[ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Rajnandani Kashyap]

Dear All
I am a PhD student who requires lots of coverslips (!!) for setting up
hanging drop crystallization. The company sells it for a huge amount. Also
there is a wide monetary difference between a normal siliconized coverslip
and a 22mm siliconized circle coverslips. We tried to search for an
alternative companies but couldn't get any one who sells coverslips with
the same dimensions (0.19-0.22mm glass thickness and 22 mm glass diameter).
Is there any alternative company (distribution in India) from where we can
buy them for a reasonable price?
Thanks in advance for sparing your valuable time and efforts.

Regards
Rajnandani Kashyap
India



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[ccp4bb] AW: [ccp4bb] 3D stereo and pymol

[Hughes, Jon]

...just open pymol, go to display - stereo mode - cross-eye then click stereo. 
it might need a little practice and it makes one look even sillier than one 
does usually, but it works, costs nothing, needs no updates and i'm told that 
it's even good for your eye muscles!
best,
jon

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jan 
Stransky
Gesendet: Mittwoch, 30. Januar 2019 11:03
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] 3D stereo and pymol


Dear all,

I started looking into the never ending story of stereo in crystallography... 
As with our standardized linux setup we probably are not willing to move to 
X.org-world, if was wondering, if anybody was succesful to make stereo working 
in Windows 10. I did read some NVIDIA forum, and it seems that 3d vision is not 
very supported by NVIDIA, even for gamers... Was anybody able to mke it work 
with Geforce cards, to save few bucks?

Best regards,

Jan
Dne 03.01.2018 v 10:42 Wim Burmeister napsal(a):
I answer a bit late, but I repost a message on 3D graphics from Mai 2017 :
Hello,
we just wanted to share our experience in finding a configuration which allows 
to use 3D graphics under linux using Nvidia GeForce 3D glasses.
We had quite a hard time to find a configurations which works correctly.
We finally used Debian linux with a xfce desktop. Other recent desktops use a 
tiling which is not compatible with 3D graphics.
The hardware consists of

  *   a DELL Precision T5810  desktop computer with an Nvidia Quadro M4000 (8 
Gbyte memory, 4 DP) graphics card
  *   Nvidia GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT) active 
stereo glasses
  *   a stereo connector PNY Quadro 4000 3D for the synchronization of graphics 
card and glasses
  *   an ASUS 24" LED 3D - VG248QE display
  *   a DisplayPort-DisplayPort cable
The Nvidia linux drivers from version 367.57 can handle the current version of 
the Nvidia glasses.
For an obscure reason a direct DP-DP connection between graphics card and 
display is absolutely required in order to obtain fully working stereo. If a 
DP-DVI dual link adapter is used, the stereo does not work on the top and the 
bottom part of the screen. This is true for a native DELL active adaptor or 
generic models. The exact reason remains unresolved, but the solution is to use 
a direct DP-DP connection. This limits the available choice of displays which 
require 120 Hz for 1080*1980 screen resolution and a DP input. We have been 
choosing a “Nvidia 3D ready” model.
There has been a considerate about of exchange about this problem on
https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/
The setup comes with a price tag of about 1600 € free of taxes.
coot, pymol and chimera work straight without problems in hardware stereo mode. 
The experience is absolutely great.
Best
Wim
--

Wim Burmeister
Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs
CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
website





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[ccp4bb] AW: [EXTERNAL] [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Herman . Schreuder]

A long time ago, before siliconized coverslips became commercially available, 
we used to siliconize coverslips ourselves. It is not really that much work and 
unsiliconized cover slips should be very cheap. If you wish, I could try to 
find back the protocol.
Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
Rajnandani Kashyap
Gesendet: Donnerstag, 31. Januar 2019 09:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Is there any alternative to siliconized glass 
coverslips for crystallization?

Dear All
I am a PhD student who requires lots of coverslips (!!) for setting up hanging 
drop crystallization. The company sells it for a huge amount. Also there is a 
wide monetary difference between a normal siliconized coverslip and a 22mm 
siliconized circle coverslips. We tried to search for an alternative companies 
but couldn't get any one who sells coverslips with the same dimensions 
(0.19-0.22mm glass thickness and 22 mm glass diameter). Is there any 
alternative company (distribution in India) from where we can buy them for a 
reasonable price?
Thanks in advance for sparing your valuable time and efforts.

Regards
Rajnandani Kashyap
India



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Re: [ccp4bb] 3D stereo and pymol

[Pedro Matias]

Hi all,

The problem with COOT stereo and Windows 10 is that the COOT binary is
not compatible with the newer OpenGL drivers or somesuch in Windows 10.
So, COOT runs fine in Windows 10 but crashes if you enter hardware
stereo mode. However, PyMOL works fine in stereo in Windows 10.

According to Bernhard Lohkamp, the Windows COOT developer, this problem
has not yet been fixed because he has no access to a Windows 10 PC.

Therefore, stick to Windows 7 if you want to run COOT stereo on a cheap
Quadro card.

Best regards,

Pedro

Às 04:38 de 31/01/2019, Jim Fairman escreveu:
> I had a Windows 7 machine that would run Quad buffered stereo back
> around 2009, haven't had a chance to try with Windows 10.
>
> On Wed, Jan 30, 2019, 02:03 Jan Stransky  > wrote:
>
> Dear all,
>
> I started looking into the never ending story of stereo in
> crystallography... As with our standardized linux setup we
> probably are not willing to move to X.org-world, if was wondering,
> if anybody was succesful to make stereo working in Windows 10. I
> did read some NVIDIA forum, and it seems that 3d vision is not
> very supported by NVIDIA, even for gamers... Was anybody able to
> mke it work with Geforce cards, to save few bucks?
>
> Best regards,
>
> Jan
>
> Dne 03.01.2018 v 10:42 Wim Burmeister napsal(a):
>> I answer a bit late, but I repost a message on 3D graphics from
>> Mai 2017 :
>>
>> Hello,
>>
>> we just wanted to share our experience in finding a configuration
>> which allows to use 3D graphics under linux using Nvidia GeForce
>> 3D glasses.
>>
>> We had quite a hard time to find a configurations which works
>> correctly.
>>
>> We finally used Debian linux with a xfce desktop. Other recent
>> desktops use a tiling which is not compatible with 3D graphics.
>>
>> The hardware consists of
>>
>>   * a DELL Precision T5810  desktop computer with an Nvidia
>> Quadro M4000 (8 Gbyte memory, 4 DP) graphics card
>>   * Nvidia GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES
>> KIT) active stereo glasses
>>   * a stereo connector PNY Quadro 4000 3D for the synchronization
>> of graphics card and glasses
>>   * an ASUS 24" LED 3D - VG248QE display
>>   * a DisplayPort-DisplayPort cable
>>
>> The Nvidia linux drivers from version 367.57 can handle the
>> current version of the Nvidia glasses.
>>
>> For an obscure reason a direct DP-DP connection between graphics
>> card and display is absolutely required in order to obtain fully
>> working stereo. If a DP-DVI dual link adapter is used, the stereo
>> does not work on the top and the bottom part of the screen. This
>> is true for a native DELL active adaptor or generic models. The
>> exact reason remains unresolved, but the solution is to use a
>> direct DP-DP connection. This limits the available choice of
>> displays which require 120 Hz for 1080*1980 screen resolution and
>> a DP input. We have been choosing a “Nvidia 3D ready” model.
>>
>> There has been a considerate about of exchange about this problem on
>>
>> 
>> https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/
>>
>> The setup comes with a price tag of about 1600 € free of taxes.
>>
>> coot, pymol and chimera work straight without problems in
>> hardware stereo mode. The experience is absolutely great.
>>
>> Best
>>
>> Wim
>>
>> -- 
>>
>> Wim Burmeister
>> Professeur
>> Institut de Biologie Structurale (IBS) CIBB
>> 71 avenue des Martyrs
>>
>> CS 20192
>> 38044 Grenoble Cedex 9, FRANCE
>> E-mail: wim.burmeis...@ibs.fr 
>> Tel:    +33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
>> website
>> 
>> 
>>
>> //
>>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
>
> 
>
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-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Tjaard Pijning]

Hi Rajnandani,

 

The cheaper DIY protocol that Herman referred to, is actually still in use by 
us. Use a siliconizing solution (e.g. Serva 35130.02 silicone solution in 
isopropanol). Put about 20-30 microliters on the coverslips, preferrably with a 
repeating pipette and in a fumehood. Then put the coverslips in an oven at 
110*C for about 75 minutes.

 

Best,

Tjaard

 

Dr. Ing. Tjaard Pijning

 

Structural Biology Group

Faculty of Science and Engineering, University of Groningen

9747 AG Groningen, The Netherlands

+31(0)50 363 4385  |  t.pijn...@rug.nl

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
herman.schreu...@sanofi.com
Sent: 31 januari 2019 10:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Is there any alternative to 
siliconized glass coverslips for crystallization?

 

A long time ago, before siliconized coverslips became commercially available, 
we used to siliconize coverslips ourselves. It is not really that much work and 
unsiliconized cover slips should be very cheap. If you wish, I could try to 
find back the protocol.

Best,

Herman

 

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
Rajnandani Kashyap
Gesendet: Donnerstag, 31. Januar 2019 09:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Is there any alternative to siliconized glass 
coverslips for crystallization?

 

Dear All

I am a PhD student who requires lots of coverslips (!!) for setting up hanging 
drop crystallization. The company sells it for a huge amount. Also there is a 
wide monetary difference between a normal siliconized coverslip and a 22mm 
siliconized circle coverslips. We tried to search for an alternative companies 
but couldn't get any one who sells coverslips with the same dimensions 
(0.19-0.22mm glass thickness and 22 mm glass diameter). Is there any 
alternative company (distribution in India) from where we can buy them for a 
reasonable price?

Thanks in advance for sparing your valuable time and efforts.

 

Regards

Rajnandani Kashyap

India

 

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[ccp4bb] old data

[Dean Derbyshire]

maybe a silly question it there a data base or other way to tell what detector 
was used to collect historic data. Image header isn't hugely helpful
ESRF is all I know for the source but I'd like to know what the detector was at 
the time... -  I'm talking 2005-2010

   Dean Derbyshire
   Principal Scientist Protein Crystallography
[X]
   Box 1086
   SE-141 22 Huddinge
   SWEDEN
   Visit: Lunastigen 7
   Direct: +46 8 54683219
   Mobile: +46731251723
   www.medivir.com
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Re: [ccp4bb] old data

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

Hi Dean

Usually there is a serial number buried somewhere in the header - many are text 
headers though some have TIFF format binary headers. Often a timestamp as well 
though this is less common

From there biosync may help e.g.

http://biosync.sbkb.org/beamlineupdatehistory.jsp?region=european&synch_id=esrf&bmln_name=BM14&height=400&width=600

(the list of ESRF MX beamlines is short so should not be too painful)

Knowing the format, filename you can probably pin it down or if you share a 
little more info someone on the BB will know

All the best Graeme



On 31 Jan 2019, at 09:38, Dean Derbyshire 
mailto:dean.derbysh...@medivir.com>> wrote:

maybe a silly question it there a data base or other way to tell what detector 
was used to collect historic data. Image header isn’t hugely helpful
ESRF is all I know for the source but I’d like to know what the detector was at 
the time… -  I’m talking 2005-2010

   Dean Derbyshire
   Principal Scientist Protein Crystallography
[X]
   Box 1086
   SE-141 22 Huddinge
   SWEDEN
   Visit: Lunastigen 7
   Direct: +46 8 54683219
   Mobile: +46731251723
   www.medivir.com
--
This transmission is intended for the person to whom or the entity
to which it is addressed and may contain information that is privileged,
confidential and exempt from disclosure under applicable law.
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Re: [ccp4bb] old data

[Pedro Matias]

It helps to know the filename extension. Opening the image with adxv may
also provide clues as to the detector type.

