:alexandra_deacone...@brown.edu>> wrote:

Hello,

Is anyone aware of a company that sells Beryllium chloride in the US? Sigma 
does not carry it any longer, and a quick Google search failed to reveal 
alternatives.

Thank you very much,

Alexandra


--
Alexandra Deaconescu, B.E., Ph.D.
Assistant Professor
Brown University

Office: (401) 863-3215
Wet Lab: (401) 863-6729
Computational Lab: (401) 863-7031

For Mail:
Laboratories of Molecular Medicine
70 Ship St. GE-4
Providence, RI 02903

For Courier:
Laboratories of Molecular Medicine
Brown University
70 Ship St., Chestnut St. Loading Dock
Providence, RI 02903

Website: www.deaconesculab.com

Admin
Ms. Christina Fournier
Email: christina_fournier[at]brown.edu
Mailing Address:
Box G-E, Brown University,
Providence, RI 02912-G
Telephone: 401-863-2782

Confidentiality Notice:
This e-mail message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain confidential, proprietary and privileged 
information. Any unauthorized review, use, disclosure or distribution is 
prohibited. If you are not the intended recipient, please contact the sender 
immediately and destroy or permanently delete all copies of the original 
message.



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UT Southwestern


Medical Center



The future of medicine, today.




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[ccp4bb] Postdoctoral Position in Biopolymer Secretion Systems

[Zimmer, Jochen (jz3x)]

Dear all,


A postdoctoral researcher position is available in the Zimmer lab at the 
University of Virginia School of Medicine. The lab explores how cells produce 
extracellular polysaccharides to form protective coats and capsules, cell 
walls, or biofilms.


Extracellular complex carbohydrates perform essential functions in all kingdoms 
of life and we strive to functionally reconstitute and structurally 
characterize various macromolecular complexes essential for their secretion. 
The lab has access to state-of-the-art cryo electron microscopy and X-ray 
crystallography facilities as well as single particle fluorescence and 
super-resolution light microscopes.


The University of Virginia has a particular strength in membrane biophysics and 
structural biology and is home to the Center for Membrane and Cell Physiology. 
The highly motivated candidate will join a diverse group working at the 
interface of structural and membrane biology, glycobiology, and biophysics. 
Candidates should have demonstrated expertise in cryo electron microscopy 
and/or crystallography, excellent skills in molecular biology and biochemistry, 
and at least one first author publication.


The University of Virginia is an equal opportunity employer. Applications from 
women and minorities are particularly welcome.


Interested candidates are encouraged to contact me directly by email for 
additional information (j...@virginia.edu).


Sincerely,

Jochen Zimmer


***

Jochen Zimmer, D. Phil.

Associate Professor

University of Virginia

Molecular Physiology & Biol. Physics

480 Ray C. Hunt Dr.

Snyder Bldg. #380

Charlottesville, VA 22908, USA

Phone: 434 243 6506



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Re: [ccp4bb] unidentified crescent-shaped electron density

[Paul Emsley]

Agreed. "PG4" - so that you don't have to go searching for it.


On 02/04/19 00:22, Peat, Tom (Manufacturing, Parkville) wrote:
>
> Hello Zhen,
>
>  
>
> PEG comes as a mixture and the weight given on the bottle is just the
> average molecular weight, so you don’t need any ‘cleavage’ to have
> smaller molecular weight PEGs present in your crystallisation cocktail.
>
> Try putting a small PEG in, it looks like it might fit.
>
> Cheers, tom
>
>  
>
> *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
> Of *Zhen Luo
> *Sent:* Tuesday, 2 April 2019 9:59 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] unidentified crescent-shaped electron density
>
>  
>
> Dear all,
>
>  
>
> Could you please shed some light on what this crescent-shaped density
> around the lysine side chain might belong to? I now have two unrelated
> protein structures where this kind of density can be found surrounding
> a lysine side chain. 
>
>  
>
>  
>
> One protein was crystallised in 0.1 M CaCl_2 and 20% PEG 3350; the
> other in 10% PEG 2, 20% PEG MME 550, 0.03 M CaCl_2 /MgCl_2 , 0.1 M
> MES/imidazole. Protein buffers contained 0.025 M HEPES and 0.15 M
> NaCl. None of these fitted in well. Could it be cleaved PEG?
>
>  
>
> Any suggestion would be greatly appreciated. Thanks in advance!
>
>  
>
> Best regards,
>
> Zhen Luo
>
>  
>
> School of Chemistry and Molecular Biosciences
>
> The University of Queensland, Australia
>
>  
>
>  
>




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Re: [ccp4bb] beryllium chloride

[Diana Tomchick]

No, that should read

[cid:2D6B8E73-AD29-4B8C-972A-06201D871588]

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Apr 1, 2019, at 5:54 PM, Keller, Jacob 
mailto:kell...@janelia.hhmi.org>> wrote:

Is that 4+ an April fools’ joke? Pretty crazy if not…can’t think of another ion 
with such a charge, well except things like DNA and proteins, but not single 
atoms.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Aaron Finke
Sent: Monday, April 1, 2019 6:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] beryllium chloride

American Elements sells BeCl2 but you’d have to check with them on what scale 
they sell it at. They tend to do custom manufacturing.

https://www.americanelements.com/beryllium-chloride-7787-47-5

BeCl2 dissociates in aqueous solution to form Be(H2O)4+ 2Cl-.

