Re: [ccp4bb] ccp4 installation problem

[Jason Key]

Hi Robert,

On Fri, Sep 16, 2022 at 4:11 PM Kay Diederichs
 wrote:
> Your real problem seems to be the Qt installation; I think that the error 
> message
> qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though 
> it was found.
> This application failed to start because no Qt platform plugin could be 
> initialized. Reinstalling the application may fix this problem.
> prevents the graphics of the CCP4 programs from working properly.

This is my thinking too - the OS seems to be missing libxcb QT plugins.

You can get better debug info from QT by setting the QT_DEBUG_PLUGINS
variable ("export QT_DEBUG_PLUGINS=1" for bash or zsh, "setenv
QT_DEBUG_PLUGINS 1" for tcsh). Then when you launch the application
you should get a much more informative message. Perhaps too
informative.

Usually the error in this case is a missing xcb library or two,
something like libxcb-icccm.so.4  No such file or directory. You
should be able to add these with your package manager.

Best,
Jason

--
Jason Key, PhD
SBGrid Consortium, Harvard Medical School



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Re: [ccp4bb] ccp4 installation problem

[Robert Gampe]

Hi Kay



Thanks again and for more insight and feedback on the Qt installation.

Reply in blue text below.

Take care,



Rob



-Original Message-
From: Kay Diederichs 
Sent: Friday, September 16, 2022 4:11 PM
To: CCP4BB@JISCMAIL.AC.UK; Robert Gampe 
Subject: Re: ccp4 installation problem



ALERT! Outside Org



Hi Robert,



you are welcome.



It seems that you own (rgampe.rgampe) the directory /software/ccp4-8.0 . You 
should revert the ownerships in /software/ccp4-8.0 from root.root with



sudo chown -R rgampe.rgampe /software/ccp4-8.0



so that in the future you don't need sudo for updates.



The above fix is along the lines Andrey provided on Aug 30.

As for your installation.

ccp4um switches to admin mode if it finds any single file inside ccp4 that does 
not belong to you. In the admin mode, it check if all files belong to the same 
user as the top ccp4-8.0 directory and changes ownership of all files that 
belong to different user. If ccp4 originally belonged to your account, not to 
root account, you can repair installation from command line using sudo chown -R 
: ccp4-8.0 arpwarp_8.0.



Your real problem seems to be the Qt installation; I think that the error 
message



qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it 
was found.

This application failed to start because no Qt platform plugin could be 
initialized. Reinstalling the application may fix this problem.



prevents the graphics of the CCP4 programs from working properly.



I have no idea, though, if your Qt is too new or too old or somehow corrupted. 
I've never heard of POP_OS or the like so maybe it's just not compatible with 
CCP4.



I will definitely have to learn more on what the Qt is and how to fix or update

GOOGLE: Qt Creator is a cross-platform integrated development environment (IDE) 
built for the maximum developer experience..



The POP_OS! system 76 is built upon Ubuntu and comes with a ready to use 
desktop.

https://pop.system76.com/

Pop!_OS is an operating system for STEM and creative professionals who use 
their computer as a tool to discover and create.



HTH,

Kay



This email originated from outside the organization. Do not click links or open 
attachments unless you recognize the sender and know the content is safe.



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Re: [ccp4bb] ccp4 installation problem

[Kay Diederichs]

Hi Robert,

you are welcome.

It seems that you own (rgampe.rgampe) the directory /software/ccp4-8.0 . You 
should revert the ownerships in /software/ccp4-8.0 from root.root with

sudo chown -R rgampe.rgampe /software/ccp4-8.0

so that in the future you don't need sudo for updates.

Your real problem seems to be the Qt installation; I think that the error 
message 

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it 
was found.
This application failed to start because no Qt platform plugin could be 
initialized. Reinstalling the application may fix this problem.

prevents the graphics of the CCP4 programs from working properly.

I have no idea, though, if your Qt is too new or too old or somehow corrupted. 
I've never heard of POP_OS or the like so maybe it's just not compatible with 
CCP4.

