[ccp4bb] binary compatibility with old Linux distributions (at synchrotrons?)

2025-03-26 Thread Kay Diederichs 
Dear all,

when compiling XDS or any other software distributed as binaries, the question 
comes up whether it will be compatible with the users' operating system.
For Linux, the main stumbling point is the GLIBC version: a binary compiled on 
a relatively new distribution (like Redhat Enterprise Linux 9 or Ubuntu 22.04) 
will not work on older distributions (like Redhat Enterprise Linux 8 or 7, or 
Ubuntu 20.04 or 18.04) because it needs "symbols" from the newer GLIBC library.
Whereas users with single or a few machines can typically upgrade with 
reasonable effort to newer distributions (e.g. from Ubuntu 20 to 22 or 24), 
some sites with many machines (e.g. synchrotrons) may be stuck with old Linux 
distributions, assuming/hoping that these do not pose security risks due to 
strict firewalls or other measures.
Therefore, developers tend to use machines with old distributions when 
preparing their binaries for public consumption. The downside of this is that 
new compilers and their features are often not available for these old 
distributions.

Since for XDS development we want to use new compiler versions, my question is: 
is there any site still using Redhat Enterprise Linux 7 (or the equivalent 
CentOS7) or Debian 9 or Ubuntu 18? Those sites that have not upgraded their 
machines are at risk not being able to use XDS in the future. Please get in 
touch with me. 

Any site with Redhat-8-compatible distribution or Ubuntu 20 or Debian 10 (or 
specifically, GLIBC 2.28 and newer) should be good for now.

Thank you,
Kay



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Re: [ccp4bb] binary compatibility with old Linux distributions (at synchrotrons?)

2025-03-26 Thread Marcin Wojdyr 
I haven't thought about ifort, so what I wrote doesn't apply here.

In general, it's common to use a different system to prepare binaries;
the overhead isn't that bad.
For example, Python wheels (binaries installed with pip) are often
built in Docker images that are maintained for this purpose here:
https://github.com/pypa/manylinux
Currently the most common Linux wheel version seems to be
manylinux2014 (a.k.a manylinux_2_17), which is built on CentOS 7 with
devtoolset-10.

Marcin

On Wed, Mar 26, 2025 at 8:30 PM Kay Diederichs
 wrote:
>
> Dear Marcin,
>
> thanks for getting back!
>
> The problem is that we want to use not only newer compilers, but also a
> newer Linux distribution for development and compilation.
>
> In my experience, CentOS 7 is showing its age. No Chrome updates, no
> ifort/ifx updates, no security updates, so not useful for our everyday
> workstation usage. GCC-13 can indeed be used but the binaries are often
> slower than those compiled with ifort.
>
> This is why we would like to upgrade our own workstations to e.g.
> Alma8/Rocky8/RHEL8 . Not being able to do this (because some users are
> stuck with CentOS7) means we need a CentOS7 VM for compilation only:
> that entails more administration, time, duplication of data, ... Our
> time would be better spent on improving the code.
>
> Best wishes,
> Kay
>
> Am 26.03.25 um 19:58 schrieb Marcin Wojdyr:
> > Dear Kay,
> >
> > do you use devtoolset (Red Hat Developer Toolset)? It's a set of
> > relatively new tools and compilers, up to GCC 12, for RHEL7. It might
> > be the best solution unless you need GCC 13+.
> >
> > Marcin
> >
> > On Wed, Mar 26, 2025 at 6:18 PM Kay Diederichs
> >  wrote:
> >>
> >> Dear all,
> >>
> >> when compiling XDS or any other software distributed as binaries, the 
> >> question comes up whether it will be compatible with the users' operating 
> >> system.
> >> For Linux, the main stumbling point is the GLIBC version: a binary 
> >> compiled on a relatively new distribution (like Redhat Enterprise Linux 9 
> >> or Ubuntu 22.04) will not work on older distributions (like Redhat 
> >> Enterprise Linux 8 or 7, or Ubuntu 20.04 or 18.04) because it needs 
> >> "symbols" from the newer GLIBC library.
> >> Whereas users with single or a few machines can typically upgrade with 
> >> reasonable effort to newer distributions (e.g. from Ubuntu 20 to 22 or 
> >> 24), some sites with many machines (e.g. synchrotrons) may be stuck with 
> >> old Linux distributions, assuming/hoping that these do not pose security 
> >> risks due to strict firewalls or other measures.
> >> Therefore, developers tend to use machines with old distributions when 
> >> preparing their binaries for public consumption. The downside of this is 
> >> that new compilers and their features are often not available for these 
> >> old distributions.
> >>
> >> Since for XDS development we want to use new compiler versions, my 
> >> question is: is there any site still using Redhat Enterprise Linux 7 (or 
> >> the equivalent CentOS7) or Debian 9 or Ubuntu 18? Those sites that have 
> >> not upgraded their machines are at risk not being able to use XDS in the 
> >> future. Please get in touch with me.
> >>
> >> Any site with Redhat-8-compatible distribution or Ubuntu 20 or Debian 10 
> >> (or specifically, GLIBC 2.28 and newer) should be good for now.
> >>
> >> Thank you,
> >> Kay
> >>
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
>
> --
> Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
> email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049
> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
>
> This e-mail is digitally signed. If your e-mail client does not have the
> necessary capabilities, just ignore the attached signature "smime.p7s".
>