Aaron
--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu

On Apr 1, 2019, at 17:07, Alexandra Deaconescu 
mailto:alexandra_deacone...@brown.edu>> wrote:
Hello,

Is anyone aware of a company that sells Beryllium chloride in the US? Sigma 
does not carry it any longer, and a quick Google search failed to reveal 
alternatives.

Thank you very much,

Alexandra


--
Alexandra Deaconescu, B.E., Ph.D.
Assistant Professor
Brown University

Office: (401) 863-3215
Wet Lab: (401) 863-6729
Computational Lab: (401) 863-7031

For Mail:
Laboratories of Molecular Medicine
70 Ship St. GE-4
Providence, RI 02903

For Courier:
Laboratories of Molecular Medicine
Brown University
70 Ship St., Chestnut St. Loading Dock
Providence, RI 02903

Website: www.deaconesculab.com

Admin
Ms. Christina Fournier
Email: christina_fournier[at]brown.edu
Mailing Address:
Box G-E, Brown University,
Providence, RI 02912-G
Telephone: 401-863-2782

Confidentiality Notice:
This e-mail message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain confidential, proprietary and privileged 
information. Any unauthorized review, use, disclosure or distribution is 
prohibited. If you are not the intended recipient, please contact the sender 
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message.



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UT Southwestern


Medical Center



The future of medicine, today.




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Re: [ccp4bb] beryllium chloride

[Keller, Jacob]

Is that 4+ an April fools’ joke? Pretty crazy if not…can’t think of another ion 
with such a charge, well except things like DNA and proteins, but not single 
atoms.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: CCP4 bulletin board  On Behalf Of Aaron Finke
Sent: Monday, April 1, 2019 6:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] beryllium chloride

American Elements sells BeCl2 but you’d have to check with them on what scale 
they sell it at. They tend to do custom manufacturing.

https://www.americanelements.com/beryllium-chloride-7787-47-5

BeCl2 dissociates in aqueous solution to form Be(H2O)4+ 2Cl-.

Aaron
--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu

On Apr 1, 2019, at 17:07, Alexandra Deaconescu 
mailto:alexandra_deacone...@brown.edu>> wrote:
Hello,

Is anyone aware of a company that sells Beryllium chloride in the US? Sigma 
does not carry it any longer, and a quick Google search failed to reveal 
alternatives.

Thank you very much,

Alexandra


--
Alexandra Deaconescu, B.E., Ph.D.
Assistant Professor
Brown University

Office: (401) 863-3215
Wet Lab: (401) 863-6729
Computational Lab: (401) 863-7031

For Mail:
Laboratories of Molecular Medicine
70 Ship St. GE-4
Providence, RI 02903

For Courier:
Laboratories of Molecular Medicine
Brown University
70 Ship St., Chestnut St. Loading Dock
Providence, RI 02903

Website: www.deaconesculab.com

Admin
Ms. Christina Fournier
Email: christina_fournier[at]brown.edu
Mailing Address:
Box G-E, Brown University,
Providence, RI 02912-G
Telephone: 401-863-2782

Confidentiality Notice:
This e-mail message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain confidential, proprietary and privileged 
information. Any unauthorized review, use, disclosure or distribution is 
prohibited. If you are not the intended recipient, please contact the sender 
immediately and destroy or permanently delete all copies of the original 
message.



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[ccp4bb] Open Research Position in Chemical Biology/ Structural Biology at St. Jude

[Marcus Fischer]

The Fischer lab is recruiting a Staff Scientist for a project that exploits
the protein conformational landscape for ligand discovery in pediatric
cancer.

We are looking for applicants with a strong training in molecular biology,
protein biochemistry, and structural biology and a keen interest or ideally
experience in ligand discovery.



You will be part of a young, interdisciplinary team that uses
structural biology (multi-temperature and high-throughput crystallography)
to characterize disease-relevant protein states, computational methods to
analyze and exploit them, and experiments (biophysical, biochemical,
cell-based assays) to test the impact of small molecules on biology and
disease. These approaches have relevance for allosteric regulation of
proteins and protein-protein interactions.



The successful candidate has these attributes:

1) Must be able to conduct independent research in molecular biology and
protein biochemistry, including cloning and protein purification, that
enable structural studies.

2) Demonstrated experience in protein crystallography.