HTH,
Kay



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Re: [ccp4bb] ccp4 installation problem

[Kay Diederichs]

Hi Robert,

hmm, more ideas:

a) check if CCP4 directory is writable, and who the owner is: 
mount | grep software
sudo touch /software/ccp4-8.0/deleteme
ls -ld /software/ccp4-8.0 
ls -l /software/ccp4-8.0/deleteme
sudo rm  /software/ccp4-8.0/deleteme

b) try 
sudo su
ccp4um 

c) try
sudo -i
ccp4um

d) also try "ccp4um -auto" - I think this does not require the graphics

e) try
which ccp4um

HTH,
Kay



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Re: [ccp4bb] ccp4 installation problem

[Kay Diederichs]

Hi Robert,

two points -

a) before you tried to update, did you
source /where/ever/ccp4/bin/ccp4.setup-sh
? The above applies to bash; for (t)csh you need to 
source /where/ever/ccp4/bin/ccp4.setup-csh

That sets the PATH environment variable such that you don't always have to 
specify the absolute path when you want to run a CCP4 program, AND it also 
makes sure that CCP4 programs such as ccp4um find other CCP4 binaries that they 
need. Without that "sourcing" I can imagine that an update is not possible.

b) since ccp4i seems to start: did you tick the box(es) that specify the 
available update(s)? You have to do this before clicking "Proceed".

HTH,
Kay



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Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

[Dom Bellini - MRC LMB]

Hi Oleksiy,

If the Akta Start is just for loading affinity columns (without air 
sensor or software), why not to get a Cyvita peristaltic pump 
 
for £3k rather than £9k?


They are really good work horses in my experience; they are also 
overpriced but still much cheaper than the rest?


BW,

D



On 16/09/2022 15:48, Kovtun, Oleksiy wrote:

Hi Eike,

Instead of AKTA Pure I purchased a combo of AKTA Go (€24k with air 
sensor) and AKta start (€9k with frac collector). It provides two 
parallel workstations with AKTA start handling the dirty job of 
loading lysates onto affinity cartridges and the GO doing clean SEC 
stages. For multiple proteins isolation, this combo beats AKTA Pure 
flat out for half price. Note that AKTA Start can’t be equipped with 
an air sensor, and sample loading need to be done by time control. 
However, we didn’t find it to be an issue.
Also, AKTA Start needs a separate version of Uncocrn suite for an 
extra €1k. So we skipped that and control the system via the built-in 
touchscreen.


As for the longevity, we need to see. Six months into active operation 
went smooth—the only malfunction was the Windows update breaking 
network card drivers.


Best,

Oleksiy


Dr Oleksiy Kovtun
Max-Planck Research Group Leader
Molecular Mechanisms of Membrane Trafficking
Max-Planck-Institute for Multidisciplinary Sciences
City-Campus, Hermann-Rein-Str. 3, 37075 Göttingen
Germany
Email: oleksiy.kov...@mpinat.mpg.de 
https://www.mpinat.mpg.de/kovtun
Phone:+49-551-3899-410


On 16. Sep 2022, at 09:39, Schulz, Eike-Christian 
 wrote:


Dear all,
I am considering to purchase a chromatography system for routine 
protein purification. The device is supposed to be used in a 
multi-user environment, hence ease of use, ease of training and ease 
of maintenance is important. I am rather looking for a robust system 
people like to use than a system that comes with many bells and 
whistles that no one dares to touch.


  * Is there any particularly _/bad/_ experience with either system?

  * Is there any specific advantage of one system over the other?

  * Does anyone have experience about (long-term) stability /
performance of the systems?

  * Do you think the higher price-point of the Aekta systems is
justified?

With best regards,
Eike



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--
Dom Bellini, Xray Crystallography Facility (1S205)
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH
Phone 01223 267839



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Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

[Xiao, Chuan]

We have a AKTA start and a AKTA Pure. Don’t like the AKTA start at all. The 
software is buggy (command not performed correctly as it should do) but the 
touch screen is OK. By now I have changed two failed/leaking valves and the UV 
detector for the AKTA start with very light usage. AKTA start uses a 
peristaltic pump that cannot reach high pressure. The gradient is controlled by 
timing between two valves since both buffers are sucked instead of pumped out 
of A and B before mixer. I will not suggest anyone to buy AKTA start. Not a 
very good system. The company will not provide any service for you. You need to 
do all the fixing yourself. If you take out the tubing (as suggested by the 
manual) for the peristaltic pump when not using, the solution will be siphoned 
out to waste line. Poorly designed. Watch those solenoid vales, they are leaky. 
AKTA Pure is a good system but expensive.