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Re: [ccp4bb] binary compatibility with old Linux distributions (at synchrotrons?)

2025-03-26 Thread David J. Schuller 
In today's world, unsupported means insecure. CHESS is now using Alma 9 Linux.

I hope everyone out there who is still using enterprise Linux 7 has good 
backups, and keeps them offline.


===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
 schul...@cornell.edu

From: CCP4 bulletin board  on behalf of Kay Diederichs 

Sent: Wednesday, March 26, 2025 13:09
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] binary compatibility with old Linux distributions (at 
synchrotrons?)

Dear all,

when compiling XDS or any other software distributed as binaries, the question 
comes up whether it will be compatible with the users' operating system.
For Linux, the main stumbling point is the GLIBC version: a binary compiled on 
a relatively new distribution (like Redhat Enterprise Linux 9 or Ubuntu 22.04) 
will not work on older distributions (like Redhat Enterprise Linux 8 or 7, or 
Ubuntu 20.04 or 18.04) because it needs "symbols" from the newer GLIBC library.
Whereas users with single or a few machines can typically upgrade with 
reasonable effort to newer distributions (e.g. from Ubuntu 20 to 22 or 24), 
some sites with many machines (e.g. synchrotrons) may be stuck with old Linux 
distributions, assuming/hoping that these do not pose security risks due to 
strict firewalls or other measures.
Therefore, developers tend to use machines with old distributions when 
preparing their binaries for public consumption. The downside of this is that 
new compilers and their features are often not available for these old 
distributions.

Since for XDS development we want to use new compiler versions, my question is: 
is there any site still using Redhat Enterprise Linux 7 (or the equivalent 
CentOS7) or Debian 9 or Ubuntu 18? Those sites that have not upgraded their 
machines are at risk not being able to use XDS in the future. Please get in 
touch with me.

Any site with Redhat-8-compatible distribution or Ubuntu 20 or Debian 10 (or 
specifically, GLIBC 2.28 and newer) should be good for now.

Thank you,
Kay



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Re: [ccp4bb] microfluidizer

2025-03-26 Thread Rob Wheatley 
Overall when using the Microfluidizer, while clogging is definitely 
annoying, I have never found it a major problem.  My metric is: the time 
I spend unclogging the machine is less than the time an extra step to 
prevent clogging would add to the protocol. :)  I am guessing on average 
I have processed multiple liters between clogs.


