[ccp4bb] DelsaMax software

[Boniecki, Michal]

Hello,


I am looking for obsolete software from Beckman called DelsaMax. It controls 
their particle sizer DelsaMax which is also obsolete. Software used to be 
license free. However, Beckman does not store it for download anymore. If 
anyone has a copy of it please reach out.

Thank You for your help,
_
Michal T. Boniecki, Ph.D.
Professional Affiliate Department of BMI
Manager Protein Characterization and Crystallization Facility 
University of Saskatchewan
107 Wiggins Rd HLTH 3D30.11
Saskatoon, SK S7N 5E5
Canada
tel. (306) 966-2977



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Re: [ccp4bb] polarizer

[Boniecki, Michal]

You need to have crystal between polarizing plates. If you use only one on the 
top (close to your eye) and rotate filter you will “filter/polarize” all the 
light coming to your eye. What you need to buy is polarizing filter sheet 
(linear) which you place under your crystal and another one (the one that you 
submitted link) on the microscope (check size as you will have to secure it in 
order to rotate filter) The linear sheets can also be bought on amazon.

Michal

On Aug 16, 2020, at 09:47, V Nagarajan  wrote:


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Hi, place a linear polarizer below the tray and one above it, rotating the top 
one until you get the desired view.

V. Nagarajan

JANSi


On 8/16/2020 8:26 AM, Diana Tomchick wrote:
It's my understanding that you have two polarizers on your 
polarizer-microscope--one in the base, and the one that attaches to the 
magnifying lens. When you rotate the one on the lens so that it is 90 degrees 
to the one in the base, no (or very little) light should pass through to your 
eyes, unless there is a crystal that plane polarizes the light at an angle that 
differs from the two on the microscope.

What you have is just one polarizing lens. Not sure how that would work, even 
if it is a circular polarizer.

Diana

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

From: CCP4 bulletin board  
on behalf of Matthias Zeug 
Sent: Sunday, August 16, 2020 9:05 AM
To: CCP4BB@JISCMAIL.AC.UK 

Subject: [ccp4bb] polarizer


EXTERNAL MAIL

Hi all,



The polarizer-microscope in our facility is not working properly, and I have to 
check my plates using a standard stereo-microscope. As a workaround, I thought 
about buying one at Amazon, placing it on top of the plates and rotating it to 
still test for birefringence.



The product is linked below. Does anyone have some experience with this kind of 
"homemade" system? And also (this might be a stupid question), does the product 
even work? As far as I know, the polarizers in the microscopes are linear 
polarizers, whereas the product linked below is a circular polarizer. I would 
also be happy for product recommendations (optimally available at the German 
Amazon).



Cheers



Matthias



https://www.amazon.de/dp/B00XNMXYBY/ref=cm_sw_r_cp_apa_i_5YsoFbFQXTBP9



___

Buchmann Institute of Molecular Life Sciences

Goethe University Frankfurt



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The future of medicine, today.



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Re: [ccp4bb] AW: [ccp4bb] Cold cabinet recommendations for AKTA Pure

[Boniecki, Michal]

Hi Alan,
I think new AKTA collector can be refrigerated. If this is not an option, 
consider putting only collector in the cold cabinet and cooling down the 
buffers. Also, you can put only columns and fraction collector inside cabinet 
which has side port for such use. Although you will have to use small diameter 
out tubing to avoid sample dilution when use like this. System live will be 
shorter inside cold cabinet due to increased humidity.

