Re: [ccp4bb] Refmac dictionary

[Sam Tang]

Hi

My apologies. This is indeed a silly question. It appears I forgot to
remove the extra O when linking them together!

Sam


On Wed, 3 Apr 2019 at 07:21, Sam Tang  wrote:

> Dear all
>
> Hello again.
>
> We have another protein-RNA dataset which we are trying to refine. For
> this dataset we have three OMU nucleotides modelled. We got the monomer
> from Coot 'Get Monomer'. Refmac returned the following error:
> ERROR : atom :OP3  OMU 2  CCC  is absent in the library
> ERROR : atom :OP3  OMU 3  CCC  is absent in the library
>
> The library version is 5.44. I tried to download a OMU.cif (from this link
> https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/dictionary.html)
> for use in Refmac but the same error occurs.
>
> So... what should I try now?
>
> Many thanks in advance!
>
> Sam
>



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[ccp4bb] Refmac dictionary

[Sam Tang]

Dear all

Hello again.

We have another protein-RNA dataset which we are trying to refine. For this
dataset we have three OMU nucleotides modelled. We got the monomer from
Coot 'Get Monomer'. Refmac returned the following error:
ERROR : atom :OP3  OMU 2  CCC  is absent in the library
ERROR : atom :OP3  OMU 3  CCC  is absent in the library

The library version is 5.44. I tried to download a OMU.cif (from this link
https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/dictionary.html)
for use in Refmac but the same error occurs.

So... what should I try now?

Many thanks in advance!

Sam



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Re: [ccp4bb] installation of XDS

[Kay Diederichs]

Hi Nadine,

it sounds like you downloaded the tar-file that has the documentation, instead 
of the tar-file that has the binaries.

You want to download 
ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz , 
and un-tar the file at /home/Programs - this will overwrite your old binaries 
in directory XDS-INTEL64_Linux_x86_64 with the new ones.

Hope this helps,

Kay

On Tue, 2 Apr 2019 16:51:09 +0200, Nadine Gerlach  wrote:

>Hello,
>
>I need help installing XDS on the computer. Apparently the current
>lisence expired on March 31 2019, which is why I downloaded and
>extracted the XDS_html_doc.tar.gz
> from
>http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.html in
>/home/Programs/XDS-INTEL64_Linux_x86_64. This directory also contains
>the uncrompressed XDS_html_doc folder. However, if I wanna run xds I get
>the following error message:
>
>!!! ERROR !!! CANNOT OPEN OR READ XDS.INP
>
>I am not really experience with ubuntu or linux. Can someone please help
>me?
>
>Thanks in advance!
>
>Best,
>
>Nadine
>
>--
>PhD student
>Joint Research Group Marine Glycobiology
>Max Planck Institute for Marine Microbiology &
>MARUM - Center for Marine Environmental Sciences, University Bremen
>MARUM Pavillon Raum 1110
>Leobener Str. 2
>28359 Bremen, Germany
>
>
>
>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] Research Technician Position in Chromatin Biology

[Karim Armache]

A research technician position is available in the laboratory of Dr.
Karim-Jean Armache, Assistant Professor in the Structural Biology Program
at the Skirball Institute of Biomedical Research—NYU Medical Center, New
York, USA.


We are looking for creative individuals with a strong interest in protein
and nucleic acid biochemistry. A commitment of at least 2 years is
required. Ideal candidates should be highly motivated and have obtained a
B.S. or M.S. degree with a background in biochemistry or molecular biology.
Experience in molecular cloning and protein expression, as well as an
ability to maintain organized records is essential. Experience with cell
culture would be a plus. The candidate must have an excellent command of
oral and written English. Applicants should send a single PDF file
containing their CV along with a summary of their previous research
experience, accomplishments, and experimental expertise.


They should also arrange for 2-3 letters of reference to be sent directly
to Dr. Karim-Jean Armache via e-mail at:


*kjarma...@gmail.com *


The position is open immediately and applications will be reviewed until
the position is filled.



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Re: [ccp4bb] beryllium chloride

[Bernhard Rupp]

The older fellows might well remember the huge Be windows on the ADSC 
multi-wire detectors – 

miraculously we survived them simply by common sense dictating 

(i) don’t eat it, (ii) don’t breathe it,  and (iii) don’t rub your nose in it…. 