Agree with many of you. After changing to Cytiva, the customer service is 
horrible and the whole company become a money sucker. Once I was asking some 
suggestion about configuration changed for AKTA Pure. Two months passed without 
response then asking me how satisfied I was for the service. I gave zero. Then 
they contacted me and give me $3000 quote for remote consulting. I ended up 
just reimaging back the hard drive to recover the setting.

I am still maintaining an very old AKTA FPLC (dark grey machine) using parts 
from eBay. It is still a very good system.

Best,

[cid:image001.jpg@01D73AFE.96DB0800]

From: CCP4 bulletin board  On Behalf Of Kovtun, Oleksiy
Sent: Friday, September 16, 2022 8:48 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Hi Eike,

Instead of AKTA Pure I purchased a combo of AKTA Go (€24k with air sensor) and 
AKta start (€9k with frac collector). It provides two parallel workstations 
with AKTA start handling the dirty job of loading lysates onto affinity 
cartridges and the GO doing clean SEC stages. For multiple proteins isolation, 
this combo beats AKTA Pure flat out for half price. Note that AKTA Start can’t 
be equipped with an air sensor, and sample loading need to be done by time 
control. However, we didn’t find it to be an issue.
Also, AKTA Start needs a separate version of Uncocrn suite for an extra €1k. So 
we skipped that and control the system via the built-in touchscreen.

As for the longevity, we need to see. Six months into active operation went 
smooth—the only malfunction was the Windows update breaking network card 
drivers.

Best,

Oleksiy


Dr Oleksiy Kovtun
Max-Planck Research Group Leader
Molecular Mechanisms of Membrane Trafficking
Max-Planck-Institute for Multidisciplinary Sciences
City-Campus, Hermann-Rein-Str. 3, 37075 Göttingen
Germany
Email: oleksiy.kov...@mpinat.mpg.de
https://www.mpinat.mpg.de/kovtun
Phone:+49-551-3899-410


On 16. Sep 2022, at 09:39, Schulz, Eike-Christian 
mailto:eike.sch...@mpsd.mpg.de>> wrote:

Dear all,

I am considering to purchase a chromatography system for routine protein 
purification. The device is supposed to be used in a multi-user environment, 
hence ease of use, ease of training and ease of maintenance is important. I am 
rather looking for a robust system people like to use than a system that comes 
with many bells and whistles that no one dares to touch.


  *   Is there any particularly _bad_ experience with either system?


  *   Is there any specific advantage of one system over the other?


  *   Does anyone have experience about (long-term) stability / performance of 
the systems?


  *   Do you think the higher price-point of the Aekta systems is justified?


With best regards,

Eike





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Re: [ccp4bb] ccp4 installation problem

[Kay Diederichs]

Hi Robert,

Concerning PROBLEM 1: have you tried
sudo ccp4um
or 
sudo ccp4i
?

HTH,
Kay

P.S. didn't find Andrey Lebedev's reply on August 30 that you refer to

On Fri, 16 Sep 2022 14:11:34 +, Robert Gampe  wrote:

>Hello Marcin Pedro and the CCP4 community,
>
>
>
>PROBLEM 1: I have the same still unresolved problem when trying to install the 
>recent CCP-8.0 updates on a POP_OS!/Ubuntu box.
>
>
>
>The updater will not accept my SUDO password and returns to the linux prompt.
>
>
>
>Using sudo -l reports I am a sudo user for ALL commands and my sudo password 
>has worked for other sudo required actions.
>
>
>
>I also tried using sudo and root to run CCP4-8.0, but that too failed.
>
>
>
>Without the updates installed, the acedrg program does NOT start up for me, 
>but other programs, eg REFMAC, seem to start up but I have not run since I 
>need acedrg cif files.
>
>
>
>See Andrey Lebedev reply on August 30 in reply to my original post and CCP4's 
>use of ccp4um and pkexec.
>