3) Familiarity with large-scale/ high-throughput approaches, automation,
liquid handling, biophysical assays or computational approaches is
desirable.

4) Experience with expression systems other than *E. coli*and familiarity
with cell-based assays is a plus.

5) Proficiency in e.g. python or shell scripting will facilitate scaling up
data analysis.

6) Must be eager to learn and implement new techniques from those relevant
areas.



Besides working on your own projects, you will form a liaison for other lab
members and

support projects within the lab while maintaining efficient laboratory
operations.



Our group is housed in the Department of Chemical Biology and Therapeutics (
https://www.stjude.org/research/departments-divisions/chemical-biology-therapeutics.html),
and Structural Biology (
https://www.stjude.org/research/departments-divisions/structural-biology.html)
at St. Jude Children’s Research Hospital. With ongoing investments into
exceptional structural and chemical biology facilities, this is an exciting
time to join our lab to do cutting-edge research whilst living in an
affordable city.

Stable funding for this post is available.



*Minimum Experience:*

A minimum of five (5) years of relevant and productive (combined) years
postdoctoral research associate or five (5) years of combined academic
experience at the postdoctoral level or above.



Please direct your questions and application package including a cover
letter, current CV, and 3 letters of reference to: Dr. Marcus Fischer (
marcus.fisc...@stjude.org).



Relevant papers include:

• Fischer et al. (2015). One crystal, two temperatures: cryocooling
penalties alter ligand binding to transient protein sites. 1560-64.
PMID 26032594

• Merski et al. (2015). Homologous ligands accommodated by discrete
conformations of a buried cavity. PNAS 112, 5039-44. PMID 25847998

• Fischer et al. (2014). Incorporation of protein flexibility &
conformational energy penalties in docking screens to improve ligand
discovery. Nature Chemistry 6, 575-83. PMID 24950326



More info at: https://www.stjude.org/fischer



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Re: [ccp4bb] beryllium chloride

[Aaron Finke]

American Elements sells BeCl2 but you’d have to check with them on what scale 
they sell it at. They tend to do custom manufacturing.

https://www.americanelements.com/beryllium-chloride-7787-47-5

BeCl2 dissociates in aqueous solution to form Be(H2O)4+ 2Cl-.

Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu

On Apr 1, 2019, at 17:07, Alexandra Deaconescu 
mailto:alexandra_deacone...@brown.edu>> wrote:

Hello,

Is anyone aware of a company that sells Beryllium chloride in the US? Sigma 
does not carry it any longer, and a quick Google search failed to reveal 
alternatives.

Thank you very much,

Alexandra


--
Alexandra Deaconescu, B.E., Ph.D.
Assistant Professor
Brown University

Office: (401) 863-3215
Wet Lab: (401) 863-6729
Computational Lab: (401) 863-7031

For Mail:
Laboratories of Molecular Medicine
70 Ship St. GE-4
Providence, RI 02903

For Courier:
Laboratories of Molecular Medicine
Brown University
70 Ship St., Chestnut St. Loading Dock
Providence, RI 02903

Website: www.deaconesculab.com

Admin
Ms. Christina Fournier
Email: christina_fournier[at]brown.edu
Mailing Address:
Box G-E, Brown University,
Providence, RI 02912-G
Telephone: 401-863-2782

Confidentiality Notice:
This e-mail message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain confidential, proprietary and privileged 
information. Any unauthorized review, use, disclosure or distribution is 
prohibited. If you are not the intended recipient, please contact the sender 
immediately and destroy or permanently delete all copies of the original 
message.



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[ccp4bb] Coot-0.8.9.2 released

[Paul Emsley]

Dear All,

We are pleased to announce the release of Coot 0.8.9.2

Source:

https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/coot-0.8.9.2.tar.gz

Binaries:

https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/release/

More Linux binaries and Windows binaries will be forthcoming in due course.


Paul.

p.s. if you get this twice, sorry about that... I suspect that not
everyone with an interest is on the Coot mailing list.

--


  Release 0.8.9.2

  o FEATURE: LINK info added to header browser

  o FEATURE: External angle restraints are now available (corresponding
to REFMAC type
     0 restraints) - mini-rsr included [Robbie Joosten]

  o FEATURE: raster3d output now includes labels [Vito Calderone]

  o FEATURE: API for user-defined unimodal torsion restraints (for
pyranoses) [Juan Hermoso]

  o FEATURE: Consolidated Validation dialog added


  o FEATURE: "Variable" bond widths i.e. as you zoom out, the bond lines
get thinner
 [Erec Stebbins]
 (set-use-variable-bond-thickness 1)

  o CHANGE:  SF4 Iron-Sulfur clusters are now bonded using the
dictionary (and so appear "cubic")
 [Hannah Bridges]

  o CHANGE:  Edit -> Copy Fragment now has a "Move it Here" check-button

  o CHANGE:  Old interface to PRODRG removed [Elinor Breiner]