Às 09:42 de 31/01/2019, graeme.win...@diamond.ac.uk escreveu:
> Hi Dean
>
> Usually there is a serial number buried somewhere in the header - many are 
> text headers though some have TIFF format binary headers. Often a timestamp 
> as well though this is less common
>
> From there biosync may help e.g.
>
> http://biosync.sbkb.org/beamlineupdatehistory.jsp?region=european&synch_id=esrf&bmln_name=BM14&height=400&width=600
>
> (the list of ESRF MX beamlines is short so should not be too painful)
>
> Knowing the format, filename you can probably pin it down or if you share a 
> little more info someone on the BB will know
>
> All the best Graeme
>
>
>
> On 31 Jan 2019, at 09:38, Dean Derbyshire 
> mailto:dean.derbysh...@medivir.com>> wrote:
>
> maybe a silly question it there a data base or other way to tell what 
> detector was used to collect historic data. Image header isn’t hugely helpful
> ESRF is all I know for the source but I’d like to know what the detector was 
> at the time… -  I’m talking 2005-2010
>
>Dean Derbyshire
>Principal Scientist Protein Crystallography
> [X]
>Box 1086
>SE-141 22 Huddinge
>SWEDEN
>Visit: Lunastigen 7
>Direct: +46 8 54683219
>Mobile: +46731251723
>www.medivir.com
> --
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> to which it is addressed and may contain information that is privileged,
> confidential and exempt from disclosure under applicable law.
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> If you have received this transmission in error, please notify us immediately.
> Thank you for your cooperation.
>
> 
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>
-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

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http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

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Re: [ccp4bb] 3D stereo and (pymol) Win 10

[Philippe BENAS]

Dear all,
I had an HP Z620 that was dual boot Kubuntu 14.03 and Win 10. Coot was working 
in stereo mode without any problem for a year or so. But after one of their 
major updates Coot crashed as soon as the built-in IR emitter of my Asus VG278H 
turned on, as described Pedro and Jan.
My personal guess is that the new Win 10 kernels no longer accept some direct 
exchanges from programs to hardware parts, probably for safety issues. So I 
came to the same conclusion as Pedro: stick to Win 7 if you want to run Coot 
under Windows or use a linux distribution or dual boot workstation.
Nevertheless PyMol was just working fine in stereo mode under Win 10. At least 
until last september when I sold my Z620 for a Z820 (Kubuntu 18.04/Win7). May 
be PyMol developers at Schrödinger could give their tips and tricks to Bernard 
Lohkamp to whom I send my warmest aknowledgments for porting Coot under Windows.

Best regards,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
15, rue René Descartes
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/

 

Le jeudi 31 janvier 2019 à 10:18:42 UTC+1, Pedro Matias 
 a écrit :  
 
  
Hi all,
 
 
The problem with COOT stereo and Windows 10 is that the COOT binary is not 
compatible with the newer OpenGL drivers or somesuch in Windows 10. So, COOT 
runs fine in Windows 10 but crashes if you enter hardware stereo mode. However, 
PyMOL works fine in stereo in Windows 10.
 
According to Bernhard Lohkamp, the Windows COOT developer, this problem has not 
yet been fixed because he has no access to a Windows 10 PC.
 
 
Therefore, stick to Windows 7 if you want to run COOT stereo on a cheap Quadro 
card.
 
Best regards,
 
Pedro
 
 Às 04:38 de 31/01/2019, Jim Fairman escreveu:
  
 I had a Windows 7 machine that would run Quad buffered stereo back around 
2009, haven't had a chance to try with Windows 10. 
  On Wed, Jan 30, 2019, 02:03 Jan Stransky  wrote:
  
  
Dear all,
 
I started looking into the never ending story of stereo in crystallography... 
As with our standardized linux setup we probably are not willing to move to 
X.org-world, if was wondering, if anybody was succesful to make stereo working 
in Windows 10. I did read some NVIDIA forum, and it seems  that 3d vision is 
not very supported by NVIDIA, even for gamers... Was anybody able to mke it 
work with Geforce cards, to save few bucks?
 
Best regards,
 
Jan
 
 Dne 03.01.2018 v 10:42 Wim Burmeister napsal(a):
  
 I answer a bit late, but I repost a message on 3D graphics from Mai 2017 : 
 
 
Hello,
   
we just wanted to share our experience in finding a configuration which allows 
to use 3D graphics under linux using Nvidia GeForce 3D glasses.
   
We had quite a hard time to find a configurations which works correctly.
   
We finally used Debian linux with a xfce desktop. Other recent desktops use a 
tiling which is not compatible with 3D graphics.
   
The hardware consists of

   - a DELL Precision T5810  desktop computer with an Nvidia Quadro M4000 (8 
Gbyte memory, 4 DP) graphics card
   - Nvidia GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT) active 
stereo glasses
   - a stereo connector PNY Quadro 4000 3D for the synchronization of graphics 
card and glasses
   - an ASUS 24" LED 3D - VG248QE display
   - a DisplayPort-DisplayPort cable
 

 
The Nvidia linux drivers from version 367.57 can handle the current version of 
the Nvidia glasses.
   
For an obscure reason a direct DP-DP connection between graphics card and 
display is absolutely required in order to obtain fully working stereo. If a 
DP-DVI dual link adapter is used, the stereo does not work on the top and the 
bottom part of the screen. This is true for a native DELL active adaptor or 
generic models. The exact reason remains unresolved, but the solution is to use 
a direct DP-DP connection. This limits the available choice of displays which 
require 120 Hz for 1080*1980 screen resolution and a  DP input. We have been 
choosing a “Nvidia 3D ready” model.
   
There has been a considerate about of exchange about this problem on
   
https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/
   
The setup comes with a price tag of about 1600 € free of taxes.
   
coot, pymol and chimera work straight without problems in hardware stereo mode. 
The experience is absolutely great.
   
Best
   
Wim 
 -- 
 
Wim Burmeister
 Professeur
 Institut de Biologie Structurale (IBS) CIBB
 71 avenue des Martyrs
 CS 20192
 38044 Grenoble Cedex 9, FRANCE
 E-mail: wim.burmeis...@ibs.fr
 Tel:    +33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
 website
 
   
 
 
   
  
  
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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Zhijie Li]

Hi,

I believe that one can put a 50-100uL drop of  fresh SigmaCote (in a tube cap) 
with the glass pieces (surface well exposed), sealed in a dedicated (because 
the container will be coated too) container (air-tight lunch boxes).  After a 
while the SigmaCote vapor should react with the glass and bring polysiloxane 
groups to the glass surface. I have done this with microscope slips. To make a 
few hundred .22 mm cover slips I think the major challenge is to make a frame 
for supporting the separated (~1mm apart to allow free diffusion?) cover slips 
(3D print?). Dry paper may work too. If some of the cover slips tend to stick 
together, a little vacuuming can help.

SigmaCote is a chlorinated polysiloxane. The Cl-Si group allows it to react 
with the hydroxyls on glass surface. Just be aware that the same group reacts 
even more readily with water in air, making the reagent less reactive with 
glass overtime (but I have used a VERY old bottle and it worked).

References:

https://en.wikipedia.org/wiki/Chlorosilane

https://pubs.acs.org/doi/pdfplus/10.1021/j100727a046

https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Product_Information_Sheet/1/sl2pis.pdf

Zhijie


On 31/01/2019 4:16 a.m., 
herman.schreu...@sanofi.com wrote:
A long time ago, before siliconized coverslips became commercially available, 
we used to siliconize coverslips ourselves. It is not really that much work and 
unsiliconized cover slips should be very cheap. If you wish, I could try to 
find back the protocol.
Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
Rajnandani Kashyap
Gesendet: Donnerstag, 31. Januar 2019 09:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Is there any alternative to siliconized glass 
coverslips for crystallization?

Dear All
I am a PhD student who requires lots of coverslips (!!) for setting up hanging 
drop crystallization. The company sells it for a huge amount. Also there is a 
wide monetary difference between a normal siliconized coverslip and a 22mm 
siliconized circle coverslips. We tried to search for an alternative companies 
but couldn't get any one who sells coverslips with the same dimensions 
(0.19-0.22mm glass thickness and 22 mm glass diameter). Is there any 
alternative company (distribution in India) from where we can buy them for a 
reasonable price?
Thanks in advance for sparing your valuable time and efforts.

Regards
Rajnandani Kashyap
India



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Re: [ccp4bb] old data

[CCP4BB]

Hi Dean

I'd ask someone who was involved in writing the data processing programs at 
that time to have a quick shufti at the images! There are a few who read the 
BB...

Harry
--
Dr Harry Powell

> On 31 Jan 2019, at 09:38, Dean Derbyshire  wrote:
> 
> maybe a silly question it there a data base or other way to tell what 
> detector was used to collect historic data. Image header isn’t hugely helpful
> ESRF is all I know for the source but I’d like to know what the detector was 
> at the time… -  I’m talking 2005-2010
>  
>Dean Derbyshire
>Principal Scientist Protein Crystallography
> 
>Box 1086
>SE-141 22 Huddinge
>SWEDEN
>Visit: Lunastigen 7
>Direct: +46 8 54683219
>Mobile: +46731251723
>www.medivir.com
> --
> This transmission is intended for the person to whom or the entity
> to which it is addressed and may contain information that is privileged,
> confidential and exempt from disclosure under applicable law.
> If you are not the intended recipient, please be notified that any 
> dissemination,
> distribution or copying is strictly prohibited.
> If you have received this transmission in error, please notify us immediately.
> Thank you for your cooperation.
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1



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[ccp4bb] FW: [ccp4bb] old data - headers

[Dean Derbyshire]

thanks all. I recon I have the ESRF data sorted.. but Daresbury.. am I right in 
assuming MARCCD or are we going back as far as image plate?
here is the image header
Harry what do you think

HEADER_BYTES=  512;
DIM=2;
BYTE_ORDER=little_endian;
TYPE=unsigned_short;
PIXEL_SIZE=0.08160;
BIN=none;
ADC=slow;
DETECTOR_SN=421;
DATE=Wed Apr 13 17:59:22 2005;
TIME=20.00;
DISTANCE=125.000;
OSC_RANGE=1.000;
PHI=7.000;
OSC_START=7.000;
AXIS=phi;
WAVELENGTH=1.48800;
BEAM_CENTER_X=94.700;
BEAM_CENTER_Y=96.400;
UNIF_PED=1500;
SIZE1=2304;
SIZE2=2304;
CCD_IMAGE_SATURATION=65535;
}


-Original Message-
From: Dean Derbyshire 
Sent: den 31 januari 2019 10:50
To: 'graeme.win...@diamond.ac.uk' ; 'Luca Jovine' 

Subject: RE: [ccp4bb] old data

ok may have lied.. not just 1 dataset i note.

Daresbury 14-1 on 19th April 2005. (I'm assuming MAR image plate but!) 

ESRF ID23-1 on 4th September 2007.
ESRF ID23-1 on 8th November 2007.
ESRF ID23-1 on 25th June 2008.
ESRF ID23-1 on 11th February2010.

I will post the headers in a sec

:)

-Original Message-
From: graeme.win...@diamond.ac.uk [mailto:graeme.win...@diamond.ac.uk]
Sent: den 31 januari 2019 10:42
To: Dean Derbyshire 
Cc: ccp4bb@jiscmail.ac.uk
Subject: Re: [ccp4bb] old data

Hi Dean

Usually there is a serial number buried somewhere in the header - many are text 
headers though some have TIFF format binary headers. Often a timestamp as well 
though this is less common

From there biosync may help e.g.

http://biosync.sbkb.org/beamlineupdatehistory.jsp?region=european&synch_id=esrf&bmln_name=BM14&height=400&width=600

(the list of ESRF MX beamlines is short so should not be too painful)

Knowing the format, filename you can probably pin it down or if you share a 
little more info someone on the BB will know

All the best Graeme



On 31 Jan 2019, at 09:38, Dean Derbyshire 
mailto:dean.derbysh...@medivir.com>> wrote:

maybe a silly question it there a data base or other way to tell what detector 
was used to collect historic data. Image header isn’t hugely helpful ESRF is 
all I know for the source but I’d like to know what the detector was at the 
time… -  I’m talking 2005-2010

   Dean Derbyshire
   Principal Scientist Protein Crystallography [X]
   Box 1086
   SE-141 22 Huddinge
   SWEDEN
   Visit: Lunastigen 7
   Direct: +46 8 54683219
   Mobile: +46731251723
   www.medivir.com
--
This transmission is intended for the person to whom or the entity to which it 
is addressed and may contain information that is privileged, confidential and 
exempt from disclosure under applicable law.
If you are not the intended recipient, please be notified that any 
dissemination, distribution or copying is strictly prohibited.
If you have received this transmission in error, please notify us immediately.
Thank you for your cooperation.



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Re: [ccp4bb] FW: [ccp4bb] old data - headers

[Pedro Matias]

Hi Dean,

I reckon that it is an ADSC Quantum 4 or 4R CCD detector. If you open
the images with mosflm or adxv you should see the characteristic 2x2
tile pattern.

Note how the header format is similar to the one you posted from the ESRF.