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Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

[Kovtun, Oleksiy]

Hi Eike,

Instead of AKTA Pure I purchased a combo of AKTA Go (€24k with air sensor) and 
AKta start (€9k with frac collector). It provides two parallel workstations 
with AKTA start handling the dirty job of loading lysates onto affinity 
cartridges and the GO doing clean SEC stages. For multiple proteins isolation, 
this combo beats AKTA Pure flat out for half price. Note that AKTA Start can’t 
be equipped with an air sensor, and sample loading need to be done by time 
control. However, we didn’t find it to be an issue.
Also, AKTA Start needs a separate version of Uncocrn suite for an extra €1k. So 
we skipped that and control the system via the built-in touchscreen.

As for the longevity, we need to see. Six months into active operation went 
smooth—the only malfunction was the Windows update breaking network card 
drivers.

Best,

Oleksiy


Dr Oleksiy Kovtun
Max-Planck Research Group Leader
Molecular Mechanisms of Membrane Trafficking
Max-Planck-Institute for Multidisciplinary Sciences
City-Campus, Hermann-Rein-Str. 3, 37075 Göttingen
Germany
Email: oleksiy.kov...@mpinat.mpg.de
https://www.mpinat.mpg.de/kovtun
Phone:+49-551-3899-410


On 16. Sep 2022, at 09:39, Schulz, Eike-Christian 
mailto:eike.sch...@mpsd.mpg.de>> wrote:

Dear all,

I am considering to purchase a chromatography system for routine protein 
purification. The device is supposed to be used in a multi-user environment, 
hence ease of use, ease of training and ease of maintenance is important. I am 
rather looking for a robust system people like to use than a system that comes 
with many bells and whistles that no one dares to touch.


  *   Is there any particularly _bad_ experience with either system?



  *   Is there any specific advantage of one system over the other?



  *   Does anyone have experience about (long-term) stability / performance of 
the systems?



  *   Do you think the higher price-point of the Aekta systems is justified?



With best regards,

Eike






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Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

[Oganesyan, Vaheh]

Hi Stephan,

You’re mostly correct, however, gradients made on instrument with one pump are 
less reliable.

Thank you.

Vaheh

From: CCP4 bulletin board  On Behalf Of Stephan Rempel
Sent: Friday, September 16, 2022 7:38 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Hi,

I had some experience for about 2-3 years with the BioRad systems before I 
moved on and they worked just fine like the AKTAs. At the time, the price point 
was a huge plus over the AKTA Pure and in my opinion for protein purification 
there was no reason to fork out the money for an AKTA Pure because you would 
never use the two pumps anyway. We had the NGC quest with multi wavelength 
detection for protein labeling, which worked fine. I liked the NGCs a lot, they 
were reliable, and I would be happy to get one any time.

In the meantime, Cytiva has released the AKTA Go, which is a scaled down 
version of the Pure with only one pump. And I would give this one a thought if 
you only want to purify proteins.

It is a great (!) little system for protein purification and the price is very 
reasonable in my opinion. Our version with the additional inlet sample valve 
(allows for scouting over night), air detector (very convenient when loading 
large lysate volumes on IMAC columns), and column valve was in the region of 
20-25k. You also have the choice between a simpler fraction collector and the 
one from the AKTA Pure. The only caveat is that they only offer a fixed 
wavelength detector. After two years, we had not a single fault (they have been 
on the market for 2.5-3 years). I very much like the Unicorn software.

I hope this helps,
Stephan.





Stephan Rempel, PhD
Senior Scientist, FoRx Therapeutics AG

Lichtstrasse 35, WSJ-350.3.10
4056 Basel, Switzerland
stephan.rem...@forxtherapeutics.com
www.forxtherapeutics.com

  [cid:image001.png@01D8C9B6.8D851690]

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Marko Hyvonen
Sent: Friday, 16 September 2022 13:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Hello Eike,

A couple of comments on the AKTA Pures (while I have not experience with the 
BioRad systems).

We have a couple of AKTA Pures and we (and another lab close to us) had a 
catastrophic failure of the 3-wavelength detector “block”. Price tag for the 
replacement part (apparently a black box  with nothing accessible for repair – 
happy to hear if this was misinformation!) was over £12,000. Someone commented 
that they had even more eye-watering price tag for an upgrade to triple 
wavelength. We switched to a single wavelength detector at £5k and I will get 
these from now on only.