  o CHANGE:  Jiggle-fit speed up by using backbone mode if possible

  o CHANGE:  Forwards-fitting a terminal residue now correctly positions
the O atom
 of the current residue that corresponds to the new residue

  o CHANGE:  Planar peptide restraints now apply to PTRANS restraints as
well as TRANS
 restraints

  o CHANGE:  "Linear" refine no longer exists, the refinement button now
uses the same
 interface as sphere refine. Residues now have environments
but "finding peptide
 links by residue number, no matter how far the residues are
away from each
 other" has been removed

  o CHANGE: Difference map peaks are now a shade of yellow and purple
[Keith Wilson]


  o CHANGE:  Squares to circles in the Ramachandran Plot

  o CHANGE:  Default is now not to generate a monomer on reading a
dictionary cif file

  o CHANGE:  More functions added to the coot_extended python module

  o CHANGE:  RCrane restored

  o CHANGE:  Add link-by-torsion-to-NAG-core-NAG-SER.tab so that
add_linked_residue()
 can link a NAG to a SER

  o CHANGE:  CA Zone -> Main-chain builds in both directions

  o CHANGE:  Alignment gap penalty changed to -3.0

  o CHANGE:  Merging a ligand molecule now adds the ligand to the
closest chain - unless
 a merging molecule ligand has been specified

  o BUG-FIX: the H atom in a peptide is now moved along with the other
peptide atoms
 on a cis->trans conversion (and vice versa)

  o BUG-FIX: align-and-mutate occasional reversing of residues fixed
[Rob Kirchdoerfer]

  O BUG-FIX: Using PDB-REDO now loads an anomalous map also (if
possible) [Robbie Joosten]

  o BUG-FIX: Fix typo in template-keybindings-to-preferences that causes
initial
 installation of key-bindings to fail sometimes [Colin Palmer].

  o BUG-FIX: The slow update on deleting deviant extra distance
restraints has been
 been replaced with a faster version [JED]

  o BUG-FIX: db_mainchain() fragment/chain indexing bug fixed [Oliver
Clarke]

  o BUG-FIX: db_mainchain() no longer crashes when using negative
residue numbers
 [Oliver Clarke]

  o BUG-FIX: Delete All Carbohydrate now works with carbohydrate with
insertion codes



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Re: [ccp4bb] beryllium chloride

[CRAIG A BINGMAN]

You can purchase beryllium oxide through a number of vendors. After careful 
neutralization with an appropriate amount of HCl, you should have BeCl2 in 
solution. I usually use pH paper to check the pH in such small volume 
operations.

> On Apr 1, 2019, at 4:07 PM, Alexandra Deaconescu 
>  wrote:
> 
> Hello,
> 
> Is anyone aware of a company that sells Beryllium chloride in the US? Sigma 
> does not carry it any longer, and a quick Google search failed to reveal 
> alternatives.
> 
> Thank you very much,
> 
> Alexandra
> 
> 
> -- 
> Alexandra Deaconescu, B.E., Ph.D.
> Assistant Professor
> Brown University
> 
> Office: (401) 863-3215
> Wet Lab: (401) 863-6729
> Computational Lab: (401) 863-7031
> 
> For Mail:
> Laboratories of Molecular Medicine
> 70 Ship St. GE-4
> Providence, RI 02903
> 
> For Courier:
> Laboratories of Molecular Medicine
> Brown University
> 70 Ship St., Chestnut St. Loading Dock
> Providence, RI 02903
> 
> Website: www.deaconesculab.com
> 
> Admin
> Ms. Christina Fournier
> Email: christina_fournier[at]brown.edu
> Mailing Address:
> Box G-E, Brown University,
> Providence, RI 02912-G
> Telephone: 401-863-2782
> 
> Confidentiality Notice:
> This e-mail message, including any attachments, is for the sole use of the 
> intended recipient(s) and may contain confidential, proprietary and 
> privileged information. Any unauthorized review, use, disclosure or 
> distribution is prohibited. If you are not the intended recipient, please 
> contact the sender immediately and destroy or permanently delete all copies 
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Re: [ccp4bb] beryllium chloride

[Daniel Anderson]

Is this for standard crystals? I think people used to use "basic 
beryllium acetate" for that application. A quick Google search got me 
nowhere.


-Dan


On 4/1/19 2:07 PM, Alexandra Deaconescu wrote:

Hello,

Is anyone aware of a company that sells Beryllium chloride in the US? 
Sigma does not carry it any longer, and a quick Google search failed 
to reveal alternatives.


Thank you very much,

Alexandra






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[ccp4bb] beryllium chloride

[Alexandra Deaconescu]

Hello,

Is anyone aware of a company that sells Beryllium chloride in the US? 
Sigma does not carry it any longer, and a quick Google search failed to 
reveal alternatives.