What interaction chamber are you using?  For cell lysis, (E. coli, 
yeast, etc.) my testing has always found an H10Z  (100 um) more than 
sufficient.  Note that chambers differ in both channel size and 
geometry  (Y or Z configuration). Speaking of chambers, with the LM20 
you can also add an APM (auxilliary processing module) upstream of the Z 
interaction chamber to preprocess the sample.  In my experience the 
Microfluidics sales reps have always been quite helpful in letting you 
test various chambers without purchasing these rather costly items.


Besides the actual equipment, I would think about the preceding steps.  
If the cells are harvested by centrifugation, perhaps preparing a more 
loosely packed pellet (shorter centrifugation time, lower rcf) would 
make it easier to resuspend?  In general with a relatively stable 
proteins I do stir the suspension on ice for a while, until most clumps 
are disrupted.  One other thing that might help with frozen E. coli 
cells is adding some nuclease while resuspending the cells  to break up 
the 'gloopiness' formed by DNA release during the freeze/thaw cycle.


Good luck,

Rob


On 3/25/2025 12:43 AM, M T wrote:

Dear Cyprian,

I recommend to users to use a Potter-Elvehjem homogenizer before to 
use the LM20, or even (in case of non fragile protein) to do some 
cycle of sonicator.


I advice also to pay attention to the anti-drop ring of the used 
bottle. Because in case of old one, you may have some plastic 
particles which falls in the sample and clog the LM20 cell. Of course, 
dust is not welcome neither…


To unclog the cell there is no other choice than to invert it. In case 
of severe clogging, the water-bath sonicator can help (gentle heating 
and sonication), before to retry to unclog the cell mounted in a 
reverse way.


Best.

Michel.

Le 25 mars 2025 à 07:09, Cyprian Cukier  
a écrit :




Dear Community,

First of all, apologies for the slightly off-topic question, which is 
related to protein purification rather than crystallography.


I am seeking your advice on preparing the cell pellets for the lysis 
process. We have an LM20 microfluidizer and we experience quite 
frequent clogging of the system that is tedious to remove. This 
happens particularly with the E. coli pellets, but from time to time 
the eukaryotic cells are also problematic. Does anyone have 
well-established protocols on how to handle the cell pellets before 
applying them to the lysis process in the microfluidizer?


I should add that of course we follow the manufacturer's 
recommendations to have a homogenous suspension, which is not too dense.


I would also appreciate any advice on how you clean your systems 
(regularly or in case of clogging).


Best regards

Cyprian




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[ccp4bb] PSB Symposium “Machine Learning in Cellular Structural Biology”, EPN Campus Grenoble, 26-27 June 2025

2025-03-26 Thread Florent Bernaudat 

Dear colleagues,

We are thrilled to announce the scientific programme of the PSB 
Symposium "Machine Learning in Cellular Structural Biology", EPN Campus 
Grenoble, France, 26-27 June 2025, is now out.


The aim of this meeting is to highlight recent developments at the 
intersection of computational and experimental approaches in structural 
biology and sub-cellular imaging. We seek to showcase the application of 
artificial intelligence and machine learning in fundamental molecular 
and cellular research and emphasize their use in translational and 
therapeutic contexts.


The selection of invited speakers and programme can be found here: 
https://www.psb-grenoble.eu/psbsymposium2025/


Main session topics include: [1]

* Computational Tools and Databases
* Proteome Wide Approaches
* Applied protein design
* Integrated Approaches in Life Science

Early Bird rate until 15 April (registration deadline 25 May 2015). 
https://www.psb-grenoble.eu/psbsymposium2025/


Participants will have the possibility to present their own research in 
a poster session, and selected abstracts will be invited to give a short 
talks.