Pedro

Às 10:21 de 31/01/2019, Dean Derbyshire escreveu:
> thanks all. I recon I have the ESRF data sorted.. but Daresbury.. am I right 
> in assuming MARCCD or are we going back as far as image plate?
> here is the image header
> Harry what do you think
>
> HEADER_BYTES=  512;
> DIM=2;
> BYTE_ORDER=little_endian;
> TYPE=unsigned_short;
> PIXEL_SIZE=0.08160;
> BIN=none;
> ADC=slow;
> DETECTOR_SN=421;
> DATE=Wed Apr 13 17:59:22 2005;
> TIME=20.00;
> DISTANCE=125.000;
> OSC_RANGE=1.000;
> PHI=7.000;
> OSC_START=7.000;
> AXIS=phi;
> WAVELENGTH=1.48800;
> BEAM_CENTER_X=94.700;
> BEAM_CENTER_Y=96.400;
> UNIF_PED=1500;
> SIZE1=2304;
> SIZE2=2304;
> CCD_IMAGE_SATURATION=65535;
> }
>
>
> -Original Message-
> From: Dean Derbyshire 
> Sent: den 31 januari 2019 10:50
> To: 'graeme.win...@diamond.ac.uk' ; 'Luca 
> Jovine' 
> Subject: RE: [ccp4bb] old data
>
> ok may have lied.. not just 1 dataset i note.
>
> Daresbury 14-1 on 19th April 2005. (I'm assuming MAR image plate but!) 
>
> ESRF ID23-1 on 4th September 2007.
> ESRF ID23-1 on 8th November 2007.
> ESRF ID23-1 on 25th June 2008.
> ESRF ID23-1 on 11th February2010.
>
> I will post the headers in a sec
>
> :)
>
> -Original Message-
> From: graeme.win...@diamond.ac.uk [mailto:graeme.win...@diamond.ac.uk]
> Sent: den 31 januari 2019 10:42
> To: Dean Derbyshire 
> Cc: ccp4bb@jiscmail.ac.uk
> Subject: Re: [ccp4bb] old data
>
> Hi Dean
>
> Usually there is a serial number buried somewhere in the header - many are 
> text headers though some have TIFF format binary headers. Often a timestamp 
> as well though this is less common
>
> From there biosync may help e.g.
>
> http://biosync.sbkb.org/beamlineupdatehistory.jsp?region=european&synch_id=esrf&bmln_name=BM14&height=400&width=600
>
> (the list of ESRF MX beamlines is short so should not be too painful)
>
> Knowing the format, filename you can probably pin it down or if you share a 
> little more info someone on the BB will know
>
> All the best Graeme
>
>
>
> On 31 Jan 2019, at 09:38, Dean Derbyshire 
> mailto:dean.derbysh...@medivir.com>> wrote:
>
> maybe a silly question it there a data base or other way to tell what 
> detector was used to collect historic data. Image header isn’t hugely helpful 
> ESRF is all I know for the source but I’d like to know what the detector was 
> at the time… -  I’m talking 2005-2010
>
>Dean Derbyshire
>Principal Scientist Protein Crystallography [X]
>Box 1086
>SE-141 22 Huddinge
>SWEDEN
>Visit: Lunastigen 7
>Direct: +46 8 54683219
>Mobile: +46731251723
>www.medivir.com
> --
> This transmission is intended for the person to whom or the entity to which 
> it is addressed and may contain information that is privileged, confidential 
> and exempt from disclosure under applicable law.
> If you are not the intended recipient, please be notified that any 
> dissemination, distribution or copying is strictly prohibited.
> If you have received this transmission in error, please notify us immediately.
> Thank you for your cooperation.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
>
> --
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you are not the intended addressee or an authorised recipient of the 
> addressee please notify us of receipt by returning the e-mail and do not use, 
> copy, retain, distribute or disclose the information in or attached to the 
> e-mail.
> Any opinions expressed within this e-mail are those of the individual and not 
> necessarily of Diamond Light Source Ltd. 
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any 
> attachments are free from viruses and we cannot accept liability for 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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> Wales with its registered office at Diamond House, Harwell Science and 
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
> 
>
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Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 4

Re: [ccp4bb] FW: [ccp4bb] old data - headers

[Dean Derbyshire]

huge thanks everyone.. what a response.  All good now
:)


-Original Message-
From: Pedro Matias [mailto:mat...@itqb.unl.pt] 
Sent: den 31 januari 2019 11:46
To: Dean Derbyshire ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] FW: [ccp4bb] old data - headers

Hi Dean,

I reckon that it is an ADSC Quantum 4 or 4R CCD detector. If you open the 
images with mosflm or adxv you should see the characteristic 2x2 tile pattern.

Note how the header format is similar to the one you posted from the ESRF.

Pedro

Às 10:21 de 31/01/2019, Dean Derbyshire escreveu:
> thanks all. I recon I have the ESRF data sorted.. but Daresbury.. am I right 
> in assuming MARCCD or are we going back as far as image plate?
> here is the image header
> Harry what do you think
>
> HEADER_BYTES=  512;
> DIM=2;
> BYTE_ORDER=little_endian;
> TYPE=unsigned_short;
> PIXEL_SIZE=0.08160;
> BIN=none;
> ADC=slow;
> DETECTOR_SN=421;
> DATE=Wed Apr 13 17:59:22 2005;
> TIME=20.00;
> DISTANCE=125.000;
> OSC_RANGE=1.000;
> PHI=7.000;
> OSC_START=7.000;
> AXIS=phi;
> WAVELENGTH=1.48800;
> BEAM_CENTER_X=94.700;
> BEAM_CENTER_Y=96.400;
> UNIF_PED=1500;
> SIZE1=2304;
> SIZE2=2304;
> CCD_IMAGE_SATURATION=65535;
> }
>
>
> -Original Message-
> From: Dean Derbyshire
> Sent: den 31 januari 2019 10:50
> To: 'graeme.win...@diamond.ac.uk' ; 'Luca 
> Jovine' 
> Subject: RE: [ccp4bb] old data
>
> ok may have lied.. not just 1 dataset i note.
>
> Daresbury 14-1 on 19th April 2005. (I'm assuming MAR image plate but!)
>
> ESRF ID23-1 on 4th September 2007.
> ESRF ID23-1 on 8th November 2007.
> ESRF ID23-1 on 25th June 2008.
> ESRF ID23-1 on 11th February2010.
>
> I will post the headers in a sec
>
> :)
>
> -Original Message-
> From: graeme.win...@diamond.ac.uk [mailto:graeme.win...@diamond.ac.uk]
> Sent: den 31 januari 2019 10:42
> To: Dean Derbyshire 
> Cc: ccp4bb@jiscmail.ac.uk
> Subject: Re: [ccp4bb] old data
>
> Hi Dean
>
> Usually there is a serial number buried somewhere in the header - many 
> are text headers though some have TIFF format binary headers. Often a 
> timestamp as well though this is less common
>
> From there biosync may help e.g.
>
> http://biosync.sbkb.org/beamlineupdatehistory.jsp?region=european&sync
> h_id=esrf&bmln_name=BM14&height=400&width=600
>
> (the list of ESRF MX beamlines is short so should not be too painful)
>
> Knowing the format, filename you can probably pin it down or if you 
> share a little more info someone on the BB will know
>
> All the best Graeme
>
>
>
> On 31 Jan 2019, at 09:38, Dean Derbyshire 
> mailto:dean.derbysh...@medivir.com>> wrote:
>
> maybe a silly question it there a data base or other way to tell what 
> detector was used to collect historic data. Image header isn’t hugely 
> helpful ESRF is all I know for the source but I’d like to know what 
> the detector was at the time… -  I’m talking 2005-2010
>
>Dean Derbyshire
>Principal Scientist Protein Crystallography [X]
>Box 1086
>SE-141 22 Huddinge
>SWEDEN
>Visit: Lunastigen 7
>Direct: +46 8 54683219
>Mobile: +46731251723
>www.medivir.com
> --
>  This transmission is intended for the person to whom or the 
> entity to which it is addressed and may contain information that is 
> privileged, confidential and exempt from disclosure under applicable law.
> If you are not the intended recipient, please be notified that any 
> dissemination, distribution or copying is strictly prohibited.
> If you have received this transmission in error, please notify us immediately.
> Thank you for your cooperation.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
>
> --
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you are not the intended addressee or an authorised recipient of the 
> addressee please notify us of receipt by returning the e-mail and do not use, 
> copy, retain, distribute or disclose the information in or attached to the 
> e-mail.
> Any opinions expressed within this e-mail are those of the individual and not 
> necessarily of Diamond Light Source Ltd. 
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any 
> attachments are free from viruses and we cannot accept liability for any 
> damage which you may sustain as a result of software viruses which may be 
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in 
> England and Wales with its registered office at Diamond House, Harwell 
> Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United 
> Kingdom
>
> ##
> ##
>
> To unsubscribe from the CCP4BB list, click the following link:
> http

Re: [ccp4bb] FW: [ccp4bb] old data - headers

[Harry Powell]

Hi

This looks like it was on beamline 7.2 (which had a fixed wavelength of 1.488Å, 
according to an article written by Liz Duke - see 
https://www.ccp4.ac.uk/newsletters/newsletter37/11_beamline14.html); I can't 
remember if detector 421 was a Q4 or a Q4R, but (again, according to the same 
article) Daresbury certainly had at least one of each at some time!

BL 7.2 was actually the only beamline at Daresbury that I collected my own data 
on (before I worked on Mosflm) - using an Arndt-Wonacott camera and film...

Harry

On 31 Jan 2019, at 10:48, Dean Derbyshire wrote:

> huge thanks everyone.. what a response.  All good now
> :)
> 
> 
> -Original Message-
> From: Pedro Matias [mailto:mat...@itqb.unl.pt] 
> Sent: den 31 januari 2019 11:46
> To: Dean Derbyshire ; CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] FW: [ccp4bb] old data - headers
> 
> Hi Dean,
> 
> I reckon that it is an ADSC Quantum 4 or 4R CCD detector. If you open the 
> images with mosflm or adxv you should see the characteristic 2x2 tile pattern.
> 
> Note how the header format is similar to the one you posted from the ESRF.
> 
> Pedro
> 
> Às 10:21 de 31/01/2019, Dean Derbyshire escreveu:
>> thanks all. I recon I have the ESRF data sorted.. but Daresbury.. am I right 
>> in assuming MARCCD or are we going back as far as image plate?
>> here is the image header
>> Harry what do you think
>> 
>> HEADER_BYTES=  512;
>> DIM=2;
>> BYTE_ORDER=little_endian;
>> TYPE=unsigned_short;
>> PIXEL_SIZE=0.08160;
>> BIN=none;
>> ADC=slow;
>> DETECTOR_SN=421;
>> DATE=Wed Apr 13 17:59:22 2005;
>> TIME=20.00;
>> DISTANCE=125.000;
>> OSC_RANGE=1.000;
>> PHI=7.000;
>> OSC_START=7.000;
>> AXIS=phi;
>> WAVELENGTH=1.48800;
>> BEAM_CENTER_X=94.700;
>> BEAM_CENTER_Y=96.400;
>> UNIF_PED=1500;
>> SIZE1=2304;
>> SIZE2=2304;
>> CCD_IMAGE_SATURATION=65535;
>> }
>> 
>> 
>> -Original Message-
>> From: Dean Derbyshire
>> Sent: den 31 januari 2019 10:50
>> To: 'graeme.win...@diamond.ac.uk' ; 'Luca 
>> Jovine' 
>> Subject: RE: [ccp4bb] old data
>> 
>> ok may have lied.. not just 1 dataset i note.
>> 
>> Daresbury 14-1 on 19th April 2005. (I'm assuming MAR image plate but!)
>> 
>> ESRF ID23-1 on 4th September 2007.
>> ESRF ID23-1 on 8th November 2007.
>> ESRF ID23-1 on 25th June 2008.
>> ESRF ID23-1 on 11th February2010.
>> 
>> I will post the headers in a sec
>> 
>> :)
>> 
>> -Original Message-
>> From: graeme.win...@diamond.ac.uk [mailto:graeme.win...@diamond.ac.uk]
>> Sent: den 31 januari 2019 10:42
>> To: Dean Derbyshire 
>> Cc: ccp4bb@jiscmail.ac.uk
>> Subject: Re: [ccp4bb] old data
>> 
>> Hi Dean
>> 
>> Usually there is a serial number buried somewhere in the header - many 
>> are text headers though some have TIFF format binary headers. Often a 
>> timestamp as well though this is less common
>> 
>> From there biosync may help e.g.
>> 
>> http://biosync.sbkb.org/beamlineupdatehistory.jsp?region=european&sync
>> h_id=esrf&bmln_name=BM14&height=400&width=600
>> 
>> (the list of ESRF MX beamlines is short so should not be too painful)
>> 
>> Knowing the format, filename you can probably pin it down or if you 
>> share a little more info someone on the BB will know
>> 
>> All the best Graeme
>> 
>> 
>> 
>> On 31 Jan 2019, at 09:38, Dean Derbyshire 
>> mailto:dean.derbysh...@medivir.com>> wrote:
>> 
>> maybe a silly question it there a data base or other way to tell what 
>> detector was used to collect historic data. Image header isn’t hugely 
>> helpful ESRF is all I know for the source but I’d like to know what 
>> the detector was at the time… -  I’m talking 2005-2010
>> 
>>   Dean Derbyshire
>>   Principal Scientist Protein Crystallography [X]
>>   Box 1086
>>   SE-141 22 Huddinge
>>   SWEDEN
>>   Visit: Lunastigen 7
>>   Direct: +46 8 54683219
>>   Mobile: +46731251723
>>   www.medivir.com
>> --
>>  This transmission is intended for the person to whom or the 
>> entity to which it is addressed and may contain information that is 
>> privileged, confidential and exempt from disclosure under applicable law.
>> If you are not the intended recipient, please be notified that any 
>> dissemination, distribution or copying is strictly prohibited.
>> If you have received this transmission in error, please notify us 
>> immediately.
>> Thank you for your cooperation.
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>> 
>> 
>> --
>> This e-mail and any attachments may contain confidential, copyright and or 
>> privileged material, and are for the use of the intended addressee only. If 
>> you are not the intended addressee or an authorised recipient of the 
>> addressee please notify us of receipt by returning the e-mail and do not 
>> use, copy, retain, distribute or disclose the information in or attached to 
>> the e-mail.
>> Any opin

[ccp4bb] Nanodrop-1000 lamp

[Bärbel Blaum]

Dear all,

 

does anyone happen to know exactly which Xe flash lamp is (or better: was) 
being used in the discontinued Nanodrop-1000? 