Thank you very much,

Alexandra


--
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Brown University

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Re: [ccp4bb] Backup of whole synchrotrons

[Aaron Finke]

Not to toot our own horn too much, but CHESS has been ahead of the curve on 
this for at least 30 years. As an academic facility, we simply take our 
limitless supply of graduate students, wipe their memory, upload what we need, 
and lock them in dimly-lit facilities. No freezing in liquid nitrogen 
necessary, and all they require for subsistence are cheap coffee and free pizza.

To date, nobody has noticed.

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu

On Mar 31, 2019, at 11:59 PM, Petr Kolenko 
mailto:petr.kole...@fjfi.cvut.cz>> wrote:

Dear colleagues,
We all are very happy about the storage of raw crystallographic datasets. But, 
is it really enough? No! Can we do better? Yes, of course!
The problem is that the crystal after the measurement is usually burned. It 
does not make sense to store them any more. But, in order to maximize 
reproducibility and increase the reliability of all our results, the committee 
of the Czech and Slovak Crystallographic Association has decided to force our 
researchers to back up the whole experimental station (including synchrotrons 
and their storage rings) after each crystal, each use. Storage of synchrotrons 
under liquid nitrogen is welcomed, but not necessary, yet. For the next decade, 
in-house storage of complete XFELs is expected (EU project Horizon 2030, 
proposal EC.2030.14.1.CZ.004).
Best regards,
Petr



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[ccp4bb] Ubiquitin & Friends Symposium 2019 (Vienna), register until 7th April

[Clausen,Tim]

Dear Colleagues,

I would like to remind you to the "Ubiquitin & Friends Symposium" that will 
take place in Vienna on May 20-21, 2019. In fact, the deadline for 
registration, the 1st of April, is not too strict, such that you can sign-in 
until the 7th.

As implied by the meeting's name, you will have the chance to enjoy exciting 
science in a relaxed, family-like atmosphere and learn more about ubiquitin 
(structural) biology in health and disease. A major intention is to give each 
participant the opportunity to discuss her/his research with colleagues, 
friends, and ubiquitin heroes. And be aware - this is not a 1st-April joke 
(still waiting for it ...) but rather a comment from our former keynote speaker 
Rachel Klevit - most of us are working on a ubiquitin project, but not knowing 
it.

With best regards,

Tim

\\\

Ubiquitin & Friends Symposium 2019 (Vienna), register until 7th April

Closely packed in a 11/2 days meeting, you will have the chance to listen to 
outstanding experts in the field including

  *   Alfred Goldberg (Harvard Medical School, USA)
  *   Ramanujan Hegde (University of Cambridge, UK)
  *   Katrin Rittinger (Francis Crick Institute, UK)
  *   Elif Karagoz (MFPL, Austria)
  *   Ivan Dikic (Institute of Biochemistry II (IBC2), Goethe University 
Frankfurt, Germany)
  *   Anne Simonsen (Institute of Basic Medical Sciences, Norway)
  *   Eilika Weber-Ban (ETH Zuerich, Switzerland)
  *   Hermann Steller (Rockefeller University, USA)
  *   Fumiyo Ikeda (IMBA - Institute of Molecular Biotechnology, Austria)

This year, the Ubiquitin & Friends symposium will take place in the 
"Billrothhaus", the house of physicians in Vienna. It's a truly historic place 
featuring a majestic lecture hall, where already Freud, Landsteiner and 
Rokitansky presented their studies. In fact, the Billrothhaus lectures are 
famous to stimulate extensive discussions and combine science with culture, 
thus fitting perfectly to the scope of the Viennese Ubiquitin meeting. An 
evening poster reception plus a follow-up dinner will provide ample of 
opportunities to discuss science, not only related to ubiquitin, and make new 
friends. Further information, photos of the wonderful location and the 
registration link you can find at https://ubiquitin.at/symposium/  ... and, 
travel awards are still available!




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Re: [ccp4bb] Backup of whole synchrotrons

[Fred Vellieux]

Hi,

We already have problems with the volume taken by our standard backups 
(they take too much space and we haven't been able to push the walls 
outwards in the Institute - I don't know why they keep telling us that 
our data should be in some clouds up in the sky). Hence I was wondering 
about space considerations: can the backups of the synchrotrons and 
X-FELs be miniature versions (obtained by clever dehydration methods)? 
If you need to access the backup then simply rehydrate and you'll get 
the full size backup appearing in the garden of your Institute... If 
your Institute doesn't have a garden of the proper size, then it's time 
to talk to the administrator. It should be fairly easy to convice 
her/him that the acquisition of a garden is really a must now.


F.