Best wishes,

The organising committee

Florent Bernaudat, European Synchrotron Radiation Facility
Leandro Estrozi, Institut de Biologie Structurale
Frank Gabel, Insititut Laue Langevin
Eva Kowalinski, EMBL Grenoble
Igor Melnikov , European Synchrotron Radiation Facility
--

PSB Symposium on Machine Learning in Cellular Structural Biology
26-27 June 2025, EPN Campus, Grenoble, France
https://www.psb-grenoble.eu/psbsymposium2025/


Florent Bernaudat, PhD
PSB Scientific Coordinator/Animator

Partnership for Structural Biology
Carl-Ivar Brändén Building- office 018
71, Avenue des Martyrs,
CS 90181
38042 Grenoble cedex 9
France

http://www.psb-grenoble.eu
Phone: 33 (0) 476 20 94 08
Fax: 33 (0) 476 20 94 00

Links:
--
[1] https://www.psb-grenoble.eu/psbsymposium2025/



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Re: [ccp4bb] binary compatibility with old Linux distributions (at synchrotrons?)

2025-03-26 Thread Kay Diederichs 

Dear Marcin,

thanks for getting back!

The problem is that we want to use not only newer compilers, but also a 
newer Linux distribution for development and compilation.


In my experience, CentOS 7 is showing its age. No Chrome updates, no 
ifort/ifx updates, no security updates, so not useful for our everyday 
workstation usage. GCC-13 can indeed be used but the binaries are often 
slower than those compiled with ifort.


This is why we would like to upgrade our own workstations to e.g. 
Alma8/Rocky8/RHEL8 . Not being able to do this (because some users are 
stuck with CentOS7) means we need a CentOS7 VM for compilation only: 
that entails more administration, time, duplication of data, ... Our 
time would be better spent on improving the code.


Best wishes,
Kay

Am 26.03.25 um 19:58 schrieb Marcin Wojdyr:

Dear Kay,

do you use devtoolset (Red Hat Developer Toolset)? It's a set of
relatively new tools and compilers, up to GCC 12, for RHEL7. It might
be the best solution unless you need GCC 13+.

Marcin

On Wed, Mar 26, 2025 at 6:18 PM Kay Diederichs
 wrote:


Dear all,

when compiling XDS or any other software distributed as binaries, the question 
comes up whether it will be compatible with the users' operating system.
For Linux, the main stumbling point is the GLIBC version: a binary compiled on a 
relatively new distribution (like Redhat Enterprise Linux 9 or Ubuntu 22.04) will not 
work on older distributions (like Redhat Enterprise Linux 8 or 7, or Ubuntu 20.04 or 
18.04) because it needs "symbols" from the newer GLIBC library.
Whereas users with single or a few machines can typically upgrade with 
reasonable effort to newer distributions (e.g. from Ubuntu 20 to 22 or 24), 
some sites with many machines (e.g. synchrotrons) may be stuck with old Linux 
distributions, assuming/hoping that these do not pose security risks due to 
strict firewalls or other measures.
Therefore, developers tend to use machines with old distributions when 
preparing their binaries for public consumption. The downside of this is that 
new compilers and their features are often not available for these old 
distributions.

Since for XDS development we want to use new compiler versions, my question is: 
is there any site still using Redhat Enterprise Linux 7 (or the equivalent 
CentOS7) or Debian 9 or Ubuntu 18? Those sites that have not upgraded their 
machines are at risk not being able to use XDS in the future. Please get in 
touch with me.

Any site with Redhat-8-compatible distribution or Ubuntu 20 or Debian 10 (or 
specifically, GLIBC 2.28 and newer) should be good for now.

Thank you,
Kay



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--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

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[ccp4bb] Hanging drop plates - cheaper alternatives

2025-03-26 Thread Johannes Claudio Sigl 

Dear fellow hanging-droppers,

for quiet some time we use 15 well hanging-drop plates with screw-cap 
lids and are very happy with their convenience and performance, yet 
those are very pricey (20 plates + lids >2k€). Anyone has 
expierence/knows a cheaper option of this system?


(we also have pre-greased plates, which are good, yet less convenient 
and give more drop-smearing)


Kind Regards

Johannes



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