 

Thanks for your help! 

 

Bärbel

 

-- 

Bärbel Blaum, PhD

Inthera Bioscience AG

Einsiedlerstrasse 34

CH-8820 Waedenswil

Switzerland

E-Mail: baerbel.bl...@intherabio.com

Phone: +41 76 568 6384

--

 

 




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[ccp4bb] Research Associate Position in Chemical Glycobiology (Francis Crick Institute)

[Omur Tastan]

>>

Deadline 1 Feb, 2019

https://www.imperial.ac.uk/jobs/description/NAT00344/research-associate-position-chemical-glycobiology-francis-crick-institute/


Job Summary:

Up to two Postdoctoral Research Associate positions are available in the
Chemical Glycobiology Laboratory hosted by the Department of Chemistry at
Imperial College London and located at the Francis Crick Institute, one of
the world’s leading biomedical research institutes (
https://www.crick.ac.uk/research/labs/ben-schumann).

The Chemical Biology Lab led by Dr Ben Schumann is performing research at
the interface between chemistry and state-of-the-art biology. Our
integration in a network of world-class biomedical research at the Francis
Crick Institute is a unique opportunity to approach problems at the
forefront of biology. Our association with Imperial College London enables
frequent exchange with pre-eminent chemists and chemical biologists. The
posts are fully core-funded, including access to outstanding Science
Technology Platforms at the Francis Crick Institute with state-of-the-art
equipment in all areas of chemical and biological research.

We are aspiring to close the gap between glycan chemistry and modern
biology by developing novel “precision tools” to understand the role of
glycans in biological processes in unprecedented detail. To this end, we
combine techniques of chemical or chemo-enzymatic synthesis, bioorthogonal
ligation, protein engineering, molecular and cell biology including
CRISPR-based genome engineering, imaging and structural biology. Our focus
lies in understanding the intricacies of glycosylation in the secretory
pathway. As an example, we engineer enzymes involved in the formation of
glycoconjugates and use them in combination with chemically modified
substrates to unravel how specific glycan subsets modulate biological
processes. These studies are essential to develop new disease biomarkers
and glycan-based therapies.

Highly motivated candidates with a strong background in chemical biology,
biochemistry, organic chemistry or glycobiology are encouraged to apply. A
strong interest in interdisciplinary, glycan-based research is expected and
should be reflected in the application.
*Duties and responsibilities*

   - To lead, conduct and record research at the forefront of modern
   chemical glycobiology
   - To contribute to other projects, internal and external, on a
   collaborative basis
   - To draft and submit publications to refereed journals
   - To actively engage in promoting the lab’s research
   - To actively learn new skills and integrate them in the lab’s research
   - To champion a motivating, collaborative work environment
   - To co-supervise PhD, Masters and undergraduate students

*Essential requirements*

   - A PhD or equivalent level of professional qualifications in a relevant
   field (e.g. chemical biology, chemistry, biochemistry)
   - A strong interest in chemical glycobiology
   - Practical experience in leading a multi-disciplinary research project
   - A proven publication track record in their respective field (where
   publications are under preparation, please provide a concise research
   summary of not more than two pages). Please indicate own contributions.
   - Ability to work independently and within a team
   - Eagerness to learn new techniques

*Further information*

Candidates who have not yet been officially awarded their PhD will be
appointed as Research Assistant within the salary range £33,380 - £35,061
per annum.

The Department of Chemistry proudly holds an Athena SWAN Gold Award and
strives to provide a working environment where all our staff feel fully
supported to flourish and excel. The Department of Chemistry is committed
to promoting the wide range of Family Friendly policies and associated
initiatives offered by the College.

For informal enquiries about this position please contact Dr Ben Schumann (
ben.schum...@crick.ac.uk).

For any technical queries during the application process please contact:
recruitm...@imperial.ac.uk.

For other queries, please contact Nayrin Noori: n.no...@imperial.ac.uk.


Committed to equality and valuing diversity. Imperial College is also an
Athena SWAN Silver Award winner, a Stonewall Diversity Champion, a
Disability Confident Employer and is working in partnership with GIRES to
promote respect for trans people.

The College is a proud signatory to the San-Francisco Declaration on
Research Assessment (DORA), which means that in hiring and promotion
decisions, we evaluate applicants on the quality of their work, not the
journal impact factor where it is published. For more information, see
https://www.imperial.ac.uk/research-and-innovation/about-imperial-research/research-evaluation/

The College believes that the use of animals in research is vital to
improve human and animal health and welfare. Animals may only be used in
research programmes where their use is shown to be necessary for developing
new treatments and makin

[ccp4bb] ESRF workshop on sample preparation for Cryo-EM, May 21-23, 2019

[David FLOT]

Dear All,

We are pleased to announce a 2.5 day practical workshop on sample 
preparation for cryo-EM single particle data collection jointly 
organised by the ESRF, IBS and the EMBL Grenoble. This is the second of 
a series of practical hands-on workshops started in 2018. This workshop 
is aimed at PhDs, PostDocs and young scientists new to the field of 
single particle cryo-EM and will be held at the European Synchrotron and 
the Institut de Biologie Structurale (IBS) in Grenoble, France from *May 
21^st to 23^rd , 2019*. During the course, participants will learn 
theoretical and practical aspects of sample preparation for single 
particle cryo-EM including prior quality control by negative staining.


There is *no registration fee* and meals and accommodation during the 
workshop will be provided free of charge. However, participants should 
arrange and pay for their own travel to/from Grenoble. A maximum of 12 
participants will be selected and we will accept a limited number of 
participants’ samples to be tested during the workshop. In the case that 
you plan to bring your own sample, please clearly mention this in your 
cover letter, also indicating the importance of the project.


Application for the workshop will be open from today, January 31^st , 
2019 using the link http://www.esrf.fr/events/conferences/ and the 
deadline for application is *March 10^th , 2019*. Successful candidates 
will be informed during the first week after the deadline.


Best regards,

Isai

(on behalf of the organizers)

--
Eaazhisai KANDIAH
ESRF Cryo-EM beamline Scientist

Address: ESRF
71 Avenue des Martyrs, 38000 Grenoble

Telephone: +33 476 882691
Email:eaazhisai.kand...@esrf.fr

--

 
Dr David FLOT

Beam-Line Operation Manager Tel : (+33) 4 76 88 17 63
Structural Biology GroupFax : (+33) 4 76 88 26 24
ESRF
e-mail : david.f...@esrf.fr http://www.esrf.eu
Room: 30.1.13

Physical addressPostal address
ESRF-The European Synchrotron   ESRF-The European Synchrotron
71, Avenue des Martyrs  CS40220
Grenoble, France38043 Grenoble Cedex 9
France




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[ccp4bb] Postdoctoral position University of Oxford (UK)

[Denis Ptchelkine]

Title:  Postdoctoral position University of Oxford (UK)



Weatherall Institute of Molecular Medicine (University of Oxford, UK) offers an 
outstanding opportunity for a highly motivated and talented Postdoctoral 
Scientist specialized in structural biology to join a research project on a 
multiprotein complex involved in the transcriptional regulation of blood stem 
cell development in normal and malignant conditions. It will employ molecular, 
biochemical, biophysical and cryo-EM studies. This high impact study will 
provide essential details for a mechanistic understanding of the 
transcriptional activities of this blood stem cell-specific complex.


Prior experience in cryo-EM or/and X-ray crystallography is desirable. 
Successful candidate will be familiar with transcription regulation field, have 
broad experience in structural biology, strong knowledge of biophysical 
methods, protein co-expression and purification of protein complexes.


This exciting project, at the forefront of its field, will be co-surpervised by 
Prof. Catherine Porcher and Dr. Denis Ptchelkine


Please apply via this link:  


https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=139214



__


Dr. Denis Ptchelkine
Senior Postdoctoral Scientist

Prof. Peter McHugh lab
Weatherall Institute of Molecular Medicine,
Dept. of Oncology
University of Oxford
John Radcliffe Hospital/Headley Way,
Oxford OX3 9DS





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[ccp4bb] Open positions in diffractive imaging method development at MPSD Hamburg

[Kartik Ayyer]

Hi All,

There are 3 open positions in my group in the Max Planck Institute for the
Structure and Dynamics of Matter (MPSD) in Hamburg. All positions involve
developing and implementing algorithms for new diffractive imaging
techniques. You can find more information about the institute at
https://www.mpsd.mpg.de/en and about the research of my group at
https://www.kartikayyer.com

The available positions are:
 - Post-doctoral researcher for X-ray single particle imaging
https://jobs.b-ite.com/jobposting/7a006d6630b34711384e34fc427eb17bf0847353

 - Post-doctoral researcher working on interpreting protein crystal diffuse
scattering
https://www.uni-hamburg.de/uhh/stellenangebote/wissenschaftliches-personal/exzellenzcluster-cui/01-03-19-76-en.pdf

 - PhD student for proof-of-principle experiments using incoherent
diffractive imaging:
https://www.uni-hamburg.de/uhh/stellenangebote/wissenschaftliches-personal/exzellenzcluster-cui/01-03-19-75-en.pdf

Even though there are deadlines attached to the job advertisements, the
positions will remain open until filled.

Thank you for your interest.

Regards
Kartik Ayyer



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[ccp4bb] ECM32, Vienna

[Kristina Djinovic Carugo]

Deal all,*
*

I would like to bring your attention to

*32^nd European Crystallographic Meeting@ University of Vienna, 18^th to 
23^th August 2019*


The 32^nd European Crystallographic Meeting, ECM32, will take place in 
Vienna, Austria, from 18^th to 23^rd of August 2019. The organizers of 
the conference plan an attractive programme covering the latest advances 
in crystallography and related scientific fields. We invite scientist to 
submit contributions of their latest scientific research and companies 
to introduce their newest developments. Join us in August for the 
conference and bring your kids! We will offer a dedicated accompanying 
people programme and a specific programme for children care and 
activities. Details how to register and submit your abstract starting 
31^st January 2019 can be found on: https://ecm2019.org.


For a limited number of young scientists (age < 35 years) and travel 
costs support can be granted. The conditions and the process to apply 
for financial support will be announced on the conference webpage 
together with the start of the registration. The grant of the financial 
support will be decided by a grant panel.