 

Cheers, BR

 

 

From: CCP4 bulletin board  On Behalf Of Ian Tickle
Sent: Tuesday, April 2, 2019 5:39 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] beryllium chloride

 

 

Yes both soluble beryllium salts and powdered beryllium metal even applied to 
the skin are known to cause sensitization and is a route into the bloodstream 
where it is highly carcinogenic (I am not speaking from experience!).

 

Yet strangely the one source of beryllium that many people (at least the more 
well-off among us) commonly come into contact with, namely the gemstone emerald 
Be3Al2(SiO3)6 obviously has no known toxic effects whatosever!  Apparently even 
gemstone grinders show no ill effects!  I guess it's the free Be2+ ion that's 
so toxic.

 

Cheers

 

-- Ian

 

 

 

On Tue, 2 Apr 2019 at 13:07, Aaron Finke mailto:af...@cornell.edu> > wrote:

1. Yes, I meant the tetrahydrate, [Be(H2O)4]2+ 2Cl- 

 

2. Bob, I studied that page, and couldn’t get past  BeCl2 is known to have a 
“sweetish taste.” I’m very glad chemists no longer characterize chemicals by 
their taste anymore...

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


On Apr 1, 2019, at 22:37, 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

 

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 mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Diana Tomchick mailto:diana.tomch...@utsouthwestern.edu> >
Sent: Monday, April 1, 2019 7:03 PM
To: CCP4BB@JISCMAIL.AC.UK  
Subject: Re: [ccp4bb] beryllium chloride 

 

No, that should read  

 



 

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 <  
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 < 
 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 

Re: [ccp4bb] beryllium chloride

[Aaron Finke]

There are plenty of heavy metals that have little to no physiological 
significance, because biomes evolved in their absence. But beryllium is 
interesting because it’s so light and nonabundant in comparison to related 
elements like Li or Mg. So since mammals never evolved with free Be2+ around, 
it can run amok, interacting with DNA and inhibiting enzymes.

That said, I am sure there is a cave somewhere on earth, full of emeralds and 
other beryl minerals, where microbes evolved to handily deal with the beryllium 
monster. We just haven’t found it yet. As Ian Malcolm said, “Life, uh, finds a 
way.”

I also just read that beryllium used to be called glucinium after the Greek for 
“sweet,” because many beryllium salts taste sweet. Yikes.

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

On Apr 2, 2019, at 11:32 AM, Keller, Jacob 
mailto:kell...@janelia.hhmi.org>> wrote:

I remember from biochemistry class that it’s the one element that has no known 
physiological role—is that still true?

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: Tuesday, April 2, 2019 11:21 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] beryllium chloride

The lung disease is called berylliosis and is an allergic-type response that 
leads to fibrosis in the lungs. A significant percentage of the population has 
allergic reactions to beryllium, but there is no very accurate method for 
prescreening this; I read somewhere even lung biopsies are only about 80% 
accurate for beryllium sensitivity. Beryllium metal readily oxidizes in air and 
BeO is the typical inhlation vector.

Mind you, this is on top of the carginogenic properties of beryllium and its 
compounds. It’s just nasty stuff. Shame it’s so useful...

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


On Apr 2, 2019, at 10:21 AM, Zhijie Li 
mailto:zhijie...@utoronto.ca>> wrote:

Sometime ago when I was watching a Youtube video on magnetron I learnt that at 
least at at certain point of time the antenna port of the magnetron was sealed 
using beryllium oxide ceramic(probably for its high thermal conductivity). The 
video maker warned that this ceramic was extremely dangerous. Further wikipedia 
and internet reading confirmed that fine beryllium oxide powder does cause 
something called beryllium disease and cancer (the latter in a way similar to 
that of asbestos? I guessed). However the sintered ceramic form is probably as 
safe as emerald unless you have to grind it and breath the dust every day. (I 
think most jewellers would always use some grinding liquid when honing their 
stones.)
The wikipedia page on beryllium oxide has some really interesting facts. Also 
if one is desperate for some beryllium salt it hints dissolving a magnetron 
antenna sealing ring in hot concentrated solution of H2SO4 and (NH4)2SO4.

My 2 cents.