Michal

On Jun 21, 2020, at 11:10, Hughes, Jonathan 
 wrote:


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hi alan,
why do you want to put the thing in a cold cabinet? if you have protease 
problems, there are better ways to get rid of them than exploiting Q10. on the 
other hand, you'll increase viscosity and thus slow down the flow rates. also, 
the high humidity will reduce the lifetime of your Äkta dramatically (ours has 
been running almost continuously for 20 years at room temperature and is still 
going strong [thanks to tina!]). if you really to need to keep the sample at 4 
°C, you can put the buffer(s) on ice and cool the column with a jacket.
best
jon

Von: CCP4 bulletin board  Im Auftrag von Paula Salgado
Gesendet: Sonntag, 21. Juni 2020 18:50
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Cold cabinet recommendations for AKTA Pure

Hi Alan

We got one a few years back, from Fisher, although I think Thermo are the 
manufacturer's:

Refrigerator FRCR4504W Forma chromatography THERMO SCIENTIFIC FORMA FRCR4504W

They also arranged for a heavy metal shelf to hold the AKTA as the normal 
shelves won't hold the weight.

We only have one AKTA Pure there, with a fraction collector and the rest of the 
cabinet holds all the columns.

Hope that helps
Paula


===

Dr Paula S. Salgado
Senior Lecturer in Macromolecular Crystallography
Molecular Mechanisms of Life Lead
During the current COVID-19 crisis, my working hours tend to focus on early 
afternoons and evenings, so please bear with me if my reply is delayed and if I 
email outside your normal working hours. In any case, I do not expect a 
response outside those hours. Stay home if you're not involved in essential 
work, stay safe.


Newcastle University Biosciences Institute
Faculty of Medical Sciences
2nd Floor Cookson Building
Newcastle University
Newcastle upon Tyne, NE2 4HH, UK

Tel: +44 (0)191 208 7432
Email: paula.salg...@ncl.ac.uk



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Alan Cheung mailto:alan.che...@ucl.ac.uk>>
Sent: 21 June 2020 08:12
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] Cold cabinet recommendations for AKTA Pure


⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.
Dear All

Apologies for being wildly off topic, but we're trying to find a decent cold 
cabinet for 2x AKTA Pure + F9C + sample pump.  Does anyone have any 
recommendations, especially for sliding door models?

Cheers,
Alan



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Re: [ccp4bb] powdery residue on pucks?

[Boniecki, Michal]

I have noticed it with new pucks (most likely some kind  of grease from 
manufacturing) and later on when used in dry shipping dewars that has old 
absorbent coating. Also it might be that your dewar is not holding vacuum very 
well. Usually it can be cleaned with compressed air but have decided to change 
dewar anyway and problem disappeared.


Michal

On Feb 21, 2020, at 18:40, Diana Tomchick  
wrote:


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I believe my technician decided that it was due to the breakdown of the 
adsorbent foam in our oldish shipping dewar, as it stopped happening once we 
replaced that particular dewar.

But I would be open to other explanations.

Diana

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

On Feb 21, 2020, at 6:33 PM, Emilia C. Arturo (Emily) 
mailto:ecgart...@gmail.com>> wrote:


EXTERNAL MAIL

Hi All,

We have been noticing lately that our crystal pucks return from different 
beamlines coated with the same powdery material. For the record, we typically 
undo our pucks, clean the assemblies and dry out the pucks within a day of 
receiving the shipping dewar, but notice the same thing regardless of how long 
between receiving the dewar and disassembling the pucks. Have any of you 
experienced this sort of thing, or have suggestions of what might be the cause 
and/or the powdery material?

Regards,
Emily.

--
"Study as if you were going to live forever; live as if you were going to die 
tomorrow." - Maria Mitchell

"I'm not afraid of storms for I'm learning to sail my ship."  - Louisa May 
Alcott




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The future of medicine, today.



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[ccp4bb] 2019 PSFaM meeting

[Boniecki, Michal]

To ccp4 community,

Please distribute invitation to the 7th Annual Meeting in Protein 
Structure, Function and Malfunction (PSFaM) organized by College of 
Medicine, University of Saskatchewan. June 20-21, 2019, Saskatoon.

link:

http://cmcf.lightsource.ca/psfam/

registration is free.

