Re: [ccp4bb] Reg. ITC machine

[Christian Roth]

We had a PEAQ and a bit of bad luck. Broken Peltier, which means the
instrument can only be replaced by a new one. Happened in a neighbouring
University as well.
Currently we have a Nano ITC from TA, It works fine. The software is more
customizable. The syringe loading is not my favourite procedure. You need
to be very careful and on average you need a bit more lingad solution. But
apart from that, the results are good and comparable to the PEAQ.

Cheers
Christian

On Mon, Aug 21, 2023 at 12:44 PM Kelvin Lau <
5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk> wrote:

> The PEAQ even though a bit old is quite robust compared to the 200. I
> would definitely go with that. The cleaning system with the pumps is well
> built compared to the 200 and over years haven’t had any problems. Also the
> new needle adapter is great, not a single broken needle in 5 years compared
> to the 200 where I think in my PhD I replaced over 10.
>
> TA, only used their VP equivalent (2 mL volume) and the way it’s set up
> its not my favourite.
>
> PEAQ for sure.
>
>
> --
> Kelvin Lau
> Protein production and structure core facility - PTPSP
> EPFL SV PTECH PTPSP
> AI 2146 (Bâtiment AI)
> Station 19
> CH-1015 Lausanne
> Switzerland
> Email: kelvin@epfl.ch
> Phone (office) : +41 21 69 30267
> Phone (everywhere else) : +41 21 69 34494
>
>
>
> On 21 Aug 2023, at 12:00, Sebastiano Pasqualato <
> sebastiano.pasqual...@gmail.com> wrote:
>
> Hello Sivaraman,
> I completely second Matthew’s message, having had the same experience he
> had, in two different workplaces and with two different Malvern PEAQ-ITC
> instruments.
> I have one anecdotal, and not direct, unpleasant feedback from TA
> instrument users.
> Ciao,
> S
>
>
> On 9 Aug 2023, at 18:05, Matthew Whitley <
> a8ed4e9d4a1a-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hello Sivaraman,
>
> We have a Malvern MicroCal PEAQ-ITC system in our lab that is used
> regularly.  In general, we are pleased with the machine.  We have
> experienced no major problems with the instrument, the data quality is
> good, and replicate measurements yield very similar results.  I have never
> used the Affinity ITC from TA Instruments, so I cannot comment on that
> system.
>
> Matthew
>
> 
>
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[ccp4bb] Cloud workshop IGBMC, Illkirch, France

[Maria Fando - STFC UKRI]

WORKSHOP


CCP4 Cloud for structure solution



Tuesday 26 September 2023
Auditorium, IGBMC


Maria Fando and Eugene Krissinel

CCP4, UKRI-STFC, Rutherford Appleton Laboratory, Didcot, United Kingdom



The workshop will begin at 10:30 am with a lecture overview of the development 
of structural solution projects using CCP4 Cloud (IGBMC Auditorium) and a 
hands-on session (2:00 pm) where participants can learn about CCP4 Cloud 
through tutorials or develop their own structural solution projects (E1031 CBI)



Free attendance but mandatory registration

Abstract here
Registration link




Hosted by Bulat 
FATKHULLIN


View on IGBMC 
website




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[ccp4bb] Cloud workshop IGBMC, Illkirch, France

[Maria Fando - STFC UKRI]

WORKSHOP


CCP4 Cloud for structure solution




Tuesday 26 September 2023
Auditorium, IGBMC


Maria Fando and Eugene Krissinel

CCP4, UKRI-STFC, Rutherford Appleton Laboratory, Didcot, United Kingdom



The workshop will begin at 10:30 am with a lecture overview of the development 
of structural solution projects using CCP4 Cloud (IGBMC Auditorium) and a 
hands-on session (2:00 pm) where participants can learn about CCP4 Cloud 
through tutorials or develop their own structural solution projects (E1031 CBI)



Free attendance but mandatory registration

Abstract here
Registration link




Hosted by Bulat 
FATKHULLIN


View on IGBMC 
website





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Re: [ccp4bb] CentOS 7 end of life (july 2024)

[Guillaume Gaullier]

Hello,


I have never tried any of the migration tools you listed, so can't advise on 
their use.


But regarding your first option of doing a backup, reformatting from btrfs to a 
different filesystem, restoring the backup and proceeding with the upgrade with 
a non-official tool: you might as well do a clean install of the new OS 
(whichever you choose) instead, then restore your backup.