Zhijie



On Apr 2, 2019, at 8:39 AM, Ian Tickle 
mailto:ianj...@gmail.com>> wrote:

Yes both soluble beryllium salts and powdered beryllium metal even applied to 
the skin are known to cause sensitization and is a route into the bloodstream 
where it is highly carcinogenic (I am not speaking from experience!).

Yet strangely the one source of beryllium that many people (at least the more 
well-off among us) commonly come into contact with, namely the gemstone emerald 
Be3Al2(SiO3)6 obviously has no known toxic effects whatosever!  Apparently even 
gemstone grinders show no ill effects!  I guess it's the free Be2+ ion that's 
so toxic.

Cheers

-- Ian



On Tue, 2 Apr 2019 at 13:07, Aaron Finke 
mailto:af...@cornell.edu>> wrote:
1. Yes, I meant the tetrahydrate, [Be(H2O)4]2+ 2Cl-

2. Bob, I studied that page, and couldn’t get past  BeCl2 is known to have a 
“sweetish taste.” I’m very glad chemists no longer characterize chemicals by 
their taste anymore...
--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu

On Apr 1, 2019, at 22:37, Sweet, Robert 

Re: [ccp4bb] unidentified crescent-shaped electron density

[Holton, James M]

Has anyone ever done the experiment of switching precipitants/cryoprotectants 
and verifying that this crown-of-PEG around lysine goes away when you do?

Just curious,

-James Holton
MAD Scientist

On 4/1/2019 4:26 PM, Paul Emsley wrote:


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 CaCl2 and 20% PEG 3350; the other in 10% 
PEG 2, 20% PEG MME 550, 0.03 M CaCl2/MgCl2, 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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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] beryllium chloride

[Keller, Jacob]

I remember from biochemistry class that it’s the one element that has no known 
physiological role—is that still true?

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: Tuesday, April 2, 2019 11:21 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] beryllium chloride

The lung disease is called berylliosis and is an allergic-type response that 
leads to fibrosis in the lungs. A significant percentage of the population has 
allergic reactions to beryllium, but there is no very accurate method for 
prescreening this; I read somewhere even lung biopsies are only about 80% 
accurate for beryllium sensitivity. Beryllium metal readily oxidizes in air and 
BeO is the typical inhlation vector.

Mind you, this is on top of the carginogenic properties of beryllium and its 
compounds. It’s just nasty stuff. Shame it’s so useful...

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


On Apr 2, 2019, at 10:21 AM, Zhijie Li 
mailto:zhijie...@utoronto.ca>> wrote:

Sometime ago when I was watching a Youtube video on magnetron I learnt that at 
least at at certain point of time the antenna port of the magnetron was sealed 
using beryllium oxide ceramic(probably for its high thermal conductivity). The 
video maker warned that this ceramic was extremely dangerous. Further wikipedia 
and internet reading confirmed that fine beryllium oxide powder does cause 
something called beryllium disease and cancer (the latter in a way similar to 
that of asbestos? I guessed). However the sintered ceramic form is probably as 
safe as emerald unless you have to grind it and breath the dust every day. (I 
think most jewellers would always use some grinding liquid when honing their 
stones.)
The wikipedia page on beryllium oxide has some really interesting facts. Also 
if one is desperate for some beryllium salt it hints dissolving a magnetron 
antenna sealing ring in hot concentrated solution of H2SO4 and (NH4)2SO4.

My 2 cents.

Zhijie



On Apr 2, 2019, at 8:39 AM, Ian Tickle 
mailto:ianj...@gmail.com>> wrote:

Yes both soluble beryllium salts and powdered beryllium metal even applied to 
the skin are known to cause sensitization and is a route into the bloodstream 
where it is highly carcinogenic (I am not speaking from experience!).

Yet strangely the one source of beryllium that many people (at least the more 
well-off among us) commonly come into contact with, namely the gemstone emerald 
Be3Al2(SiO3)6 obviously has no known toxic effects whatosever!  Apparently even 
gemstone grinders show no ill effects!  I guess it's the free Be2+ ion that's 
so toxic.