Sincerely,

Michal Boniecki

-- 
Michal T. Boniecki, Ph.D.
University of Saskatchewan
Department of Biochemistry, Microbiology and Immunology
Manager Protein Characterization and Crystallization Facility
Health Sciences Building 3D40
107 Wiggins Rd.
Saskatoon, SK S7N 5E5
Canada
tel.(306)966-6307




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Re: [ccp4bb] Fishing crystals from volatile solvent as precipitant

[Boniecki, Michal]

In my case what simply worked is to put your solution with 40% glycerol on the 
side of the drop and wait for crystals to stop dancing. Fish them out swiping 
through the side were you have put your solution. Or I have used MPD as 
cryoprotectant and freeze them in cold room (4C) its amazing what cold air 
humidity can do for your drop. No problem with dancing crystals.

Michal Boniecki

On Aug 23, 2018, at 11:38, James Holton 
mailto:jmhol...@slac.stanford.edu>> wrote:


Ahh, yes, the "dancing crystals problem".  The good news is alcohols are really 
good cryoprotectants as well as excellent precipitants.  Shame their use has 
fallen out of favor over the years, but I guess as drop sizes got smaller the 
evaporation problems got worse and worse.

In my humble opinion, this is just an extreme case of a problem we all have 
already.  Evaporation during harvesting is an insidious issue that is hard to 
monitor.  It's not just alcohol, but water that evaporates, and some buffers 
are volatile too (like ammonium and acetate ions).  Volatile buffers mean the 
pH changes over time.  All this can easily lead to non-isomorphism between the 
first crystal you mount vs the last.  An excellent review is: 
https://dx.doi.org/10.1107%2FS1399004714012310

It has already been suggested that you surround your harvesting environment 
with a wet towel (aka Kimwipe) soaked with the well solution, and this is a 
good idea to try and keep the local humidity (or alcohol-idity?) up.  Another 
possibility is to make up 30-40 mL of your well solution, put that into a 50 mL 
conical tube and use one of those stone fish-tank aerators to bubble air or N2 
gas through the appropriate solution for generating just the right 
"atomosphere" that your crystals are used to (see attached photo).  You can 
then direct that gas through an additional length of hose in the general 
direction of your well before you crack it open.  The point is to keep your 
crystals unaware of the fact that they are about to be harvested for as long as 
possible.

In your case you have an excellent assay for when you have kept the harvesting 
environment properly controlled: the crystals will stop dancing.

There are some devices on the market now, such as the "HC1" from Arinax, or the 
"Watershed" from MiTeGen that are a much more sophisticated way to do this, but 
check with the vendor before filling it with alcohol.  Some seals don't like 
non-aqueous liquids.  I expect there may be a safety concern about generating 
large amounts of alcohol vapor, especially isopropanol.  You don't want to 
breathe that in.  Best to keep away from open flames and work in a 
well-ventilated area, like the hood.  Ethanol is less toxic but on a per-capita 
basis more dangerous.  At the very least, don't drive yourself home afterwards.

-James Holton
MAD Scientist


On 8/14/2018 1:58 PM, Thomas Krey wrote:
Dear crystallization experts,

We have 3D protein crystals grown from a microseed matrix screening vapor 
diffusion experiment in either

15% (v/v) Reagent alcohol
HEPES Na pH 7.5
0.2 M MgCl2

or in

27% Isopropanol
0.18 M MgCl2
90 mM HEPES Na pH 7.5
10% Glycerol

Upon opening the corresponding wells these crystals move quite a bit – 
presumably due to the volatility of the alcohols. Does anyone have a good 
suggestion to stabilize the swirling movements? Does anyone have experience, 
whether these conditions alone can serve as cryo-protectant (i.e., do we really 
have to fish, move into cryo solution and fish again)?
Any suggestion or input would be highly welcome.

Thank you very much in advance.

Thomas


Prof. Dr. Thomas Krey
Hannover Medical School
Institute of Virology
Structural Virology Group
Carl-Neuberg-Str. 1
D-30625 Hannover
phone: +49 (0) 511 - 532 4308
email: krey.tho...@mh-hannover.de




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