>From my understanding, RHEL derivatives are not designed for automatic upgrade 
>between major versions, they expect you to backup your /home and do a clean 
>install. The justification is that they have very long support (the 
>earlier-than-originally-planned end of life of CentOS is a consequence of 
>recent policy changes since IBM bought Red Hat, and hopefully only an 
>outlier), so you only rarely need to do this tedious clean install and porting 
>of your old configuration.

Debian, on the other hand, is designed to handle upgrades between major 
versions (I would still do a backup before attempting this) and smoothly 
migrate configuration, so maybe this is the OS you want from now on.


Backing up data is not too difficult (but check your backups). Configuration is 
more difficult, especially because defaults change between versions, so the 
configuration files you back up are not guaranteed to play well with the new 
system. It is tedious to have to configure a freshly installed OS, but on the 
other hand the really critical pieces of configuration are often not that many, 
and you might be better off porting them to a freshly installed system than 
trying to keep your old configuration files in place during an upgrade.


I hope this helps,


Guillaume



From: CCP4 bulletin board  on behalf of Fred Vellieux 

Sent: Friday, August 18, 2023 10:43:34 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CentOS 7 end of life (july 2024)

Hi,

Other people on this BB may run into the same problem.

CentOS 7 end of life is announced to happen in July 2024.

I have to migrate my Linux box to another Linux "flavour".

I've had a look at the possibilities:

- migrate to another RHEL (rpm-based) Linux, with "elevate-linux" and
"leapp".
Here on this Linux box the problem I have is that the disk partition
mounted as / uses btrfs. btrfs has been deprecated starting at versions
8 (RHEL8, CentOS 8, Alma etc). This means first to copy all that is
present on / somewhere, change the file system (for example to ext4) and
restore everything.

- migrate to Debian, that supports btrfs. There are utilities,
"debtakeover" and "debootstrap" that are supposed to install Debian 8.11
(jessie).

Has anyone performed such a migration without data loss (files,
pathways, configurations)? If so I'd like to know what was successful.

Thank you.

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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[ccp4bb] 3 Year Structural Biologist Position in Australia

[Wai Hong Tham]

An opportunity exists for Postdoctoral Fellow (Structural Biologist) to join 
the research laboratory of Professor Wai-Hong Tham in the Department of 
Biomedical Sciences and Biochemistry, Research School of Biology at the 
Australian National University.

The Tham Laboratory works on infectious diseases, with an emphasis on 
understanding how pathogens infect their hosts. In particular, we focus on 
development of human antibodies and nanobodies that prevent pathogens from 
infecting and transmitting within their hosts.

We are looking for a postdoc with expertise in structural biology and 
crystallography techniques and experience in variety of protein expression 
systems. Proficiency in cryo-EM and phage display approaches is highly 
desirable.

AUD $78,940 - $99,083 per annum, Full Time, Fixed Term (up 36 months) , Closing 
date: Oct 1st

More details here: 
https://jobs.anu.edu.au/jobs/postdoctoral-fellow-tham-canberra-act-act-australia





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[ccp4bb] mmciif pdb file editor.

[Krishnan Raman]

How do I edit mmcif files from pdb?  Is there a editor for download from pdb 
website? Thanks krish



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[ccp4bb] Determining Second Lattice

[Matt McLeod]

Hi all,

I have a lot of large datasets that I want to screen to determine if there are 
one or two lattices in the diffraction.  I was wondering if there was a simple 
and quick way to do so.

Currently, I am processing with DIALS and getting to the indexing where the 
percent indexed indicates if there is potentially a second lattice - and then 
visually inspected when there is a significant number of rejection.

I have autoprocess log files ie aimless.log, autoindex.log, fast_dp.log that 
were generated at the beamline but I cannot see a similar metric suggesting 
second lattices. 

Any insight would be appreciated!
Matt



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Re: [ccp4bb] CentOS 7 end of life (july 2024)

[Frederic Vellieux]

Hi and thanks for the reply.

In case others on the bb face the same problem before july 2024, this is 
what I can write about the process of migrating to a more recent Linux 
distro:


"elevate-release", not "elevate-linux"... Poor memory of mine.

The debtakeover and debootstrap route failed with a cryptic message.

The btrfs partition is really preventing direct upgrade to more recent 
RHEL-based distributions (Alma-Linux for example). In the end I 
installed a Debian 12 distribution (the home directory partition was on 
another physical "disk" so it was easy to mount). The root partition fs 
was changed to ext4 in the process.