Cheers

-- Ian



On Tue, 2 Apr 2019 at 13:07, Aaron Finke 
mailto:af...@cornell.edu>> wrote:
1. Yes, I meant the tetrahydrate, [Be(H2O)4]2+ 2Cl-

2. Bob, I studied that page, and couldn’t get past  BeCl2 is known to have a 
“sweetish taste.” I’m very glad chemists no longer characterize chemicals by 
their taste anymore...
--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu

On Apr 1, 2019, at 22:37, 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

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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Diana Tomchick 
mailto:diana.tomch...@utsouthwestern.edu>>
Sent: Monday, April 1, 2019 7:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] beryllium chloride

No, that should read



Diana

Re: [ccp4bb] beryllium chloride

[Aaron Finke]

The lung disease is called berylliosis and is an allergic-type response that 
leads to fibrosis in the lungs. A significant percentage of the population has 
allergic reactions to beryllium, but there is no very accurate method for 
prescreening this; I read somewhere even lung biopsies are only about 80% 
accurate for beryllium sensitivity. Beryllium metal readily oxidizes in air and 
BeO is the typical inhlation vector.

Mind you, this is on top of the carginogenic properties of beryllium and its 
compounds. It’s just nasty stuff. Shame it’s so useful...

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

On Apr 2, 2019, at 10:21 AM, Zhijie Li 
mailto:zhijie...@utoronto.ca>> wrote:

Sometime ago when I was watching a Youtube video on magnetron I learnt that at 
least at at certain point of time the antenna port of the magnetron was sealed 
using beryllium oxide ceramic(probably for its high thermal conductivity). The 
video maker warned that this ceramic was extremely dangerous. Further wikipedia 
and internet reading confirmed that fine beryllium oxide powder does cause 
something called beryllium disease and cancer (the latter in a way similar to 
that of asbestos? I guessed). However the sintered ceramic form is probably as 
safe as emerald unless you have to grind it and breath the dust every day. (I 
think most jewellers would always use some grinding liquid when honing their 
stones.)
The wikipedia page on beryllium oxide has some really interesting facts. Also 
if one is desperate for some beryllium salt it hints dissolving a magnetron 
antenna sealing ring in hot concentrated solution of H2SO4 and (NH4)2SO4.

My 2 cents.

Zhijie



On Apr 2, 2019, at 8:39 AM, Ian Tickle 
mailto:ianj...@gmail.com>> wrote:


Yes both soluble beryllium salts and powdered beryllium metal even applied to 
the skin are known to cause sensitization and is a route into the bloodstream 
where it is highly carcinogenic (I am not speaking from experience!).

Yet strangely the one source of beryllium that many people (at least the more 
well-off among us) commonly come into contact with, namely the gemstone emerald 
Be3Al2(SiO3)6 obviously has no known toxic effects whatosever!  Apparently even 
gemstone grinders show no ill effects!  I guess it's the free Be2+ ion that's 
so toxic.

Cheers

-- Ian



On Tue, 2 Apr 2019 at 13:07, Aaron Finke 
mailto:af...@cornell.edu>> wrote:
1. Yes, I meant the tetrahydrate, [Be(H2O)4]2+ 2Cl-

2. Bob, I studied that page, and couldn’t get past  BeCl2 is known to have a 
“sweetish taste.” I’m very glad chemists no longer characterize chemicals by 
their taste anymore...

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

On Apr 1, 2019, at 22:37, 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

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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Diana Tomchick 
mailto:diana.tomch...@utsouthwestern.edu>>
Sent: Monday, April 1, 2019 7:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] beryllium chloride

No, that should read



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 

Re: [ccp4bb] installation of XDS

[graeme.win...@diamond.ac.uk]

Hi Nadine

The program is probably correct - I suspect you have no XDS.INP in there

I recommend using e.g. generate_XDS.INP for this purpose

https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP

You may find the wider XDS wiki worth a read

Best wishes Graeme


On 2 Apr 2019, at 15:51, Nadine Gerlach 
mailto:ngerl...@marum.de>> wrote:


Hello,

I need help installing XDS on the computer. Apparently the current lisence 
expired on March 31 2019, which is why I downloaded and extracted the 
XDS_html_doc.tar.gz
  from http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.html in 
/home/Programs/XDS-INTEL64_Linux_x86_64. This directory also contains the 
uncrompressed XDS_html_doc folder. However, if I wanna run xds I get the 
following error message:

!!! ERROR !!! CANNOT OPEN OR READ XDS.INP

I am not really experience with ubuntu or linux. Can someone please help me?