Looking forward to having you inVienna,

Kristina Djinovic Carugo
(Chair of Programme Committee)

--
Department of Structural and Computational Biology
Max F. Perutz Laboratories
University of Vienna
Campus Vienna Biocenter 5
A-1030 Vienna
Austria


e-mail: kristina.djino...@univie.ac.at
Phone: +43-1-4277-52203
Phone: +43-1-4277-52201 (secretary)
Mobile A: +43-664-602 77-522 03
Fax: +43-1-4277-9522




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Re: [ccp4bb] FW: [ccp4bb] old data - headers

[Jrh Gmail]

Hello Harry
I used SRS 7.2 and 9.6 at a wide variety of monochromatic wavelengths for 
resonant scattering (AD) studies. But I can imagine high intensity application 
PX measurements were made at those specific wavelengths which you mention.
Greetings from Novosibirsk,
John 

Emeritus Professor of Chemistry John R Helliwell DSc_Physics 




> On 31 Jan 2019, at 18:02, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi
> 
> This looks like it was on beamline 7.2 (which had a fixed wavelength of 
> 1.488Å, according to an article written by Liz Duke - see 
> https://www.ccp4.ac.uk/newsletters/newsletter37/11_beamline14.html); I can't 
> remember if detector 421 was a Q4 or a Q4R, but (again, according to the same 
> article) Daresbury certainly had at least one of each at some time!
> 
> BL 7.2 was actually the only beamline at Daresbury that I collected my own 
> data on (before I worked on Mosflm) - using an Arndt-Wonacott camera and 
> film...
> 
> Harry
> 
>> On 31 Jan 2019, at 10:48, Dean Derbyshire wrote:
>> 
>> huge thanks everyone.. what a response.  All good now
>> :)
>> 
>> 
>> -Original Message-
>> From: Pedro Matias [mailto:mat...@itqb.unl.pt] 
>> Sent: den 31 januari 2019 11:46
>> To: Dean Derbyshire ; CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] FW: [ccp4bb] old data - headers
>> 
>> Hi Dean,
>> 
>> I reckon that it is an ADSC Quantum 4 or 4R CCD detector. If you open the 
>> images with mosflm or adxv you should see the characteristic 2x2 tile 
>> pattern.
>> 
>> Note how the header format is similar to the one you posted from the ESRF.
>> 
>> Pedro
>> 
>> Às 10:21 de 31/01/2019, Dean Derbyshire escreveu:
>>> thanks all. I recon I have the ESRF data sorted.. but Daresbury.. am I 
>>> right in assuming MARCCD or are we going back as far as image plate?
>>> here is the image header
>>> Harry what do you think
>>> 
>>> HEADER_BYTES=  512;
>>> DIM=2;
>>> BYTE_ORDER=little_endian;
>>> TYPE=unsigned_short;
>>> PIXEL_SIZE=0.08160;
>>> BIN=none;
>>> ADC=slow;
>>> DETECTOR_SN=421;
>>> DATE=Wed Apr 13 17:59:22 2005;
>>> TIME=20.00;
>>> DISTANCE=125.000;
>>> OSC_RANGE=1.000;
>>> PHI=7.000;
>>> OSC_START=7.000;
>>> AXIS=phi;
>>> WAVELENGTH=1.48800;
>>> BEAM_CENTER_X=94.700;
>>> BEAM_CENTER_Y=96.400;
>>> UNIF_PED=1500;
>>> SIZE1=2304;
>>> SIZE2=2304;
>>> CCD_IMAGE_SATURATION=65535;
>>> }
>>> 
>>> 
>>> -Original Message-
>>> From: Dean Derbyshire
>>> Sent: den 31 januari 2019 10:50
>>> To: 'graeme.win...@diamond.ac.uk' ; 'Luca 
>>> Jovine' 
>>> Subject: RE: [ccp4bb] old data
>>> 
>>> ok may have lied.. not just 1 dataset i note.
>>> 
>>> Daresbury 14-1 on 19th April 2005. (I'm assuming MAR image plate but!)
>>> 
>>> ESRF ID23-1 on 4th September 2007.
>>> ESRF ID23-1 on 8th November 2007.
>>> ESRF ID23-1 on 25th June 2008.
>>> ESRF ID23-1 on 11th February2010.
>>> 
>>> I will post the headers in a sec
>>> 
>>> :)
>>> 
>>> -Original Message-
>>> From: graeme.win...@diamond.ac.uk [mailto:graeme.win...@diamond.ac.uk]
>>> Sent: den 31 januari 2019 10:42
>>> To: Dean Derbyshire 
>>> Cc: ccp4bb@jiscmail.ac.uk
>>> Subject: Re: [ccp4bb] old data
>>> 
>>> Hi Dean
>>> 
>>> Usually there is a serial number buried somewhere in the header - many 
>>> are text headers though some have TIFF format binary headers. Often a 
>>> timestamp as well though this is less common
>>> 
>>> From there biosync may help e.g.
>>> 
>>> http://biosync.sbkb.org/beamlineupdatehistory.jsp?region=european&sync
>>> h_id=esrf&bmln_name=BM14&height=400&width=600
>>> 
>>> (the list of ESRF MX beamlines is short so should not be too painful)
>>> 
>>> Knowing the format, filename you can probably pin it down or if you 
>>> share a little more info someone on the BB will know
>>> 
>>> All the best Graeme
>>> 
>>> 
>>> 
>>> On 31 Jan 2019, at 09:38, Dean Derbyshire 
>>> mailto:dean.derbysh...@medivir.com>> wrote:
>>> 
>>> maybe a silly question it there a data base or other way to tell what 
>>> detector was used to collect historic data. Image header isn’t hugely 
>>> helpful ESRF is all I know for the source but I’d like to know what 
>>> the detector was at the time… -  I’m talking 2005-2010
>>> 
>>>  Dean Derbyshire
>>>  Principal Scientist Protein Crystallography [X]
>>>  Box 1086
>>>  SE-141 22 Huddinge
>>>  SWEDEN
>>>  Visit: Lunastigen 7
>>>  Direct: +46 8 54683219
>>>  Mobile: +46731251723
>>>  www.medivir.com
>>> --
>>>  This transmission is intended for the person to whom or the 
>>> entity to which it is addressed and may contain information that is 
>>> privileged, confidential and exempt from disclosure under applicable law.
>>> If you are not the intended recipient, please be notified that any 
>>> dissemination, distribution or copying is strictly prohibited.
>>> If you have received this transmission in error, please notify us 
>>> immediately.
>>> Thank you for your cooperation.
>>> 
>

Re: [ccp4bb] old data - headers

[Pierre Rizkallah]

Hi Dean, Harry,

Station 14.1 was also run at 1.488A, partly to maintain the lower energy 
capacity that disappeared with the closure of 7.2. We are talking here about 
the last period of SRS Daresbury, in 2005 when staffing and equipment were in 
'high flux'. Marccd never went on 14.1, it was ADSC Q4 detector, maybe from the 
second generation of that particular brand. Note that 2304 pixels times 0.0816 
mm per pixel would come to about 188 mm square face of the detector, hence the 
beam centre, read from the header, being slightly away from 94 x 94 mm.

This is certainly fin de siècle feeling! A far cry from where we are now. 
Please do mention the venerable 14.1 beamline when it comes to depositing your 
data. Best wishes.

Pierre
***
Dr Pierre Rizkallah, Senior Lecturer Structural Biology 
Institute of Infection & Immunology, Sir Geraint Evans Building, 
School of Medicine, Heath Campus, Cardiff, CF14 4XN
email: rizkall...@cardiff.ac.uk        phone: +44 29 2074 2248
http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre

-Original Message-
From: CCP4 bulletin board  On Behalf Of Dean Derbyshire
Sent: 31 January 2019 10:21
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] FW: [ccp4bb] old data - headers

thanks all. I recon I have the ESRF data sorted.. but Daresbury.. am I right in 
assuming MARCCD or are we going back as far as image plate?
here is the image header
Harry what do you think

HEADER_BYTES=  512;
DIM=2;
BYTE_ORDER=little_endian;
TYPE=unsigned_short;
PIXEL_SIZE=0.08160;
BIN=none;
ADC=slow;
DETECTOR_SN=421;
DATE=Wed Apr 13 17:59:22 2005;
TIME=20.00;
DISTANCE=125.000;
OSC_RANGE=1.000;
PHI=7.000;
OSC_START=7.000;
AXIS=phi;
WAVELENGTH=1.48800;
BEAM_CENTER_X=94.700;
BEAM_CENTER_Y=96.400;
UNIF_PED=1500;
SIZE1=2304;
SIZE2=2304;
CCD_IMAGE_SATURATION=65535;
}


-Original Message-
From: Dean Derbyshire 
Sent: den 31 januari 2019 10:50
To: 'graeme.win...@diamond.ac.uk' ; 'Luca Jovine' 

Subject: RE: [ccp4bb] old data

ok may have lied.. not just 1 dataset i note.

Daresbury 14-1 on 19th April 2005. (I'm assuming MAR image plate but!) 

ESRF ID23-1 on 4th September 2007.
ESRF ID23-1 on 8th November 2007.
ESRF ID23-1 on 25th June 2008.
ESRF ID23-1 on 11th February2010.

I will post the headers in a sec

:)

-Original Message-
From: graeme.win...@diamond.ac.uk [mailto:graeme.win...@diamond.ac.uk]
Sent: den 31 januari 2019 10:42
To: Dean Derbyshire 
Cc: ccp4bb@jiscmail.ac.uk
Subject: Re: [ccp4bb] old data

Hi Dean

Usually there is a serial number buried somewhere in the header - many are text 
headers though some have TIFF format binary headers. Often a timestamp as well 
though this is less common

From there biosync may help e.g.

https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiosync.sbkb.org%2Fbeamlineupdatehistory.jsp%3Fregion%3Deuropean%26synch_id%3Desrf%26bmln_name%3DBM14%26height%3D400%26width%3D600&data=01%7C01%7Crizkallahp%40CARDIFF.AC.UK%7Cee66117ff0164e4b1aaf08d68765e7a1%7Cbdb74b3095684856bdbf06759778fcbc%7C1&sdata=SErBfjWMz6%2FS%2B7F%2F92N5UPThLB3pjf%2BuaLg5taSabRo%3D&reserved=0

(the list of ESRF MX beamlines is short so should not be too painful)

Knowing the format, filename you can probably pin it down or if you share a 
little more info someone on the BB will know

All the best Graeme



On 31 Jan 2019, at 09:38, Dean Derbyshire 
mailto:dean.derbysh...@medivir.com>> wrote:

maybe a silly question it there a data base or other way to tell what detector 
was used to collect historic data. Image header isn’t hugely helpful ESRF is 
all I know for the source but I’d like to know what the detector was at the 
time… -  I’m talking 2005-2010

   Dean Derbyshire
   Principal Scientist Protein Crystallography [X]
   Box 1086
   SE-141 22 Huddinge
   SWEDEN
   Visit: Lunastigen 7
   Direct: +46 8 54683219
   Mobile: +46731251723
   
https://emea01.safelinks.protection.outlook.com/?url=www.medivir.com&data=01%7C01%7Crizkallahp%40CARDIFF.AC.UK%7Cee66117ff0164e4b1aaf08d68765e7a1%7Cbdb74b3095684856bdbf06759778fcbc%7C1&sdata=ALjE7DR%2FSccWm7lejdFHiMbmCF3fzgLgZHVSUmD6fG0%3D&reserved=0
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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Nagarajan V]

I know of Rain-X being used.
V. Nagarajan

On Thu, Jan 31, 2019 at 1:17 AM  wrote:

> A long time ago, before siliconized coverslips became commercially
> available, we used to siliconize coverslips ourselves. It is not really
> that much work and unsiliconized cover slips should be very cheap. If you
> wish, I could try to find back the protocol.
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Rajnandani Kashyap
> *Gesendet:* Donnerstag, 31. Januar 2019 09:17
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] [ccp4bb] Is there any alternative to siliconized
> glass coverslips for crystallization?
>
>
>
> Dear All
>
> I am a PhD student who requires lots of coverslips (!!) for setting up
> hanging drop crystallization. The company sells it for a huge amount. Also
> there is a wide monetary difference between a normal siliconized coverslip
> and a 22mm siliconized circle coverslips. We tried to search for an
> alternative companies but couldn't get any one who sells coverslips with
> the same dimensions (0.19-0.22mm glass thickness and 22 mm glass diameter).
> Is there any alternative company (distribution in India) from where we can
> buy them for a reasonable price?
>
> Thanks in advance for sparing your valuable time and efforts.
>
>
>
> Regards
>
> Rajnandani Kashyap
>
> India
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 
>
> --
>
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>



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[ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Hughes, Jon]

yes, rain-x is excellent (also for PAGE gel plates). a little bottle costs 
almost nothing and will last you a lifetime.
best
jon

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
Nagarajan V
Gesendet: Donnerstag, 31. Januar 2019 16:14
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Is there any alternative to 
siliconized glass coverslips for crystallization?

I know of Rain-X being used.
V. Nagarajan

On Thu, Jan 31, 2019 at 1:17 AM 
mailto:herman.schreu...@sanofi.com>> wrote:
A long time ago, before siliconized coverslips became commercially available, 
we used to siliconize coverslips ourselves. It is not really that much work and 
unsiliconized cover slips should be very cheap. If you wish, I could try to 
find back the protocol.
Best,
Herman

Von: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
Rajnandani Kashyap
Gesendet: Donnerstag, 31. Januar 2019 09:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Is there any alternative to siliconized glass 
coverslips for crystallization?