On 4/1/19 12:22 PM, Robbie Joosten wrote:

Hi Peter,

The copies are only indistinguishable after they have been produced. So there 
has to be good record keeping during production. It's as easy as hanging on to 
rich meta-data. There was another post today on what to store in mmCIF, I'm 
sure we can have another record in there to cover this.
You do touch the subject of FAIR data here, for reproducibility, do we need to 
keep the copy and spawn a new copy with the update? Or can we keep update the 
'original' copy with a well-defined downgrade path. Off course the meta-data 
for the original copy needs to be retained in such a case.
I hope it is obvious to everyone that we have to keep the copies in stasis, we 
cannot have them running around to change all the time. This is not just a 
methodological issue of being able to keep an experiment reproducible, but it 
is also an HR nightmare. It would require a lot of extra salaries. I mean, 
copies have rights and what will the unions think? If only we had thought of 
backing up crystallographers earlier, then we would have a copy of Margaret 
Thatcher to deal with the unions!  Instead, I guess today is a good day to 
invest in cryo-stasis technology.

Cheers,
Robbie

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Peter Keller
Sent: Monday, April 01, 2019 12:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Backup of whole synchrotrons

Hi Robbie,

On 01/04/2019 07:23, Robbie Joosten wrote:

I don't think making this GDOR complient is that hard. It's all pretty
well defined what you store (everything), where you store it, and why.
There are some philosophical problems with allowing users to have
their data deleted. Assuming the copy is good enough to reproducing
the experiment. Deleting a copy would constitute murder.

You have correctly identified the underlying philosophical issue: it is a 
variant
of what is now known as the "Teletransportation paradox", see
.

  From the point of view of methods developers like you and me, there is an
additional issue: with insufficient raw data to work with, we are required to
create living experimenters as part of our development work.
For the most accurate results, these should be faithful copies of real
synchrotron visitors and beamline scientists, who in many cases are
personally known to us. How should we handle these copies when we need
to release new or updated methods? Since these copies need to be
indistinguishable from the originals, how can we tell whether we are
upgrading the copy or the original?

Regards,
Peter.

   This means that the

backups have to be stored in a rather libertarian "state" like Sealand
or Somalia.
Keeping that in mind, perrhaps this sort of backup should first be
implemented with the future African synchrotron.

Cheers,
Robbie

On 1 Apr 2019 07:46, "graeme.win...@diamond.ac.uk"
 wrote:

 While this may sound absurd, the principle of incremental backups
 can help out a great deal here. Like Apple’s Time Machine, all we
 need to do is store a copy of the things which have changed rather
 than the entire facility, which reduces the burden by at least a few
 orders of magnitude. Such efficiency savings will I am sure be of
 great interest in this project. Surely though we could save a copy
 of the experimental Eigenstate before the experiment too, offering
 the option of going back and having another go - every
 experimentalists dream!

 I do however take issue with your hypothesis that only the
 experimental equipment need be backed up - surely the experimenters
 also need to be archived, to allow the question “What were you
 thinking??” to be accurately answered when the reviewer’s questions
 come back. Unfortunately due to quantum entanglement issues this
 would probably require archiving the mind-state of dozens of people
 every time you hit “go” with the associated data protection issues -
 I for one would not like to fill in the GDPR section of that EU
 application :-)

 Anyhow, best of luck with your application,

 Graeme

 

Re: [ccp4bb] OT: Terminal Command-P

[Stefano Trapani]

 

Le 2019-04-01 08:53, Paul Emsley a écrit : 

> Dear All, Sometime I use a Mac. A niggling issue I have is that, in a 
> Terminal, Command-P doesn't act like Alt-P in (say) a gnome-terminal

try ESC-p (not simultaneously) 

---
Stefano Trapani

Maître de Conférences
http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
-
Centre de Biochimie Structurale (CBS)
29 rue de Navacelles
34090 MONTPELLIER Cedex, France

Tel : +33 (0)4 67 41 77 29
Fax : +33 (0)4 67 41 79 13
-
Université de Montpellier
CNRS UMR 5048
INSERM UMR 1054
-

 
-- 
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dangerous content by MailScanner, and is
believed to be clean.




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Re: [ccp4bb] Backup of whole synchrotrons

[Robbie Joosten]

Hi Peter,

The copies are only indistinguishable after they have been produced. So there 
has to be good record keeping during production. It's as easy as hanging on to 
rich meta-data. There was another post today on what to store in mmCIF, I'm 
sure we can have another record in there to cover this. 
You do touch the subject of FAIR data here, for reproducibility, do we need to 
keep the copy and spawn a new copy with the update? Or can we keep update the 
'original' copy with a well-defined downgrade path. Off course the meta-data 
for the original copy needs to be retained in such a case. 
I hope it is obvious to everyone that we have to keep the copies in stasis, we 
cannot have them running around to change all the time. This is not just a 
methodological issue of being able to keep an experiment reproducible, but it 
is also an HR nightmare. It would require a lot of extra salaries. I mean, 
copies have rights and what will the unions think? If only we had thought of 
backing up crystallographers earlier, then we would have a copy of Margaret 
Thatcher to deal with the unions!  Instead, I guess today is a good day to 
invest in cryo-stasis technology.  