Thanks in advance!

Best,

Nadine

--
PhD student
Joint Research Group Marine Glycobiology
Max Planck Institute for Marine Microbiology &
MARUM - Center for Marine Environmental Sciences, University Bremen
MARUM Pavillon Raum 1110
Leobener Str. 2
28359 Bremen, Germany



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[ccp4bb] installation of XDS

[Nadine Gerlach]

Hello,

I need help installing XDS on the computer. Apparently the current 
lisence expired on March 31 2019, which is why I downloaded and 
extracted the XDS_html_doc.tar.gz 
 from 
http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.html in 
/home/Programs/XDS-INTEL64_Linux_x86_64. This directory also contains 
the uncrompressed XDS_html_doc folder. However, if I wanna run xds I get 
the following error message:


!!! ERROR !!! CANNOT OPEN OR READ XDS.INP

I am not really experience with ubuntu or linux. Can someone please help 
me?


Thanks in advance!

Best,

Nadine

--
PhD student
Joint Research Group Marine Glycobiology
Max Planck Institute for Marine Microbiology &
MARUM - Center for Marine Environmental Sciences, University Bremen
MARUM Pavillon Raum 1110
Leobener Str. 2
28359 Bremen, Germany



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

Re: [ccp4bb] beryllium chloride

[Zhijie Li]

Sometime ago when I was watching a Youtube video on magnetron I learnt that at 
least at at certain point of time the antenna port of the magnetron was sealed 
using beryllium oxide ceramic(probably for its high thermal conductivity). The 
video maker warned that this ceramic was extremely dangerous. Further wikipedia 
and internet reading confirmed that fine beryllium oxide powder does cause 
something called beryllium disease and cancer (the latter in a way similar to 
that of asbestos? I guessed). However the sintered ceramic form is probably as 
safe as emerald unless you have to grind it and breath the dust every day. (I 
think most jewellers would always use some grinding liquid when honing their 
stones.)
The wikipedia page on beryllium oxide has some really interesting facts. Also 
if one is desperate for some beryllium salt it hints dissolving a magnetron 
antenna sealing ring in hot concentrated solution of H2SO4 and (NH4)2SO4.

My 2 cents.

Zhijie



On Apr 2, 2019, at 8:39 AM, Ian Tickle 
mailto:ianj...@gmail.com>> wrote:


Yes both soluble beryllium salts and powdered beryllium metal even applied to 
the skin are known to cause sensitization and is a route into the bloodstream 
where it is highly carcinogenic (I am not speaking from experience!).

Yet strangely the one source of beryllium that many people (at least the more 
well-off among us) commonly come into contact with, namely the gemstone emerald 
Be3Al2(SiO3)6 obviously has no known toxic effects whatosever!  Apparently even 
gemstone grinders show no ill effects!  I guess it's the free Be2+ ion that's 
so toxic.

Cheers

-- Ian



On Tue, 2 Apr 2019 at 13:07, Aaron Finke 
mailto:af...@cornell.edu>> wrote:
1. Yes, I meant the tetrahydrate, [Be(H2O)4]2+ 2Cl-

2. Bob, I studied that page, and couldn’t get past  BeCl2 is known to have a 
“sweetish taste.” I’m very glad chemists no longer characterize chemicals by 
their taste anymore...

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

On Apr 1, 2019, at 22:37, 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


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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Diana Tomchick 
mailto:diana.tomch...@utsouthwestern.edu>>
Sent: Monday, April 1, 2019 7:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] beryllium chloride

No, that should read



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

Re: [ccp4bb] modelling of modified RNA

[Paul Emsley]

On 02/04/2019 14:28, Sam Tang wrote:

Hello


Hello.



I have been refining a protein-RNA complex with Refmac. The RNA we used was tagged with a Cy label. I 
modelled the RNA in Coot using the RCrane add-on and manually built the Cy tag. However after Refmac (also 
via Coot) the linkage between Cy and the RNA was always broken.


I guess I must have missed something obvious.


Maybe.