Dear All
I am a PhD student who requires lots of coverslips (!!) for setting up hanging 
drop crystallization. The company sells it for a huge amount. Also there is a 
wide monetary difference between a normal siliconized coverslip and a 22mm 
siliconized circle coverslips. We tried to search for an alternative companies 
but couldn't get any one who sells coverslips with the same dimensions 
(0.19-0.22mm glass thickness and 22 mm glass diameter). Is there any 
alternative company (distribution in India) from where we can buy them for a 
reasonable price?
Thanks in advance for sparing your valuable time and efforts.

Regards
Rajnandani Kashyap
India



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[ccp4bb] ISBC2019 Granada

[Jose A. Gavira]

Dear Colleague,
  We are pleased to announce the 7th International School on Biological Crystallization (ISBC2019), to be held in Granada (Spain) during May 26th to 31st, 2019 (http://www.isbcgranada.org/). 
  The School will provide five days of lectures, posters and practical demonstrations focused on the fundamentals of crystallization. The aim of the School is to introduce all participants into the fundamental knowledge about the behaviour of crystallizing solutions and their applications to the field of biological crystallization, including large crystals for neutron diffraction, tiny crystals for XFEL, and EM sample preparation/characterization. 
Looking forward to seeing you in Granada.
Best regards,
ISBC 2019 Organizing Committee
INVITED SPEAKERS

Bernhard Rupp, k. k. Hofkristallamt, US.
Terese Bergfors, Uppsala University,  Sweden.
Janet  Newman, CSIRO, Australia.
Martin  Caffrey, Trinity College Dublin, Ireland.
Petra  Fromme, Arizona State University, US.
Juan Manuel Garcia-Ruiz, IACT, CSIC-UGR, Spain.
Joseph  Ng, University of Alabama, US.
Jeroen  Mesters, University of Lüebeck, Germany.
Marc  Pusey, iXpressGenes, Huntsville, US.
Howard  Einspahr, IUCr Journal Comission, US.
José A.  Gavira, IACT, CSIC-UGR, Spain.
Hudel  Luecke, University of Oslo, Norway.
Naoko  Mizuno, Max Planck Institute, Germany.
Sergio  Martínez, UGR, Spain.
Ivana  K. Smatanova, University of South Bohemia, Czech Republic.
Nadine Candoni, CINam-Marseille, France. 
Claude  Sauter, IBMC, CNRS, France.
Christian  Betzel, University of Hamburg, Germany.
Fermin  Otálora, IACT, CSIC-UGR, Spain.
Christian  Biertümpfel, Max Planck Institute, Germany.
Edward  H. Snell, Hauptman-Woodward Institute, Buffalo, US.
May  Marsh, Swiss Light Source at Paul Scherrer Institut, Swiss.
Jose  Manuel Martin-Garcia, Arizona State University, US.
Katsuo  Tsukamoto, Osaka University, Japan
Lata Govada, Imperial Collague, London, UK.
Guillermo  Calero, University of Pittsburg, US.
Monica  Budayova-Spano, Université Grenoble Alpes, France.
Pavlína  Řezáčová, University of Prague, Czech Republic.
Abel Moreno, Universidad Autónoma de México, México.
Crissy  Tarver, University of Alabama in Huntsville, USA.
Tom Peat, CSIRO, Australia.

TOPICS

   Nucleation: Classical and non-classical approaches.
   Crystal growth kinetics and mechanisms.
   Properties of macromolecular solutions (DLS/SAXS).
   Screening: The search for crystallization conditions
   Crystallization techniques: Batch, Vapour and Counter Diffusion, MMS, How do they work?
   Crystallization and diffusion transport: gels, microfluidics and microgravity.
   Crystallization of large crystals for Neutron diffraction.
   In vivo crystallization of tiny crystals for XFEL.
   Serial Crystallography.
   Polymorphism in protein crystals.
   Membrane protein crystallization: Lipid cubic phase, bicelles and detergents.
   Crystallization of Macromolecular Complexes.
   Electron microscopy for structural studies
   Sample manipulation, preparation and characterization by electron microscopy.






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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Mitchell D. Miller]

We used to use dichlorodimethylsilane in toluene to siliconize both
coverslips and the special glass capillaries for crystal mounting.
I don't have the protocol we used anymore, but the one listed on
protocolpedia sounds familiar.
https://www.protocolpedia.com/blog/2017/05/11/siliconized-coverslips-2/
I recall we often baked the items afterwards.

We used to use staining racks to hold the coverslips and a staining
vessel to hold the solution (in a hood). The racks looked like
https://www.thomassci.com/Equipment/Histology/_/THOMAS-COVER-GLASS-STAINING-OUTFITS?q=Cover%20Glass%20Rack
it looks like sigma also has a poly-propylene rack that is much
less expensive,
https://www.sigmaaldrich.com/catalog/product/sigma/z688568?lang=en®ion=US&cm_sp=Insite-_-recent_fixed-_-recent5-5
but they may be incompatible with toluene.

Regards,
Mitch

Quoting Zhijie Li :


Hi,

I believe that one can put a 50-100uL drop of  fresh SigmaCote (in a  
tube cap) with the glass pieces (surface well exposed), sealed in a  
dedicated (because the container will be coated too) container  
(air-tight lunch boxes).  After a while the SigmaCote vapor should  
react with the glass and bring polysiloxane groups to the glass  
surface. I have done this with microscope slips. To make a few  
hundred .22 mm cover slips I think the major challenge is to make a  
frame for supporting the separated (~1mm apart to allow free  
diffusion?) cover slips (3D print?). Dry paper may work too. If some  
of the cover slips tend to stick together, a little vacuuming can  
help.


SigmaCote is a chlorinated polysiloxane. The Cl-Si group allows it  
to react with the hydroxyls on glass surface. Just be aware that the  
same group reacts even more readily with water in air, making the  
reagent less reactive with glass overtime (but I have used a VERY  
old bottle and it worked).


References:

https://en.wikipedia.org/wiki/Chlorosilane

https://pubs.acs.org/doi/pdfplus/10.1021/j100727a046

https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Product_Information_Sheet/1/sl2pis.pdf

Zhijie


On 31/01/2019 4:16 a.m.,  
herman.schreu...@sanofi.com wrote:
A long time ago, before siliconized coverslips became commercially  
available, we used to siliconize coverslips ourselves. It is not  
really that much work and unsiliconized cover slips should be very  
cheap. If you wish, I could try to find back the protocol.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag  
von Rajnandani Kashyap

Gesendet: Donnerstag, 31. Januar 2019 09:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Is there any alternative to siliconized  
glass coverslips for crystallization?


Dear All
I am a PhD student who requires lots of coverslips (!!) for setting  
up hanging drop crystallization. The company sells it for a huge  
amount. Also there is a wide monetary difference between a normal  
siliconized coverslip and a 22mm siliconized circle coverslips. We  
tried to search for an alternative companies but couldn't get any  
one who sells coverslips with the same dimensions (0.19-0.22mm glass  
thickness and 22 mm glass diameter). Is there any alternative  
company (distribution in India) from where we can buy them for a  
reasonable price?

Thanks in advance for sparing your valuable time and efforts.

Regards
Rajnandani Kashyap
India



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Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Holton, James M]

plastic.

Plastic cover slips are no good for UV or polarization, but they are way better 
than glass if you happen to want to try in-situ diffraction. 
(https://doi.org/10.1107/S002188981254)

If you can't afford commercial ones, then you can always cut up some inkjet 
transparency film sheets like McPherson did in the above reference.  Then after 
you've made a few hundred you can ask yourself how much you'd be willing to pay 
somebody else to do it for you.  There is no wrong answer to that question, but 
it will determine which route you take.

-James Holton
MAD Scientist

On 1/31/2019 12:17 AM, Rajnandani Kashyap wrote:
Dear All
I am a PhD student who requires lots of coverslips (!!) for setting up hanging 
drop crystallization. The company sells it for a huge amount. Also there is a 
wide monetary difference between a normal siliconized coverslip and a 22mm 
siliconized circle coverslips. We tried to search for an alternative companies 
but couldn't get any one who sells coverslips with the same dimensions 
(0.19-0.22mm glass thickness and 22 mm glass diameter). Is there any 
alternative company (distribution in India) from where we can buy them for a 
reasonable price?
Thanks in advance for sparing your valuable time and efforts.

Regards
Rajnandani Kashyap
India



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Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Goldman, Adrian]

When I was a graduate student, about 150,000 years ago, we took regular 
coverslips and doused them in ?silane to make siliconised ones.  You then let 
them sit in a rack to dry.  It was a bit tedious but not horrendously so.  
After a while, I stopped doing it altogether, because IMHO it didn’t make a 
massive amount of difference to the behaviour of the solution on the cover 
slip.  It would bead up, or not, depending on what it was.

So my advice would be: 1) siliconise yourself; 2) compare siliconised versus 
non and decide if you can be bothered.

Adrian Goldman


On 31 Jan 2019, at 16:02, Holton, James M 
<270165b9f4cf-dmarc-requ...@jiscmail.ac.uk>
 wrote:

plastic.

Plastic cover slips are no good for UV or polarization, but they are way better 
than glass if you happen to want to try in-situ diffraction. 
(https://doi.org/10.1107/S002188981254)

If you can't afford commercial ones, then you can always cut up some inkjet 
transparency film sheets like McPherson did in the above reference.  Then after 
you've made a few hundred you can ask yourself how much you'd be willing to pay 
somebody else to do it for you.  There is no wrong answer to that question, but 
it will determine which route you take.

-James Holton
MAD Scientist

On 1/31/2019 12:17 AM, Rajnandani Kashyap wrote:
Dear All
I am a PhD student who requires lots of coverslips (!!) for setting up hanging 
drop crystallization. The company sells it for a huge amount. Also there is a 
wide monetary difference between a normal siliconized coverslip and a 22mm 
siliconized circle coverslips. We tried to search for an alternative companies 
but couldn't get any one who sells coverslips with the same dimensions 
(0.19-0.22mm glass thickness and 22 mm glass diameter). Is there any 
alternative company (distribution in India) from where we can buy them for a 
reasonable price?
Thanks in advance for sparing your valuable time and efforts.

Regards
Rajnandani Kashyap
India



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Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Mathews, Irimpan I.]

Long back we used Prosil solution (I think,  1% solution) for siliconization. 
Mathews


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Goldman, 
Adrian
Sent: Thursday, January 31, 2019 8:43 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Is there any alternative to siliconized glass coverslips 
for crystallization?

When I was a graduate student, about 150,000 years ago, we took regular 
coverslips and doused them in ?silane to make siliconised ones.  You then let 
them sit in a rack to dry.  It was a bit tedious but not horrendously so.  
After a while, I stopped doing it altogether, because IMHO it didn’t make a 
massive amount of difference to the behaviour of the solution on the cover 
slip.  It would bead up, or not, depending on what it was.

So my advice would be: 1) siliconise yourself; 2) compare siliconised versus 
non and decide if you can be bothered.

Adrian Goldman



On 31 Jan 2019, at 16:02, Holton, James M 
<270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> wrote:

plastic.

Plastic cover slips are no good for UV or polarization, but they are 
way better than glass if you happen to want to try in-situ diffraction. 
(https://doi.org/10.1107/S002188981254)

If you can't afford commercial ones, then you can always cut up some 
inkjet transparency film sheets like McPherson did in the above reference.  
Then after you've made a few hundred you can ask yourself how much you'd be 
willing to pay somebody else to do it for you.  There is no wrong answer to 
that question, but it will determine which route you take.

-James Holton
MAD Scientist


On 1/31/2019 12:17 AM, Rajnandani Kashyap wrote:


Dear All 
I am a PhD student who requires lots of coverslips (!!) for 
setting up hanging drop crystallization. The company sells it for a huge 
amount. Also there is a wide monetary difference between a normal siliconized 
coverslip and a 22mm siliconized circle coverslips. We tried to search for an 
alternative companies but couldn't get any one who sells coverslips with the 
same dimensions (0.19-0.22mm glass thickness and 22 mm glass diameter). Is 
there any alternative company (distribution in India) from where we can buy 
them for a reasonable price?
Thanks in advance for sparing your valuable time and efforts.

Regards
Rajnandani Kashyap

India





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Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Goldman, Adrian]

Yes, that was it! I just couldn’t remember the name.