Cheers,
Robbie
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Peter Keller
> Sent: Monday, April 01, 2019 12:04
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Backup of whole synchrotrons
> 
> Hi Robbie,
> 
> On 01/04/2019 07:23, Robbie Joosten wrote:
> > I don't think making this GDOR complient is that hard. It's all pretty
> > well defined what you store (everything), where you store it, and why.
> > There are some philosophical problems with allowing users to have
> > their data deleted. Assuming the copy is good enough to reproducing
> > the experiment. Deleting a copy would constitute murder.
> 
> You have correctly identified the underlying philosophical issue: it is a 
> variant
> of what is now known as the "Teletransportation paradox", see
> .
> 
>  From the point of view of methods developers like you and me, there is an
> additional issue: with insufficient raw data to work with, we are required to
> create living experimenters as part of our development work.
> For the most accurate results, these should be faithful copies of real
> synchrotron visitors and beamline scientists, who in many cases are
> personally known to us. How should we handle these copies when we need
> to release new or updated methods? Since these copies need to be
> indistinguishable from the originals, how can we tell whether we are
> upgrading the copy or the original?
> 
> Regards,
> Peter.
> 
>   This means that the
> > backups have to be stored in a rather libertarian "state" like Sealand
> > or Somalia.
> > Keeping that in mind, perrhaps this sort of backup should first be
> > implemented with the future African synchrotron.
> >
> > Cheers,
> > Robbie
> >
> > On 1 Apr 2019 07:46, "graeme.win...@diamond.ac.uk"
> >  wrote:
> >
> > While this may sound absurd, the principle of incremental backups
> > can help out a great deal here. Like Apple’s Time Machine, all we
> > need to do is store a copy of the things which have changed rather
> > than the entire facility, which reduces the burden by at least a few
> > orders of magnitude. Such efficiency savings will I am sure be of
> > great interest in this project. Surely though we could save a copy
> > of the experimental Eigenstate before the experiment too, offering
> > the option of going back and having another go - every
> > experimentalists dream!
> >
> > I do however take issue with your hypothesis that only the
> > experimental equipment need be backed up - surely the experimenters
> > also need to be archived, to allow the question “What were you
> > thinking??” to be accurately answered when the reviewer’s questions
> > come back. Unfortunately due to quantum entanglement issues this
> > would probably require archiving the mind-state of dozens of people
> > every time you hit “go” with the associated data protection issues -
> > I for one would not like to fill in the GDPR section of that EU
> > application :-)
> >
> > Anyhow, best of luck with your application,
> >
> > Graeme
> >
> > On 1 Apr 2019, at 04:59, Petr Kolenko
> > mailto:petr.kole...@fjfi.cvut.cz>>
> wrote:
> >
> > Dear colleagues,
> > We all are very happy about the storage of raw crystallographic
> > datasets. But, is it really enough? No! Can we do better? Yes, of
> > course!
> > The problem is that the crystal after the measurement is usually
> > burned. It does not make sense to store them any more. But, in order
> > to maximize reproducibility and increase the reliability of all our
> > results, the committee of the Czech and Slovak Crystallographic
> > Association has decided to force our 

Re: [ccp4bb] Backup of whole synchrotrons

[Peter Keller]

Hi Robbie,

On 01/04/2019 07:23, Robbie Joosten wrote:
I don't think making this GDOR complient is that hard. It's all pretty 
well defined what you store (everything), where you store it, and why.
There are some philosophical problems with allowing users to have their 
data deleted. Assuming the copy is good enough to reproducing the 
experiment. Deleting a copy would constitute murder.


You have correctly identified the underlying philosophical issue: it is 
a variant of what is now known as the "Teletransportation paradox", see 
.


From the point of view of methods developers like you and me, there is 
an additional issue: with insufficient raw data to work with, we are 
required to create living experimenters as part of our development work. 
For the most accurate results, these should be faithful copies of real 
synchrotron visitors and beamline scientists, who in many cases are 
personally known to us. How should we handle these copies when we need 
to release new or updated methods? Since these copies need to be 
indistinguishable from the originals, how can we tell whether we are 
upgrading the copy or the original?


Regards,
Peter.

 This means that the
backups have to be stored in a rather libertarian "state" like Sealand 
or Somalia.
Keeping that in mind, perrhaps this sort of backup should first be 
implemented with the future African synchrotron.


Cheers,
Robbie

On 1 Apr 2019 07:46, "graeme.win...@diamond.ac.uk" 
 wrote:


While this may sound absurd, the principle of incremental backups
can help out a great deal here. Like Apple’s Time Machine, all we
need to do is store a copy of the things which have changed rather
than the entire facility, which reduces the burden by at least a few
orders of magnitude. Such efficiency savings will I am sure be of
great interest in this project. Surely though we could save a copy
of the experimental Eigenstate before the experiment too, offering
the option of going back and having another go - every
experimentalists dream!