I really dislike the database system used in new Unicorn for storing data etc: 
another black box. I much prefer the way older Unicorns worked, but maybe that 
is just me being old and grumpy and stuck in my ways. That reminds also that we 
tend to source computers separately. Much better systems available for less 
money and with MUCH smaller footprint.

The price tags on Pures (like almost everything else with Cytiva) are in my 
opinion a reflection of the market dominance. I wish there was more competition 
(bring back Biocad!). Service contracts with Cytiva are also ridiculously 
expensive – we have, luckily,  a very knowledgeable company here that does all 
the servicing and maintenance, at less than half the price.

Having just complained, I do like AKTA Pures and there is much to like in them. 
Time will tell if these will be as robust as the original “grey” AKTA 
purifiers. Several of ours Purifiers still running perfectly after over 15 
years. As long as the detector works and flow is accurate, the proteins elute 
just the same from the columns. However, once you have even one of the shinier 
systems around, those old ones start collecting dust very soon.

Hth, Marko


Marko Hyvonen
Department of Biochemistry
University of Cambridge
https://hyvonen.bioc.cam.ac.uk
@HyvonenGroup
mh...@cam.ac.uk




From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Schulz, Eike-Christian
Sent: 16 September 2022 08:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Dear all,

I am considering to purchase a chromatography system for routine protein 
purification. The device is supposed to be used in a multi-user environment, 
hence ease of use, ease of training and ease of maintenance is important. I am 
rather looking for a robust system people like to use than a system that comes 
with many bells and whistles that no one dares to touch.


·   Is there any particularly _bad_ experience with either system?


·   Is there any specific 

Re: [ccp4bb] Problem downloading models maps in from PDBe in Coot

[Paul Emsley]

Hopefully 0.9.8.4 should fix that.

Paul.

On 16/09/2022 13:54, Jan Dohnalek wrote:

This has been quite variable in (several?) last versions of Coot.
I have some three latest versions available and when one does not work 
I start another one. Sad but true.


Jan


On Thu, Sep 15, 2022 at 11:39 AM Robbie Joosten 
 wrote:


Not sure if this is a PDBe bug or a Coot bug (or a combination
thereof)...

I'm using the latest WinCoot in CCP4 8.0. When I try to 'Fetch PDB
using Accession Code', I do not get any models so I guess the
target URL is wrong.
When I use Fetch PDB & Map using EDS, I sometimes get a map (1cbs,
3fvl), sometimes I don't (1ctn, 1lee and many more). All of these
maps used to be available and PDB-REDO versions of all these
entries exist. Does anyone know what is going on?

Cheers,
Robbie



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--
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

[Mark J. van Raaij]

Hi Eike,
we bought a Biorad back in 2005 or so, an Akta Purifier in 2011 and recently an 
Akta Go (2020). All work(ed) well, the latter two are in use. Don't know about 
the Biorad, it's in Santiago de Compostela. Both the Biorad and Purifier have 
been used a lot, the Akta Go not that much so far. Just because the programs 
are set up for the Purifier I think, not because people like it more per se.
For "normal" protein purifications all are fine. We've had breakdowns in both 
the Biorad and Purifier, which could be fixed with not too much spending.
I'm not sure about this kind of equipment in a multi-user environment, best to 
keep it in one group I think, otherwise it's difficult people feel responsible 
enough to use them properly. This is even more important for columns, they are 
easily ruined if just once an incorrectly prepared sample is run through.
Price: we got very good deals on the two Akta systems we bought, not more 
expensive than a comparable Biorad. But Cytiva service/repair is very expensive.
Good luck,
Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/
https://namedrop.io/markvanraaij