> On 31 Jan 2019, at 17:04, Mathews, Irimpan I. 
> <2add487f8799-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Long back we used Prosil solution (I think,  1% solution) for siliconization. 
> Mathews
> 
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
> Goldman, Adrian
> Sent: Thursday, January 31, 2019 8:43 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Is there any alternative to siliconized glass 
> coverslips for crystallization?
> 
> When I was a graduate student, about 150,000 years ago, we took regular 
> coverslips and doused them in ?silane to make siliconised ones.  You then let 
> them sit in a rack to dry.  It was a bit tedious but not horrendously so.  
> After a while, I stopped doing it altogether, because IMHO it didn’t make a 
> massive amount of difference to the behaviour of the solution on the cover 
> slip.  It would bead up, or not, depending on what it was.
> 
> So my advice would be: 1) siliconise yourself; 2) compare siliconised versus 
> non and decide if you can be bothered.
> 
> Adrian Goldman
> 
> 
> 
>   On 31 Jan 2019, at 16:02, Holton, James M 
> <270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
>   plastic.
>   
>   Plastic cover slips are no good for UV or polarization, but they are 
> way better than glass if you happen to want to try in-situ diffraction. 
> (https://doi.org/10.1107/S002188981254)
>   
>   If you can't afford commercial ones, then you can always cut up some 
> inkjet transparency film sheets like McPherson did in the above reference.  
> Then after you've made a few hundred you can ask yourself how much you'd be 
> willing to pay somebody else to do it for you.  There is no wrong answer to 
> that question, but it will determine which route you take.
>   
>   -James Holton
>   MAD Scientist
>   
>   
>   On 1/31/2019 12:17 AM, Rajnandani Kashyap wrote:
>   
> 
>   Dear All 
>   I am a PhD student who requires lots of coverslips (!!) for 
> setting up hanging drop crystallization. The company sells it for a huge 
> amount. Also there is a wide monetary difference between a normal siliconized 
> coverslip and a 22mm siliconized circle coverslips. We tried to search for an 
> alternative companies but couldn't get any one who sells coverslips with the 
> same dimensions (0.19-0.22mm glass thickness and 22 mm glass diameter). Is 
> there any alternative company (distribution in India) from where we can buy 
> them for a reasonable price?
>   Thanks in advance for sparing your valuable time and efforts.
> 
>   Regards
>   Rajnandani Kashyap
>   
>   India
>   
> 
> 
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 
> 
> 
> 
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 
> 
> 
> 
> 
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Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Patrick Shaw Stewart]

For the last 150,000 years we've been using the Hampton THICK siliconized
coverslips - I'm told they're one of the many crystallization tricks/gizmos
that Alan D'Arcy invented.  We quite often recycle them - and I've never
seen any problems.  The thick ones are very easy to use because you can jam
your thumb down on them without any danger of either cutting your thumb or
losing your crystals.  Alan (or someone) told me that the original ones
were standard microscope (long) SLIDES cut into square sections by hand
with a glass cutter.  Hampton's are either round or square and some have
beautiful flame-polished edges.

A chemist told me that once you siliconize glass you can never get the
silane groups off again by any normal chemical means.  He didn't see any
need for eg rinsing with methanol and baking after treatment, which I had
been doing.

If recycling however the surface can become contaminated with grease and
denatured protein.  Either put them through a dishwasher (I've heard) or
rub them hard with something soft.

Thx, Patrick


On Thu, 31 Jan 2019 at 17:14, Goldman, Adrian 
wrote:

> Yes, that was it! I just couldn’t remember the name.
>
> > On 31 Jan 2019, at 17:04, Mathews, Irimpan I. <
> 2add487f8799-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> > Long back we used Prosil solution (I think,  1% solution) for
> siliconization.
> > Mathews
> >
> >
> > -Original Message-
> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Goldman, Adrian
> > Sent: Thursday, January 31, 2019 8:43 AM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Is there any alternative to siliconized glass
> coverslips for crystallization?
> >
> > When I was a graduate student, about 150,000 years ago, we took regular
> coverslips and doused them in ?silane to make siliconised ones.  You then
> let them sit in a rack to dry.  It was a bit tedious but not horrendously
> so.  After a while, I stopped doing it altogether, because IMHO it didn’t
> make a massive amount of difference to the behaviour of the solution on the
> cover slip.  It would bead up, or not, depending on what it was.
> >
> > So my advice would be: 1) siliconise yourself; 2) compare siliconised
> versus non and decide if you can be bothered.
> >
> > Adrian Goldman
> >
> >
> >
> >   On 31 Jan 2019, at 16:02, Holton, James M <
> 270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> >   plastic.
> >
> >   Plastic cover slips are no good for UV or polarization, but they
> are way better than glass if you happen to want to try in-situ diffraction.
> (https://doi.org/10.1107/S002188981254)
> >
> >   If you can't afford commercial ones, then you can always cut up
> some inkjet transparency film sheets like McPherson did in the above
> reference.  Then after you've made a few hundred you can ask yourself how
> much you'd be willing to pay somebody else to do it for you.  There is no
> wrong answer to that question, but it will determine which route you take.
> >
> >   -James Holton
> >   MAD Scientist
> >
> >
> >   On 1/31/2019 12:17 AM, Rajnandani Kashyap wrote:
> >
> >
> >   Dear All
> >   I am a PhD student who requires lots of coverslips (!!)
> for setting up hanging drop crystallization. The company sells it for a
> huge amount. Also there is a wide monetary difference between a normal
> siliconized coverslip and a 22mm siliconized circle coverslips. We tried to
> search for an alternative companies but couldn't get any one who sells
> coverslips with the same dimensions (0.19-0.22mm glass thickness and 22 mm
> glass diameter). Is there any alternative company (distribution in India)
> from where we can buy them for a reasonable price?
> >   Thanks in advance for sparing your valuable time and
> efforts.
> >
> >   Regards
> >   Rajnandani Kashyap
> >
> >   India
> >
> >
> > 
> >
> >
> >   To unsubscribe from the CCP4BB list, click the following
> link:
> >
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >
> >
> >
> > 
> >
> >   To unsubscribe from the CCP4BB list, click the following link:
> >   https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >
> >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >
> >
> > 
> >
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> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
>
> 
>
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>


-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.

[ccp4bb] AW: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Hughes, Jon]

in my experience using silane with PAGE plates, rain-x is much better (at least 
in that case).
jon

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Goldman, 
Adrian
Gesendet: Donnerstag, 31. Januar 2019 17:43
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Is there any alternative to siliconized glass coverslips 
for crystallization?

When I was a graduate student, about 150,000 years ago, we took regular 
coverslips and doused them in ?silane to make siliconised ones.  You then let 
them sit in a rack to dry.  It was a bit tedious but not horrendously so.  
After a while, I stopped doing it altogether, because IMHO it didn’t make a 
massive amount of difference to the behaviour of the solution on the cover 
slip.  It would bead up, or not, depending on what it was.

So my advice would be: 1) siliconise yourself; 2) compare siliconised versus 
non and decide if you can be bothered.

Adrian Goldman



On 31 Jan 2019, at 16:02, Holton, James M 
<270165b9f4cf-dmarc-requ...@jiscmail.ac.uk>
 wrote:

plastic.

Plastic cover slips are no good for UV or polarization, but they are way better 
than glass if you happen to want to try in-situ diffraction. 
(https://doi.org/10.1107/S002188981254)

If you can't afford commercial ones, then you can always cut up some inkjet 
transparency film sheets like McPherson did in the above reference.  Then after 
you've made a few hundred you can ask yourself how much you'd be willing to pay 
somebody else to do it for you.  There is no wrong answer to that question, but 
it will determine which route you take.

-James Holton
MAD Scientist
On 1/31/2019 12:17 AM, Rajnandani Kashyap wrote:
Dear All
I am a PhD student who requires lots of coverslips (!!) for setting up hanging 
drop crystallization. The company sells it for a huge amount. Also there is a 
wide monetary difference between a normal siliconized coverslip and a 22mm 
siliconized circle coverslips. We tried to search for an alternative companies 
but couldn't get any one who sells coverslips with the same dimensions 
(0.19-0.22mm glass thickness and 22 mm glass diameter). Is there any 
alternative company (distribution in India) from where we can buy them for a 
reasonable price?
Thanks in advance for sparing your valuable time and efforts.

Regards
Rajnandani Kashyap
India


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[ccp4bb] Postdoctoral Research Associate: Oak Ridge National Laboratory

[Myles, Dean A A]

Dear Colleagues,

The Diffraction Group in the Neutron Scattering Division (NSD) at Oak Ridge 
National Laboratory (ORNL) has an immediate opening for a Postdoctoral Research 
Associate in macromolecular crystallography and/or structural biology to 
investigate the structure and function of biological complexes involved in 
catalysis, membrane transport and light harvesting systems. You will join a 
multi-disciplinary research team that is developing and applying isotopic 
labeling and neutron diffraction and scattering techniques to understand and 
control the structure, function and dynamics of complex biological systems. As 
an ORNL postdoctoral fellow you will have access to state-of-the-art facilities 
for isotopic labeling, biophysical characterization and X-ray diffraction, as 
well as access to world class facilities for neutron diffraction and scattering.
Applicants should have received a Ph.D. in structural biology, protein 
chemistry, biophysics or related science field within the last five years and 
should have extensive experience  in biophysical characterization using 
diffraction or scattering techniques. Experience in protein expression, 
purification and crystallization is desired.

For informal enquiries please contact Dean Myles 
(myle...@ornl.gov)

For further details and to apply, please see link below:

https://jobs.ornl.gov/job/Oak-Ridge-Postdoctoral-Research-Associate-Structural-Biology-TN-37831/533212900/






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Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Daniel M. Himmel, Ph. D.]

Fisher Scientific makes 22 inch square plastic cover slips, which are
labeled "Fisherbrand Unbreakable
Cover Slips".

I and my colleagues have used them for over 15 years instead of siliconized
glass coverslips.
Just dip each one in ethanol to clean before use, dry with an air blower,
and use it to set up
your drops.  They work like a charm.  They come 100 to a box.  Check the
Fisher Scientific catalog.

-Daniel


On Thu, Jan 31, 2019 at 3:17 AM Rajnandani Kashyap <
kashyap.rajnand...@gmail.com> wrote:

> Dear All
> I am a PhD student who requires lots of coverslips (!!) for setting up
> hanging drop crystallization. The company sells it for a huge amount. Also
> there is a wide monetary difference between a normal siliconized coverslip
> and a 22mm siliconized circle coverslips. We tried to search for an
> alternative companies but couldn't get any one who sells coverslips with
> the same dimensions (0.19-0.22mm glass thickness and 22 mm glass diameter).
> Is there any alternative company (distribution in India) from where we can
> buy them for a reasonable price?
> Thanks in advance for sparing your valuable time and efforts.
>
> Regards
> Rajnandani Kashyap
> India
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Minmin Yu]

Yeah I used to use Fisher Scientific square plastic cover slips. Now I am using 
Sigma 22x22mm (Z36,590-4, 100 each Lot10B084279) smaller sized ones. These 
plastic ones are much more durable than the glass ones and are very easy to be 
handled. They work very well for both hanging drops or for sitting drops 
sealing with grease. 

Minmin

> On 31 Jan 2019, at 21:14, Daniel M. Himmel, Ph. D.  
> wrote:
> 
> Fisher Scientific makes 22 inch square plastic cover slips, which are labeled 
> "Fisherbrand Unbreakable
> Cover Slips".
> 
> I and my colleagues have used them for over 15 years instead of siliconized 
> glass coverslips.
> Just dip each one in ethanol to clean before use, dry with an air blower, and 
> use it to set up 
> your drops.  They work like a charm.  They come 100 to a box.  Check the 
> Fisher Scientific catalog.
> 
> -Daniel
> 
> 
> On Thu, Jan 31, 2019 at 3:17 AM Rajnandani Kashyap 
> mailto:kashyap.rajnand...@gmail.com>> wrote:
> Dear All
> I am a PhD student who requires lots of coverslips (!!) for setting up 
> hanging drop crystallization. The company sells it for a huge amount. Also 
> there is a wide monetary difference between a normal siliconized coverslip 
> and a 22mm siliconized circle coverslips. We tried to search for an 
> alternative companies but couldn't get any one who sells coverslips with the 
> same dimensions (0.19-0.22mm glass thickness and 22 mm glass diameter). Is 
> there any alternative company (distribution in India) from where we can buy 
> them for a reasonable price?
> Thanks in advance for sparing your valuable time and efforts.
> 
> Regards
> Rajnandani Kashyap
> India
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 



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[ccp4bb] Solid-state NMR technician position @ University of Groningen (Netherlands)

[P.C.A. van der Wel]

Looking for: 

Solid-state NMR research technician (PhD/MSc)
University of Groningen, Zernike Institute for Advanced Materials
Van der Wel SSNMR group

— Deadline Feb. 14th — 

The Van der Wel solid-state NMR group at the University of Groningen 
(Netherlands) is looking for applicants with a background in NMR for a new 
research technician position in the lab. This position is funded by 
institutional support. The ideal candidate would have a MSc/PhD degree with a 
background in magic-angle-spinning solid-state NMR. However, we welcome 
applications by candidates with a strong background in NMR in general. Others 
with a potentially relevant expertise are encouraged to inquire (contact 
information below).