What CCD entry are you using for your Cy tag? What have you done to specify the link between the Cy and the 
RNA? What do you mean by "broken"? That the LINK is missing or that the distance between the linked atoms is 
too large? What did the refmac log file tell you about the distance between the atoms that you thought 
should be linked? Have you made a link using Acedrg in CCP4i2? Or Coot? (Extensions -> CCP4 -> CCP4 -> Make 
a Link via Acedrg)?


Regards,

Paul.



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[ccp4bb] PhD/ postdoc positions on studies on the life cycle and applications of virophages: Max Planck Institute, Heidelberg, Germany

[Ilme Schlichting]

Ph.D. and Postdoctoral positions dedicated to biophysical and 
spectroscopic/structural studies on the life cycle of virophages and 
their applications as nano-containers available in Jochen Reinstein's 
lab http://www.mpimf-heidelberg.mpg.de/14072516/gruppereinstein

at the Max Planck Institute for Medical Research, Heidelberg.
http://www.mpimf-heidelberg.mpg.de/en

Project Description:
Virophages are small DNA viruses of unicellular eukaryotes that 
replicate only during a coinfection with a giant virus. They propagate 
at the expense of the giant virus using its cytosolic reproduction and 
assembly machinery. Virophages encode about 20 genes including two 
capsid proteins, a protease that assists maturation and a FtsK-HerA type 
ATPase that supposedly is responsible for ATP dependent DNA transport 
into the assembled capsid.
The successful candidates will characterize capsid assembly & processing 
and active DNA transport of the Virophage. The assembly/-disassembly 
pathway will be characterized with spectroscopic, kinetic and structural 
methods with the aim to better understand the hierarchy and pathway of 
supramolecular organisation of capsid structure and what determines the 
exact size of assembled particles in the absence of a molecular ruler. 
Key to addressing these questions is the development and application of 
fluorescence based markers for FRET and Fluorescence Microscopy assays. 
The gained knowledge will be used for recruiting in vitro assembled 
capsids for in vivo studies in collaboration with Matthias Fischer 
http://www.mpimf-heidelberg.mpg.de/14071687/gruppefischer.

The department has ample synchrotron beamtime at the SLS.

Applicants:
Successful candidates have an excellent track record, high motivation, 
and broad scientific interests. They will join a multidisciplinary 
international team. They should hold a master’s (Ph.D. or equivalent for 
postdoctoral candidates) degree in Biochemistry or related fields. The 
working language of the project will be English. We offer excellent 
laboratory facilities tailored to the needs of the project. Payment is 
based on the TVöD guidelines.


Ph.D. candidates will have the opportunity to participate in one of 
several interdisciplinary Ph.D. programs in collaboration with the 
University of Heidelberg. The position is limited to three years with a 
possibility of extension.
For postdoctoral applicants, the position is limited to two years with a 
possibility of extension.


In case of questions, please contact Jochen Reinstein 
(jochen.reinst...@mpimf-heidelberg.mpg.de)


Please submit your application containing a cover letter (explaining 
background and motivation), your CV, complete transcripts (for Ph.D. 
applicants) or summary of previous research experience with a list of 
publications (for postdoctoral applicants) via e-mail as a single PDF file to


j...@vw.mpimf-heidelberg.mpg.de (reference nr. 05/2019)

The Max Planck Society is committed to increasing the number of 
individuals with disabilities in its workforce and therefore encourages 
their application. The Max Planck Society strives for gender and 
diversity equality. We welcome applications from all backgrounds. A 
daycare center for children is located close to the institute.




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[ccp4bb] modelling of modified RNA

[Sam Tang]

Hello

I have been refining a protein-RNA complex with Refmac. The RNA we used was
tagged with a Cy label. I modelled the RNA in Coot using the RCrane add-on
and manually built the Cy tag. However after Refmac (also via Coot) the
linkage between Cy and the RNA was always broken.

I guess I must have missed something obvious. Any suggestions would be
appreciated..

Sam



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

Re: [ccp4bb] beryllium chloride

[Andreas Förster]

Hi Bob,

for something probably less toxic (but also less sweet tasting), try
beryllium ortho-silicate (Be2SiO4).  Crystals of sufficient purity serve as
excellent test crystals, with low absorption and ridiculous diffraction.
You might need a jeweler to cut them down to size.

All best.