> On 16 Sep 2022, at 09:39, Schulz, Eike-Christian  
> wrote:
> 
> Dear all, 
>  
> I am considering to purchase a chromatography system for routine protein 
> purification. The device is supposed to be used in a multi-user environment, 
> hence ease of use, ease of training and ease of maintenance is important. I 
> am rather looking for a robust system people like to use than a system that 
> comes with many bells and whistles that no one dares to touch.
>  
> Is there any particularly _bad_ experience with either system?
>  
> Is there any specific advantage of one system over the other?
>  
> Does anyone have experience about (long-term) stability / performance of the 
> systems?
>  
> Do you think the higher price-point of the Aekta systems is justified?
>  
>  
> With best regards, 
>  
> Eike
>  
>  
>  
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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[ccp4bb] Open Postdoc position: 'Imaging at extreme intensities using XFEL' (Hamburg)

[CUI Career]

Dear All,

We'd like to advertise an open Postdoc position in the project "Imaging 
at extreme intensities using XFEL"  with Dr. Saša Bajt within our 
Cluster of Excellence 'CUI: Advanced Imaging of Matter' at the 
Universität Hamburg, Germany.


Please see here for further information:
https://www.uni-hamburg.de/stellenangebote/ausschreibung.html?jobID=23e41766b09a3d86af466f76976b620d856ae021

Best regards,

Jutta Voigtmann


Jutta Voigtmann
CUI Career Service

Universität Hamburg
CUI: Advanced Imaging of Matter
Luruper Chaussee 149, 22761 Hamburg
Bldg. 610, Rm. 2010
Phone: +49 40 42838-2442



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Re: [ccp4bb] Problem downloading models maps in from PDBe in Coot

[Jan Dohnalek]

This has been quite variable in (several?) last versions of Coot.
I have some three latest versions available and when one does not work I
start another one. Sad but true.

Jan


On Thu, Sep 15, 2022 at 11:39 AM Robbie Joosten 
wrote:

> Not sure if this is a PDBe bug or a Coot bug (or a combination thereof)...
>
> I'm using the latest WinCoot in CCP4 8.0. When I try to 'Fetch PDB using
> Accession Code', I do not get any models so I guess the target URL is
> wrong.
> When I use Fetch PDB & Map using EDS, I sometimes get a map (1cbs, 3fvl),
> sometimes I don't (1ctn, 1lee and many more). All of these maps used to be
> available and PDB-REDO versions of all these entries exist. Does anyone
> know what is going on?
>
> Cheers,
> Robbie
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
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>


-- 
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

[Stephan Rempel]

Hi,

I had some experience for about 2-3 years with the BioRad systems before I 
moved on and they worked just fine like the AKTAs. At the time, the price point 
was a huge plus over the AKTA Pure and in my opinion for protein purification 
there was no reason to fork out the money for an AKTA Pure because you would 
never use the two pumps anyway. We had the NGC quest with multi wavelength 
detection for protein labeling, which worked fine. I liked the NGCs a lot, they 
were reliable, and I would be happy to get one any time.

In the meantime, Cytiva has released the AKTA Go, which is a scaled down 
version of the Pure with only one pump. And I would give this one a thought if 
you only want to purify proteins.

It is a great (!) little system for protein purification and the price is very 
reasonable in my opinion. Our version with the additional inlet sample valve 
(allows for scouting over night), air detector (very convenient when loading 
large lysate volumes on IMAC columns), and column valve was in the region of 
20-25k. You also have the choice between a simpler fraction collector and the 
one from the AKTA Pure. The only caveat is that they only offer a fixed 
wavelength detector. After two years, we had not a single fault (they have been 
on the market for 2.5-3 years). I very much like the Unicorn software.

I hope this helps,
Stephan.





Stephan Rempel, PhD
Senior Scientist, FoRx Therapeutics AG

Lichtstrasse 35, WSJ-350.3.10
4056 Basel, Switzerland
stephan.rem...@forxtherapeutics.com
www.forxtherapeutics.com

  [cid:image001.png@01D8C9D1.8E327950]

From: CCP4 bulletin board  On Behalf Of Marko Hyvonen
Sent: Friday, 16 September 2022 13:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Hello Eike,

A couple of comments on the AKTA Pures (while I have not experience with the 
BioRad systems).

We have a couple of AKTA Pures and we (and another lab close to us) had a 
catastrophic failure of the 3-wavelength detector “block”. Price tag for the 
replacement part (apparently a black box  with nothing accessible for repair – 
happy to hear if this was misinformation!) was over £12,000. Someone commented 
that they had even more eye-watering price tag for an upgrade to triple 
wavelength. We switched to a single wavelength detector at £5k and I will get 
these from now on only.