The group’s research focuses on the use of multidimensional 
magic-angle-spinning NMR in diverse contexts, with focal points being 
structural biology of protein misfolding diseases (including Huntington 
disease), membrane biophysics, and self-assembling bio-/nano-materials.

More background information about the lab and the research environment is on 
the group website: https://www.vanderwellab.org  
, and the institute/university website: https://www.rug.nl/research/zernike/ 
 

Potential applicants can find specific details about the position and 
application procedures (deadline Feb. 14th 2019) at the following URL:
https://www.rug.nl/about-us/work-with-us/job-opportunities/overview?details=00347-02S0006SAP
 

 

Questions and inquiries should be sent to:
Patrick van der Wel – p.c.a.van.der@rug.nl 



 

--
Patrick C.A. van der Wel, Ph.D.
Associate Professor
Solid-state NMR spectroscopy group
Zernike Institute for Advanced Materials
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

e-mail: p.c.a.van.der@rug.nl 
phone: +31(0)50-3632683
https://www.rug.nl/staff/p.c.a.van.der.wel/ 

https://www.vanderwellab.org 




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Re: [ccp4bb] AW: [ccp4bb] 3D stereo and pymol

[Jan Stransky]

Awesome solution :-) I am sure, users will appreciate it. And I don't
need stereo personally :-)
Jan

On 1/31/19 9:26 AM, Hughes, Jon wrote:
> ...just open pymol, go to display - stereo mode - cross-eye then click
> stereo. it might need a little practice and it makes one look even
> sillier than one does usually, but it works, costs nothing, needs no
> updates and i'm told that it's even good for your eye muscles!
> 
> best,
> 
> jon
> 
>  
> 
> *Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Jan Stransky
> *Gesendet:* Mittwoch, 30. Januar 2019 11:03
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* Re: [ccp4bb] 3D stereo and pymol
> 
>  
> 
> Dear all,
> 
> I started looking into the never ending story of stereo in
> crystallography... As with our standardized linux setup we probably are
> not willing to move to X.org-world, if was wondering, if anybody was
> succesful to make stereo working in Windows 10. I did read some NVIDIA
> forum, and it seems that 3d vision is not very supported by NVIDIA, even
> for gamers... Was anybody able to mke it work with Geforce cards, to
> save few bucks?
> 
> Best regards,
> 
> Jan
> 
> Dne 03.01.2018 v 10:42 Wim Burmeister napsal(a):
> 
> I answer a bit late, but I repost a message on 3D graphics from Mai
> 2017 :
> 
> Hello,
> 
> we just wanted to share our experience in finding a configuration
> which allows to use 3D graphics under linux using Nvidia GeForce 3D
> glasses.
> 
> We had quite a hard time to find a configurations which works correctly.
> 
> We finally used Debian linux with a xfce desktop. Other recent
> desktops use a tiling which is not compatible with 3D graphics.
> 
> The hardware consists of
> 
>   * a DELL Precision T5810  desktop computer with an Nvidia Quadro
> M4000 (8 Gbyte memory, 4 DP) graphics card
>   * Nvidia GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT)
> active stereo glasses
>   * a stereo connector PNY Quadro 4000 3D for the synchronization of
> graphics card and glasses
>   * an ASUS 24" LED 3D - VG248QE display
>   * a DisplayPort-DisplayPort cable
> 
> The Nvidia linux drivers from version 367.57 can handle the current
> version of the Nvidia glasses.
> 
> For an obscure reason a direct DP-DP connection between graphics
> card and display is absolutely required in order to obtain fully
> working stereo. If a DP-DVI dual link adapter is used, the stereo
> does not work on the top and the bottom part of the screen. This is
> true for a native DELL active adaptor or generic models. The exact
> reason remains unresolved, but the solution is to use a direct DP-DP
> connection. This limits the available choice of displays which
> require 120 Hz for 1080*1980 screen resolution and a DP input. We
> have been choosing a “Nvidia 3D ready” model.
> 
> There has been a considerate about of exchange about this problem on
> 
> 
> https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/
> 
> The setup comes with a price tag of about 1600 € free of taxes.
> 
> coot, pymol and chimera work straight without problems in hardware
> stereo mode. The experience is absolutely great.
> 
> Best
> 
> Wim
> 
> -- 
> 
> Wim Burmeister
> Professeur
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs
> 
> CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeis...@ibs.fr 
> Tel:    +33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
> website
> 
> 
> 
>  
> 
>  
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 
> 
> 
> 
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> 



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Re: [ccp4bb] 3D stereo and (pymol) Win 10

[Georg Mlynek]

Dear all, I am considering to buy a new laptop and would like to install 
the latest ubuntu version and have 3D glasses. Following the discussions 
in the lasts years, this issue seems to be not trivial. Which setup of 
laptop and 3D glasses will work plug and play?


And what about VR. When is coot and pymol VR ready?

Best regards, Georg.


On 31.01.19 10:54, Philippe BENAS wrote:

Dear all,

I had an HP Z620 that was dual boot Kubuntu 14.03 and Win 10. Coot was 
working in stereo mode without any problem for a year or so. But after 
one of their major updates Coot crashed as soon as the built-in IR 
emitter of my Asus VG278H turned on, as described Pedro and Jan.


My personal guess is that the new Win 10 kernels no longer accept some 
direct exchanges from programs to hardware parts, probably for safety 
issues. So I came to the same conclusion as Pedro: stick to Win 7 if 
you want to run Coot under Windows or use a linux distribution or dual 
boot workstation.


Nevertheless PyMol was just working fine in stereo mode under Win 10. 
At least until last september when I sold my Z620 for a Z820 (Kubuntu 
18.04/Win7). May be PyMol developers at Schrödinger could give their 
tips and tricks to Bernard Lohkamp to whom I send my warmest 
aknowledgments for porting Coot under Windows.


Best regards,
Philippe


Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
15, rue René Descartes
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr 
, philippe_be...@yahoo.fr 

URLs: http://www-ibmc.u-strasbg.fr/ , 
http://www-ibmc.u-strasbg.fr/spip-arn/





Le jeudi 31 janvier 2019 à 10:18:42 UTC+1, Pedro Matias 
 a écrit :



Hi all,

The problem with COOT stereo and Windows 10 is that the COOT binary is 
not compatible with the newer OpenGL drivers or somesuch in Windows 
10. So, COOT runs fine in Windows 10 but crashes if you enter hardware 
stereo mode. However, PyMOL works fine in stereo in Windows 10.


According to Bernhard Lohkamp, the Windows COOT developer, this 
problem has not yet been fixed because he has no access to a Windows 
10 PC.


Therefore, stick to Windows 7 if you want to run COOT stereo on a 
cheap Quadro card.


Best regards,

Pedro

Às 04:38 de 31/01/2019, Jim Fairman escreveu:
I had a Windows 7 machine that would run Quad buffered stereo back 
around 2009, haven't had a chance to try with Windows 10.


On Wed, Jan 30, 2019, 02:03 Jan Stransky > wrote:


Dear all,

I started looking into the never ending story of stereo in
crystallography... As with our standardized linux setup we
probably are not willing to move to X.org-world, if was
wondering, if anybody was succesful to make stereo working in
Windows 10. I did read some NVIDIA forum, and it seems that 3d
vision is not very supported by NVIDIA, even for gamers... Was
anybody able to mke it work with Geforce cards, to save few bucks?

Best regards,

Jan

Dne 03.01.2018 v 10:42 Wim Burmeister napsal(a):

I answer a bit late, but I repost a message on 3D graphics from
Mai 2017 :

Hello,

we just wanted to share our experience in finding a
configuration which allows to use 3D graphics under linux using
Nvidia GeForce 3D glasses.

We had quite a hard time to find a configurations which works
correctly.

We finally used Debian linux with a xfce desktop. Other recent
desktops use a tiling which is not compatible with 3D graphics.

The hardware consists of

  * a DELL Precision T5810  desktop computer with an Nvidia
Quadro M4000 (8 Gbyte memory, 4 DP) graphics card
  * Nvidia GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES
KIT) active stereo glasses
  * a stereo connector PNY Quadro 4000 3D for the
synchronization of graphics card and glasses
  * an ASUS 24" LED 3D - VG248QE display
  * a DisplayPort-DisplayPort cable

The Nvidia linux drivers from version 367.57 can handle the
current version of the Nvidia glasses.

For an obscure reason a direct DP-DP connection between graphics
card and display is absolutely required in order to obtain fully
working stereo. If a DP-DVI dual link adapter is used, the
stereo does not work on the top and the bottom part of the
screen. This is true for a native DELL active adaptor or generic
models. The exact reason remains unresolved, but the solution is
to use a direct DP-DP connection. This limits the available
choice of displays which require 120 Hz for 1080*1980 screen
resolution and a DP input. We have been choosing a “Nvidia 3D
ready” model.

There has been a considerate about of exchange about this problem on


https://devtalk.nvidia.com/default/

Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Frank Von Delft]

Or do sitting drop, it's much easier all round. Frank

Sent from tiny silly touch screen

From: Minmin Yu 
Sent: Thursday, 31 January 2019 21:42
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Is there any alternative to siliconized glass coverslips 
for crystallization?

Yeah I used to use Fisher Scientific square plastic cover slips. Now I am using 
Sigma 22x22mm (Z36,590-4, 100 each Lot10B084279) smaller sized ones. These 
plastic ones are much more durable than the glass ones and are very easy to be 
handled. They work very well for both hanging drops or for sitting drops 
sealing with grease.

Minmin

On 31 Jan 2019, at 21:14, Daniel M. Himmel, Ph. D. 
mailto:danielmhim...@gmail.com>> wrote:

Fisher Scientific makes 22 inch square plastic cover slips, which are labeled 
"Fisherbrand Unbreakable
Cover Slips".

I and my colleagues have used them for over 15 years instead of siliconized 
glass coverslips.
Just dip each one in ethanol to clean before use, dry with an air blower, and 
use it to set up
your drops.  They work like a charm.  They come 100 to a box.  Check the Fisher 
Scientific catalog.

-Daniel


On Thu, Jan 31, 2019 at 3:17 AM Rajnandani Kashyap 
mailto:kashyap.rajnand...@gmail.com>> wrote:
Dear All
I am a PhD student who requires lots of coverslips (!!) for setting up hanging 
drop crystallization. The company sells it for a huge amount. Also there is a 
wide monetary difference between a normal siliconized coverslip and a 22mm 
siliconized circle coverslips. We tried to search for an alternative companies 
but couldn't get any one who sells coverslips with the same dimensions 
(0.19-0.22mm glass thickness and 22 mm glass diameter). Is there any 
alternative company (distribution in India) from where we can buy them for a 
reasonable price?
Thanks in advance for sparing your valuable time and efforts.

Regards
Rajnandani Kashyap
India



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Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

[Minmin Yu]

‎Agree. Nowadays I hardly do hanging drops and crystal clear tapes are good to seal the sitting drop plates too. I mainly use the plastic cover slips to set the cryo drops on for crystal harvesting. They can be put on any plates and the drops are good to be viewed under the microscope.  From: Frank Von DelftSent: Friday, 1 February 2019 06:13To: CCP4BB@JISCMAIL.AC.UKReply To: Frank Von DelftSubject: Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?






Or do sitting drop, it's much easier all round. Frank




Sent from tiny silly touch screen






From: Minmin Yu 
Sent: Thursday, 31 January 2019 21:42
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?





Yeah I used to use Fisher Scientific square plastic cover slips. Now I am using Sigma 22x22mm (Z36,590-4, 100 each Lot10B084279) smaller sized ones. These plastic ones are much more durable than the glass ones and
 are very easy to be handled. They work very well for both hanging drops or for sitting drops sealing with grease. 


Minmin



On 31 Jan 2019, at 21:14, Daniel M. Himmel, Ph. D.  wrote:



Fisher Scientific makes 22 inch square plastic cover slips, which are labeled "Fisherbrand Unbreakable
Cover Slips".


I and my colleagues have used them for over 15 years instead of siliconized glass coverslips.
Just dip each one in ethanol to clean before use, dry with an air blower, and use it to set up 
your drops.  They work like a charm.  They come 100 to a box.  Check the Fisher Scientific catalog.


-Daniel





On Thu, Jan 31, 2019 at 3:17 AM Rajnandani Kashyap  wrote:


Dear All
I am a PhD student who requires lots of coverslips (!!) for setting up hanging drop crystallization. The company sells it for a huge amount. Also there is a wide monetary difference between a normal siliconized coverslip and a 22mm siliconized circle coverslips.
 We tried to search for an alternative companies but couldn't get any one who sells coverslips with the same dimensions (0.19-0.22mm glass thickness and 22
 mm glass diameter). Is there any alternative company (distribution in India) from where we can buy them for a reasonable price?
Thanks in advance for sparing your valuable time and efforts.


Regards
Rajnandani Kashyap












India















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