[ccp4bb] Satellite meeting on MX raw image data formats, metadata and validation

[Andreas Förster]

Dear all,

how many times do you have to refer back to information in the most obscure
places to prepare a PDB submission?  With the right metadata associated
with your dataset, the process could be much simpler.  This is one of the
points that will be addressed during a virtual meeting on MX raw image data
formats, metadata and validation this Saturday, 22 Aug 2020, from 9 am
until 3 pm, Prague Time (GMT+2, you do the math for your time zone).

Organized and put together by Herbert Bernstein for the most part, the
meeting will put the recently published Gold standard (
https://doi.org/10.1107/S2052252520008672) before a discerning audience of
beamline scientists and crystallographers and ask how
- we can assure that all relevant experimental information is save with the
diffraction data,
- crystallographic data should be recorded to be findable, accessible,
interoperable and reusable,
- correctly recorded metadata makes automatic processing simpler,
- PDB submission can be made more automatic with the right metadata,
- chemical crystallography can benefit from the work put into the Gold
standard.

Please register for the meeting by replying to this email (include your
name and affiliation).  It's free and fun.  More information can be found
at http://www.medsbio.org/meetings/HDRMX_22Aug20.html.

In my humble opinion, everyone with responsibility for a crystallographic
beamline anywhere in the world should be interested in this topic, though I
understand that the timing of the meeting will only let the most dedicated
scientists from the US attend.

I hope to see many of you on Saturday.


Andreas



-- 

Andreas Förster, Ph.D.
Application Scientist Crystallography, Area Sales Manager Asia & Pacific
Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email:
andreas.foers...@dectris.com
DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
www.dectris.com







[image: LinkedIn]






[image:
facebook] 
 


*Confidentiality Note: This message is intended only for the use of the
named recipient(s)*
*and may contain confidential and/or privileged information. If you are not
the intended*
*recipient, please contact the sender and delete the message. Any
unauthorized use of*
*the information contained in this message is prohibited.*



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Cell disruption

[Bernhard Lechtenberg]

Dear colleagues,

The CCP4BB community is amazing, as always. I received many comments by happy 
users of the Avestin Emulsiflex C3 (and C5); not so much on the Microfluidics 
LM20. Thanks for that, it will be a great help to decide which instrument to 
purchase.

Best,
Bernhard


From: CCP4 bulletin board  on behalf of Adam Middleton 

Reply to: Adam Middleton 
Date: Tuesday, 18 August 2020 at 2:56 pm
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] Cell disruption

Hi Bernhard,

The Department has an Avestin emusiflex here, and it is kept in the cold room. 
Works great as long as your cells are properly resuspended and in a big enough 
volume. Highly recommended.

Adam



On Sun, Aug 16, 2020 at 4:48 PM Pascal Egea 
<4aa44fc90f38-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Dear Bernhard ,
I would recommend the emulsified from Avestin. It is great . Depending on your 
budget you can ask for stainless  steel (probe  to slow tear ) or ceramic 
(longer lasting but a bit more expensive).
We have the ceramic but I have worked with the stainless steel one and it is 
really good with E. coli cells. Not the best for
Yeast despite pressurizing more. Yeast are better dealt with bead beaters or 
cryo-mill grinders.
3 passes are usually sufficient to process up to 250 ml of extract in a decent 
time (15-20) minutes .

We operate ours at room temperature just cool the serpentine tubing coming out 
of the chamber in ice . There is an option to add a cooling plate but we have 
never considered it. Overheating comes from overpressurizing but for E Coli at 
15000 psi max  3 passes will do the trick without overhea tu bf the sample. I 
have processEs successfully many membrane proteins And protein complexes with 
it.

I have never seen one in a cold room to be honest but it should be fine 
although I don’t think it would be necessary . I would Ask avestin about that .
Maintenance and cleaning is simple . Once in a while I will replace the seal, 
it s not very difficult to do. The whole assembly is metal so you can sterilize 
the whole thing After complete disassembly in extreme cases . This is a bit 
more involved but not overwhelming.
The people at Avestin are super nice and responsive ( Canadians) so they will 
guide you if necessary . And we have had their engineers show up sometimes to 
just check the instrument for free . I have had this one for 10 years in my lab 
now. And before that was using one for 7 years during my post doc.  I would not 
lyse bacteria by any other method now.

I hope this helps.
All the best.
Pascal

On Sat, Aug 15, 2020 at 9:08 PM Bernhard Lechtenberg 
mailto:lechtenber...@wehi.edu.au>> wrote:
Dear colleagues,

We are currently looking to purchase a cell disruptor/homogeniser mainly for 
routinely processing a few 100 mls of E. coli suspensions. With the current 
COVID-19 restrictions it is very difficult for us to test any equipment. I thus 
hope that some of you can share their experiences with the different models. I 
found a similar thread on the CCP4BB from 2013 but wondered if anybody had had 
some more up to date information.

We are mainly looking at the Avestin Emulsiflex C3 homogeniser and the 
Microfluidics LM20 Microfluidizer. In particular we are interested to know more 
about ease of use, maintenance, reliability and if anybody operates these in a 
cold room (4°C).

Thanks in advance,

Bernhard


--
Bernhard C. Lechtenberg, Ph.D.
Laboratory Head
Ubiquitin Signalling Division
The Walter and Eliza Hall Institute
1G Royal 
Parade
Parkville VIC 
3052
Australia
Phone: +61 3 9345 2217
Email: lechtenber...@wehi.edu.au


___

The information in this email is confidential and intended solely for the 
addressee.
You must not disclose, forward, print or use it without the permission of the 
sender.

The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the 
Kulin
Nation as the traditional owners of the land where our campuses are located and
the continuing connection to country and community.
___



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
--
Pascal F. Egea, PhD
Associate Project Scientist
UCLA, David Geffen School of Medicine
Department of Biological Chemistry
Boyer Hall room 356
611 Charles E Young Drive East
Los Angeles CA 90095
office (310)-983-3515
lab  (310)-983-3516
email pegea at mednet.ucla.edu