I really dislike the database system used in new Unicorn for storing data etc: 
another black box. I much prefer the way older Unicorns worked, but maybe that 
is just me being old and grumpy and stuck in my ways. That reminds also that we 
tend to source computers separately. Much better systems available for less 
money and with MUCH smaller footprint.

The price tags on Pures (like almost everything else with Cytiva) are in my 
opinion a reflection of the market dominance. I wish there was more competition 
(bring back Biocad!). Service contracts with Cytiva are also ridiculously 
expensive – we have, luckily,  a very knowledgeable company here that does all 
the servicing and maintenance, at less than half the price.

Having just complained, I do like AKTA Pures and there is much to like in them. 
Time will tell if these will be as robust as the original “grey” AKTA 
purifiers. Several of ours Purifiers still running perfectly after over 15 
years. As long as the detector works and flow is accurate, the proteins elute 
just the same from the columns. However, once you have even one of the shinier 
systems around, those old ones start collecting dust very soon.

Hth, Marko


Marko Hyvonen
Department of Biochemistry
University of Cambridge
https://hyvonen.bioc.cam.ac.uk
@HyvonenGroup
mh...@cam.ac.uk




From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Schulz, Eike-Christian
Sent: 16 September 2022 08:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Dear all,

I am considering to purchase a chromatography system for routine protein 
purification. The device is supposed to be used in a multi-user environment, 
hence ease of use, ease of training and ease of maintenance is important. I am 
rather looking for a robust system people like to use than a system that comes 
with many bells and whistles that no one dares to touch.


· Is there any particularly _bad_ experience with either system?


· Is there any specific advantage of one system over the other?


· Does anyone have experience about (long-term) stability / performance 
of the systems?


· Do you think the higher price-point of the Aekta systems is justified?


With best regards,

Eike






To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

[Marko Hyvonen]

Hello Eike,

A couple of comments on the AKTA Pures (while I have not experience with the 
BioRad systems).

We have a couple of AKTA Pures and we (and another lab close to us) had a 
catastrophic failure of the 3-wavelength detector "block". Price tag for the 
replacement part (apparently a black box  with nothing accessible for repair - 
happy to hear if this was misinformation!) was over £12,000. Someone commented 
that they had even more eye-watering price tag for an upgrade to triple 
wavelength. We switched to a single wavelength detector at £5k and I will get 
these from now on only.

I really dislike the database system used in new Unicorn for storing data etc: 
another black box. I much prefer the way older Unicorns worked, but maybe that 
is just me being old and grumpy and stuck in my ways. That reminds also that we 
tend to source computers separately. Much better systems available for less 
money and with MUCH smaller footprint.

The price tags on Pures (like almost everything else with Cytiva) are in my 
opinion a reflection of the market dominance. I wish there was more competition 
(bring back Biocad!). Service contracts with Cytiva are also ridiculously 
expensive - we have, luckily,  a very knowledgeable company here that does all 
the servicing and maintenance, at less than half the price.

Having just complained, I do like AKTA Pures and there is much to like in them. 
Time will tell if these will be as robust as the original "grey" AKTA 
purifiers. Several of ours Purifiers still running perfectly after over 15 
years. As long as the detector works and flow is accurate, the proteins elute 
just the same from the columns. However, once you have even one of the shinier 
systems around, those old ones start collecting dust very soon.

Hth, Marko


Marko Hyvonen
Department of Biochemistry
University of Cambridge
https://hyvonen.bioc.cam.ac.uk
@HyvonenGroup
mh...@cam.ac.uk




From: CCP4 bulletin board  On Behalf Of Schulz, 
Eike-Christian
Sent: 16 September 2022 08:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Dear all,

I am considering to purchase a chromatography system for routine protein 
purification. The device is supposed to be used in a multi-user environment, 
hence ease of use, ease of training and ease of maintenance is important. I am 
rather looking for a robust system people like to use than a system that comes 
with many bells and whistles that no one dares to touch.