I do however take issue with your hypothesis that only the
experimental equipment need be backed up - surely the experimenters
also need to be archived, to allow the question “What were you
thinking??” to be accurately answered when the reviewer’s questions
come back. Unfortunately due to quantum entanglement issues this
would probably require archiving the mind-state of dozens of people
every time you hit “go” with the associated data protection issues -
I for one would not like to fill in the GDPR section of that EU
application :-)

Anyhow, best of luck with your application,

Graeme

On 1 Apr 2019, at 04:59, Petr Kolenko
mailto:petr.kole...@fjfi.cvut.cz>> wrote:

Dear colleagues,
We all are very happy about the storage of raw crystallographic
datasets. But, is it really enough? No! Can we do better? Yes, of
course!
The problem is that the crystal after the measurement is usually
burned. It does not make sense to store them any more. But, in order
to maximize reproducibility and increase the reliability of all our
results, the committee of the Czech and Slovak Crystallographic
Association has decided to force our researchers to back up the
whole experimental station (including synchrotrons and their storage
rings) after each crystal, each use. Storage of synchrotrons under
liquid nitrogen is welcomed, but not necessary, yet. For the next
decade, in-house storage of complete XFELs is expected (EU project
Horizon 2030, proposal EC.2030.14.1.CZ.004).
Best regards,
Petr




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Diamond Light Source Ltd. cannot guarantee that this e-mail or any
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any damage which you may sustain as a result of software viruses
which may be transmitted in or with the message.
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0DE, United Kingdom

[ccp4bb] OT: Terminal Command-P

[Paul Emsley]

Dear All,

Sometime I use a Mac. A niggling issue I have is that, in a Terminal, Command-P doesn't act like Alt-P in 
(say) a gnome-terminal. I'd really quite like it if it did. If you have worked out how to do this then I'd 
appreciate if you let us know (actually, I suspect that it's not possible).


Needless to say that I have already reassigned System Preferences -> Keyboard -> Shortcuts -> App Shortcuts 
-> Terminal -> Print so that I no longer get Print Screen, but it (Cmd-P) doesn't seem to get through to the 
shell (tcsh, FWIW). Also, I'd like Cmd-F, Cmd-B, Cmd-N to Do The Right Thing (not the Mac thing).


Thanks,

Paul.

p.s. this is a question about Cmd, not Option.



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Re: [ccp4bb] Backup of whole synchrotrons

[Robbie Joosten]

I don't think making this GDOR complient is that hard. It's all pretty well 
defined what you store (everything), where you store it, and why.
There are some philosophical problems with allowing users to have their data 
deleted. Assuming the copy is good enough to reproducing the experiment. 
Deleting a copy would constitute murder. This means that the backups have to be 
stored in a rather libertarian "state" like Sealand or Somalia.
Keeping that in mind, perrhaps this sort of backup should first be implemented 
with the future African synchrotron.

Cheers,
Robbie

On 1 Apr 2019 07:46, "graeme.win...@diamond.ac.uk" 
 wrote:

While this may sound absurd, the principle of incremental backups can help out 
a great deal here. Like Apple’s Time Machine, all we need to do is store a copy 
of the things which have changed rather than the entire facility, which reduces 
the burden by at least a few orders of magnitude. Such efficiency savings will 
I am sure be of great interest in this project. Surely though we could save a 
copy of the experimental Eigenstate before the experiment too, offering the 
option of going back and having another go - every experimentalists dream!

I do however take issue with your hypothesis that only the experimental 
equipment need be backed up - surely the experimenters also need to be 
archived, to allow the question “What were you thinking??” to be accurately 
answered when the reviewer’s questions come back. Unfortunately due to quantum 
entanglement issues this would probably require archiving the mind-state of 
dozens of people every time you hit “go” with the associated data protection 
issues - I for one would not like to fill in the GDPR section of that EU 
application :-)

Anyhow, best of luck with your application,

Graeme

On 1 Apr 2019, at 04:59, Petr Kolenko 
mailto:petr.kole...@fjfi.cvut.cz>> wrote:

Dear colleagues,
We all are very happy about the storage of raw crystallographic datasets. But, 
is it really enough? No! Can we do better? Yes, of course!
The problem is that the crystal after the measurement is usually burned. It 
does not make sense to store them any more. But, in order to maximize 
reproducibility and increase the reliability of all our results, the committee 
of the Czech and Slovak Crystallographic Association has decided to force our 
researchers to back up the whole experimental station (including synchrotrons 
and their storage rings) after each crystal, each use. Storage of synchrotrons 
under liquid nitrogen is welcomed, but not necessary, yet. For the next decade, 
in-house storage of complete XFELs is expected (EU project Horizon 2030, 
proposal EC.2030.14.1.CZ.004).
Best regards,
Petr



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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
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