The one problem I have is that Dassault Systemes' BIOVIA Discovery 
Studio cannot be installed on Debian boxes. Apparently some people 
manage to install it on Ubuntu.


I may try to install Alma-Linux in the end. Just so that I don't need to 
use a Windows PC when Discovery Studio is needed.


Cheers,

Fred.

On 2023-08-30 13:57, Guillaume Gaullier wrote:

Hello,

I have never tried any of the migration tools you listed, so can't
advise on their use.

But regarding your first option of doing a backup, reformatting from
btrfs to a different filesystem, restoring the backup and proceeding
with the upgrade with a non-official tool: you might as well do a
clean install of the new OS (whichever you choose) instead, then
restore your backup.

From my understanding, RHEL derivatives are not designed for automatic
upgrade between major versions, they expect you to backup your /home
and do a clean install. The justification is that they have very long
support (the earlier-than-originally-planned end of life of CentOS is
a consequence of recent policy changes since IBM bought Red Hat, and
hopefully only an outlier), so you only rarely need to do this tedious
clean install and porting of your old configuration.

Debian, on the other hand, is designed to handle upgrades between
major versions (I would still do a backup before attempting this) and
smoothly migrate configuration, so maybe this is the OS you want from
now on.

Backing up data is not too difficult (but check your backups).
Configuration is more difficult, especially because defaults change
between versions, so the configuration files you back up are not
guaranteed to play well with the new system. It is tedious to have to
configure a freshly installed OS, but on the other hand the really
critical pieces of configuration are often not that many, and you
might be better off porting them to a freshly installed system than
trying to keep your old configuration files in place during an
upgrade.

I hope this helps,

Guillaume

-

From: CCP4 bulletin board  on behalf of Fred
Vellieux 
Sent: Friday, August 18, 2023 10:43:34 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CentOS 7 end of life (july 2024)

Hi,

Other people on this BB may run into the same problem.

CentOS 7 end of life is announced to happen in July 2024.

I have to migrate my Linux box to another Linux "flavour".

I've had a look at the possibilities:

- migrate to another RHEL (rpm-based) Linux, with "elevate-linux" and
"leapp".
Here on this Linux box the problem I have is that the disk partition
mounted as / uses btrfs. btrfs has been deprecated starting at
versions
8 (RHEL8, CentOS 8, Alma etc). This means first to copy all that is
present on / somewhere, change the file system (for example to ext4)
and
restore everything.

- migrate to Debian, that supports btrfs. There are utilities,
"debtakeover" and "debootstrap" that are supposed to install Debian
8.11
(jessie).

Has anyone performed such a migration without data loss (files,
pathways, configurations)? If so I'd like to know what was successful.

Thank you.

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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[ccp4bb] Registration open for the SSRL/LCLS User Meeting

[Mooers, Blaine H.M. (HSC)]

Registration is open for the SSRL/LCLS User's Meeting, which will be September 
24-29, 2023 (https://events.bizzabo.com/SLAC-2023/home). It will be in person 
for the first time since 2019. This meeting attracts the lightsource community 
to a single scientific event that is inclusive of many disciplines. 
Participants learn about current/future facility capabilities and the latest 
user research. Of special note is an excellent series of tutorials on the 
Sunday designed by graduate students for new users of LCLS or SSRL.  There will 
be 33 workshops and a plenary session. In addition, there is a poster session 
on Wednesday, September 27th with several poster prizes. Graduate students who 
present a poster have their registration fee waived. The poster abstract 
submission deadline is September 18th.

In addition to the very popular "Metals in Structural Biology" workshop on 
Friday, September 29, I would like to draw attention to the "Computational 
Methods in Structural Biology" workshop on Monday, September 25. It is likely 
of particular interest to some members of the CCP4BB. We have the following 
distinguished set of speakers.

Marcin Wojdyr, Global Phasing
Clemens Vonrhein, Global Phasing
Carmelo Giacovazoo, U of Bari
Lance M. Westerhof, QuantumBio Inc.
Elke De Zitter, IBS, Grenoble, France
Muyuan Chen, Stanford U.
Rachael Kretsch , Stanford U.
Cathy Lawson, RCSB Protein Data Bank

Best regards,

Blaine Mooers and Tzanko Doukov
Co-Chairs of the Computational Methods in Structural Biology  Workshop.




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