·   Is there any particularly _bad_ experience with either system?


·   Is there any specific advantage of one system over the other?


·   Does anyone have experience about (long-term) stability / performance 
of the systems?


·   Do you think the higher price-point of the Aekta systems is justified?


With best regards,

Eike






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[ccp4bb] CLOSING SOON: DLS/CCP4 data analysis workshop 2022

[David Waterman]

Hi all,

The application period for the DLS/CCP4 workshop closes 17:00 (UK time) on
Tuesday the 20th. Don't leave it to the last minute to apply! :)

Cheers
-- David


On Tue, 13 Sept 2022 at 12:02, David Waterman  wrote:

> Hi folks,
>
> A reminder: there is one week left to apply for this year's DLS/CCP4
> workshop. Please see below for details.
>
> Best wishes
> -- David
>
>
> On Tue, 6 Sept 2022 at 13:31, David Waterman  wrote:
>
>> We are pleased to announce that the 9th joint Diamond-CCP4 Workshop on MX
>> data collection and structure solution is now open for applications.
>> Bringing together leading experts in the field of MX to teach best practice
>> in data collection and analysis, this course is aimed at PhD students,
>> postdocs and early career scientists who have a focus on structural biology.
>>
>> After the last two remote events limited to online-only using Zoom, we
>> are very happy to report that we intend to go back to an in-person workshop
>> this year! However, having learned from the online-only workshops, we will
>> keep two remote setup days prior to the on-site element, and we will make
>> use of a Slack workspace through the course.
>>
>> It is essential that applicants commit to attending the workshop in its
>> entirety. Please note below the workshop days and timings involved:
>>
>> - First online preparation day (before fishing crystals): Monday 17
>> October
>> - Second online preparation day (before data collection): Tuesday 22
>> November
>> - On-site: Monday 28 November to Tuesday 6 December
>> - Day off: Saturday 3 December
>>
>> There is no fee to attend this online workshop, however attendance will
>> be subject to an application process and a letter of support from the
>> attendee's supervisor will be required. Both the application form and
>> supervisor's letter of support will need to be submitted by 17:00 (UK time)
>> on 20 September 2022.
>>
>> Some prior experience of crystallography and data collection is expected,
>> and those who already have an interesting project (crystals and possibly
>> previously collected datasets) will be given priority in selection.
>>
>> - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2022/
>> - Apply at the Diamond website:
>> https://www.diamond.ac.uk/Home/Events/2022/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2022.html
>>
>> -- David (on behalf of the organisers)
>>
>>



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Re: [ccp4bb] PDBx-format utilities

[Jan Dohnalek]

We have our internal PDBCOP program that extracts all the info you need
when refining a structure, i.e. extremes of B values, of occupancies,
listing of all alternatives, all compounds found in the file and an option
to provide the largest differences between two versions of the same
structure, i.e. most of the time used to see "what really happened" during
the last refinement run.

Jan


On Thu, Sep 8, 2022 at 9:29 PM Paul Emsley 
wrote:

> A spectre is haunting structural biology - it is the spectre of the PDBx
> format.
>
> We at CCP4 are interested in providing tools that are equivalents of
> those that one might have trivially made with utilities such as grep or
> sed.
>
> For example:
>
>  delete the hydrogen atoms
>
>  extract the hydrogen atoms
>
>  extract the SD of MET
>
>  find the atoms with B-factors greater than 100.0
>
>
> So, what useful tool have you made can that works because it based on
> the PDB format - that (of course) doesn't work with PDBx?
>
>
> Thanks,
>
> Paul.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
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> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>


-- 
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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[ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

[Schulz, Eike-Christian]

Dear all,

I am considering to purchase a chromatography system for routine protein 
purification. The device is supposed to be used in a multi-user environment, 
hence ease of use, ease of training and ease of maintenance is important. I am 
rather looking for a robust system people like to use than a system that comes 
with many bells and whistles that no one dares to touch.


  *   Is there any particularly _bad_ experience with either system?


  *   Is there any specific advantage of one system over the other?


  *   Does anyone have experience about (long-term) stability / performance of 
the systems?


  *   Do you think the higher price-point of the Aekta systems is justified?


With best regards,

Eike






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