Andreas



On Tue, Apr 2, 2019 at 4:37 AM 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
>
> 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
>
>
> 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 
> 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  *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 <
> 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.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> --
>
> To unsubscribe from the CCP4BB list, click the 

Re: [ccp4bb] beryllium chloride

[Ian Tickle]

Yes both soluble beryllium salts and powdered beryllium metal even applied
to the skin are known to cause sensitization and is a route into the
bloodstream where it is highly carcinogenic (I am not speaking from
experience!).

Yet strangely the one source of beryllium that many people (at least the
more well-off among us) commonly come into contact with, namely the
gemstone emerald Be3Al2(SiO3)6 obviously has no known toxic effects
whatosever!  Apparently even gemstone grinders show no ill effects!  I
guess it's the free Be2+ ion that's so toxic.

Cheers

-- Ian



On Tue, 2 Apr 2019 at 13:07, Aaron Finke  wrote:

> 1. Yes, I meant the tetrahydrate, [Be(H2O)4]2+ 2Cl-
>
> 2. Bob, I studied that page, and couldn’t get past  BeCl2 is known to have
> a “sweetish taste.” I’m very glad chemists no longer characterize chemicals
> by their taste anymore...
>
> --
> Aaron Finke
> Staff Scientist, MacCHESS
> Cornell University
> e-mail: af...@cornell.edu
>
> On Apr 1, 2019, at 22:37, 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
>
> 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
>
>
> 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 
> 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  *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 <
> 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
> 

Re: [ccp4bb] beryllium chloride

[Aaron Finke]

1. Yes, I meant the tetrahydrate, [Be(H2O)4]2+ 2Cl-

2. Bob, I studied that page, and couldn’t get past  BeCl2 is known to have a 
“sweetish taste.” I’m very glad chemists no longer characterize chemicals by 
their taste anymore...

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

On Apr 1, 2019, at 22:37, 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


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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Diana Tomchick 
mailto:diana.tomch...@utsouthwestern.edu>>
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
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[ccp4bb] Open position structural biology at University of Milan

[stefano]

Dear,
here to advertise two postdoc positions in my lab at the Department of 
Biosciences, University of Milan, Italy.
The scientific project will deal on structural biology (Cryo-EM and 
crystallography) and biophysics of protein aggregation and amyloid fibril 
formation.
Specifically the projects will concentrate on two severe human pathologies: AL 
amyloidosis (a severe cardiac disorder) and on ALS (neurodegeneration).
Both projects will require a solid background in any of these disciplines: 
protein biochemistry, structural biology (crystallography or CryoEM), protein 
biophysics.
Specifically in both projects structural and biophysical characterisation of 
amyloidogenic proteins at the native state will be coupled with the inspection 
of the fibrillar assembly formed under pathologic conditions.
Selection will take place in the coming 2-3 months and contracts will start 
during summer (July - September).
Personal emails: stefano.rica...@unimi.it, ciciu...@hotmail.com
Personal website: https://users.unimi.it/stericagno
Structural biology Unit: https://users.unimi.it/biolstru/index.html


Here the most recent literature from my lab:
- Swuec et al Cryo-EM structure of cardiac amyloid fibrils from an 
immunoglobulin light chain AL amyloidosis patient. Nat Comm 2019
- Visconti et al Investigating the Molecular Basis of the Aggregation 
Propensity of the Pathological D76N Mutant of Beta-2 Microglobulin: Role of the 
Denatured State. IJMS 2019
- Le Marchand et al Conformational dynamics in crystals reveal the molecular 
bases for D76N beta-2 microglobulin aggregation propensity. Nat Comm 2018
- Oberti et al Concurrent structural and biophysical traits link with 
immunoglobulin light chains amyloid propensity. SciRep 2017

Best regards
SR

Stefano Ricagno, PhD
Associate Professor
Dept. of Biosciences
University of Milano
Via Celoria, 26. I-20133 Milano (Italy)
Tel. +39 02 5031 4914
https://users.unimi.it/stericagno
www.bioscienze.bio







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Re: [ccp4bb] unidentified crescent-shaped electron density

[Peer Mittl]

I have seen similar density with a fatty acid (C16 or C18). In our case 
the there was also a lysine side chain forming a salt bridge with the 
carboxylate. Furthermore, the pocket was very hydrophobic. What about 
this one?


-Peer

On 02.04.2019 03:12, Zhen Luo wrote:


Hi everyone,

Thank you very much for your help and time. A PEG fragment indeed 
seems to fit into the density. Thanks again!


Best regards,

Zhen

*From: *CCP4 bulletin board  on behalf of Zhen 
Luo 

*Reply-To: *Zhen Luo 
*Date: *Tuesday, 2 April 2019 at 9:01 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.


Protein 1cid:image009.png@01D4E932.5B911B60

Protein 2cid:image012.png@01D4E932.5B911B60

2FOFC maps were contoured at around 1.5 sigma, FOFC map at 3 sigma.

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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--

Peer Mittl, PD Dr.
Biochemisches Institut
Universität Zürich
Room 44M03
Winterthurer Strasse 190
CH-8057 Zürich

Tel.   +41-(0)44-6356559
Mobile +41-(0)76-2776566
Fax.   +41-(0)44-6356805
Mail   mi...@bioc.uzh.ch



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Re: [ccp4bb] unidentified crescent-shaped electron density

[Joel Sussman]

Please see:

Dym, O., Song, W., Felder, C., Roth, E., Shnyrov, V., Ashani, Y., Xu, Y., 
Joosten, R. P., Weiner, L., Sussman, J. L. & Silman, I. The impact of 
crystallization conditions on structure-based drug design: A case study on the 
methylene blue/acetylcholinesterase complex. Protein Sci. 25, 1096-1114 (2016).


Structure-based drug design utilizes apoprotein or complex structures retrieved 
from the PDB. >57% of crystallographic PDB entries were obtained with 
polyethylene glycols (PEGs) as precipitant and/or as cryoprotectant, but <6% of 
these report presence of individual ethyleneglycol oligomers. We report a case 
in which ethyleneglycol oligomers' presence in a crystal structure markedly 
affected the bound ligand's position. Specifically, we compared the positions 
of methylene blue and decamethonium in acetylcholinesterase complexes obtained 
using isomorphous crystals precipitated with PEG200 or ammonium sulfate. The 
ligands' positions within the active-site gorge in complexes obtained using 
PEG200 are influenced by presence of ethyleneglycol oligomers in both cases 
bound to W84 at the gorge's bottom, preventing interaction of the ligand's 
proximal quaternary group with its indole. Consequently, both ligands are ∼3.0Å 
further up the gorge than in complexes obtained using crystals precipitated 
with ammonium sulfate, in which the quaternary groups make direct π-cation 
interactions with the indole. These findings have implications for 
structure-based drug design, since data for ligand-protein complexes with 
polyethylene glycol as precipitant may not reflect the ligand's position in its 
absence, and could result in selecting incorrect drug discovery leads. Docking 
methylene blue into the structure obtained with PEG200, but omitting the 
ethyleneglycols, yields results agreeing poorly with the crystal structure; 
excellent agreement is obtained if they are included. Many proteins display 
features in which precipitants might lodge. It will be important to investigate 
presence of precipitants in published crystal structures, and whether it has 
resulted in misinterpreting electron density maps, adversely affecting drug 
design.

and the cover image showing the PEG molecules, in blue with their surrounding 
electron density, near the bound ligand,  methylene blue, in pink.

best regards
Joel
[cid:E3F7CC9E-AFE7-47B8-8E92-54FDF7658D14@weizmann.ac.il]


Prof. Joel L. Sussman  
joel.suss...@weizmann.ac.il   
www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309  
proteopedia.org
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600
-

On 2Apr, 2019, at 4:12, Zhen Luo 
mailto:z@imb.uq.edu.au>> wrote:

Hi everyone,

Thank you very much for your help and time. A PEG fragment indeed seems to fit 
into the density. Thanks again!


Best regards,
Zhen
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Zhen Luo mailto:z@imb.uq.edu.au>>
Reply-To: Zhen Luo mailto:z@imb.uq.edu.au>>
Date: Tuesday, 2 April 2019 at 9:01 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
mailto: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.




2FOFC maps were contoured at around 1.5 sigma, FOFC map at 3 sigma.


One protein was crystallised in 0.1 M CaCl2 and 20% PEG 3350; the other in 10% 
PEG 2, 20% PEG MME 550, 0.03 M CaCl2/MgCl2, 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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