Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

[Charles Ballard - STFC UKRI]

In answer to Paul, should be available soon.   Targeting Monday.

-Original Message-
From: CCP4 bulletin board  On Behalf Of Paul Emsley
Sent: 09 August 2023 15:31
To: ccp4bb 
Subject: Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement 
is broken in 0.9.8.7]

On 09/08/2023 10:54, David Lawson (JIC) wrote:
> Hi Paul,
>
> Just wondering where we are with this fix.

The blog is generally the place to turn for this sort of thing.

Having said that, I missed the post about 0.9.8.9! But I have added one for 
0.9.8.91 (that revision fixed the missing peptide omega graph and fixes 
"Replace Residue" (needed for the upcoming Summer School)).

As to if/when that gets added to CCP4, that is up to Charles.

> Is it safe to apply the latest CCP4 updates?


Isn't it always?


Paul.


>
> Many thanks
>
> Dave
>
> ---
>
> Prof. David M. Lawson
> Department of Biochemistry and Metabolism, John Innes Centre, Norwich,
> NR4 7UH, UK.
> Tel: +44-(0)1603-450725
> Web: https://www.jic.ac.uk/people/david-lawson
> Email: david.law...@jic.ac.uk
>
>
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Paul 
> Emsley
> Sent: Tuesday, July 18, 2023 5:11 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space 
> refinement is broken in 0.9.8.7]
>
> On 18/07/2023 03:55, Mark Saper wrote:
>> I reported this problem to Paul and to the group at least 2-3 months ago.
> Your email didn't arrive.
>
> Just to be clear, Coot's real space refinement is not (was not) broken, the 
> problem is that the version of Coot distributed by CCP4 and the version of 
> the monomer library distributed by CCP4 were not compatible.
>
>> It affects protein as well as [nucleic] acid.  I never heard back 
>> from Paul if a fix was in progress.
> Keitaro Yamashita alerted me to the problem in a timely fashion and an update 
> to Coot was added and documented in early June.
>
>
> [To Charles in particular] My commitments will be out of the way at 
> the end of the week and I hereby commit to making the 0.9.8.9 release 
> early next week.
>
>
> Paul.
>
> ##
> ##
>
> 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/
>
> ##
> ##
>
> 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/
>
>
> --
> CAUTION: This email originated from outside of the LMB.
> Do not click links or open attachments unless you recognize the sender and 
> know the content is safe.
> .-owner-ccp...@jiscmail.ac.uk-.



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/



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/

[ccp4bb] FW: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

[Charles Ballard - STFC UKRI]

Hi

The current version of coot in ccp4 (on osx and linux) is 0.9.8.8, since update 
12 in June

Charles

-Original Message-
From: CCP4 bulletin board  On Behalf Of Paul Emsley
Sent: 18 July 2023 17:11
To: ccp4bb 
Subject: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is 
broken in 0.9.8.7]

On 18/07/2023 03:55, Mark Saper wrote:
> I reported this problem to Paul and to the group at least 2-3 months ago.

Your email didn't arrive.

Just to be clear, Coot's real space refinement is not (was not) broken, the 
problem is that the version of Coot distributed by CCP4 and the version of the 
monomer library distributed by CCP4 were not compatible.

> It affects protein as well as [nucleic] acid.  I never heard back from 
> Paul if a fix was in progress.

Keitaro Yamashita alerted me to the problem in a timely fashion and an update 
to Coot was added and documented in early June.


[To Charles in particular] My commitments will be out of the way at the 
end of the week and I hereby commit to making the 0.9.8.9 release early 
next week.


Paul.



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/



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/

[ccp4bb] ccp4 update 009

[Charles Ballard - STFC UKRI]

Dear All

A little late, but update to 8.0 009 is now available.

Brief description:

ccp4cloud -update to 1.7.010 
https://cloud.ccp4.ac.uk/manuals/html-userguide/jscofe_version_log.html

ccp4i2 - update to v2.0.  https://ccp4i2.gitlab.io/rstdocs/updatelog/index.html


cbuccaneerNN - new model building program


pairef - update to 1.3.
ccif - update to mmcif_pdbx_v50.dic

refmac - update to cif handling and bug fixes

pandda (on osx and linux) - further python3 fixes

monomers library - new monomers, BJ3, BQG, CZU, DJ5, G5F, G7C, I1X, K39, P3C, 
UQO, WEL, WJB, ZN1, correction FES


Details of earlier updates are available at CCP4 8.0 Updates - Collaborative 
Computational Project No. 4

CCP4 Core Team



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] Coot (& phenix) on Ventura

[Charles Ballard - STFC UKRI]

Hi Pat

There may well be issues with the latest xquartz (2.8.3+) as the  libcairo 
compatibility version has changed to 1 from being 11 thousand odd.   This means 
that anything built against an older installation will fail.   The  workaround 
is to use an older xquartz, such as 2.8.0.

That pretty well summarises my knowledge, hopefully others will fill in the 
gaps.

Charles

From: CCP4 bulletin board  on behalf of Patrick Loll 

Date: Thursday, 16 February 2023 at 13:27
To: ccp4bb 
Subject: [ccp4bb] Coot (& phenix) on Ventura
Hi everyone,

I’ve been putting off upgrading to Mac OS 13 Ventura, but my computer is 
getting more and more pushy in its demands for a new OS.

Hence I ask, What’s the current status of coot running on Ventura? I’m aware of 
the issues that have been discussed in this forum, but that thread seems to 
have been quiet for a while. Are people able to get their work done under OS 
13? And have people encountered problems with any other structural biology 
programs?

Cheers,

Pat

---
Patrick J. Loll, Ph. D.  (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu



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



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] CCP4 8.0.008 Python2 <-> 3 problem

[Charles Ballard - STFC UKRI]

Hi Michael

New version coming on Friday.  Should fix the issues.

You will be able to upgrade using ccp4um

Sorry for the issues

Charles

From: CCP4 bulletin board  on behalf of Michael Weyand 

Date: Thursday, 16 February 2023 at 07:30
To: ccp4bb 
Subject: [ccp4bb] CCP4 8.0.008 Python2 <-> 3 problem
Dear colleagues,

First, I don't want to flood ccp4bb with all the concrete program error 
code(s). Therefore a more general description. I can give more details if 
needed. To the board or by direct mails to the real experts.

I would like to use the 
Panndda/PanDEMIC tools within our CCP4 
environment (version 8.0.008) but I ran in some Python issues, although CCP4 
patch 8.0.005 claimed various py3 Python fixes for Pandda. Even more by using 
the 2to3 Python version converter 
I found a number of Python3 (syntax and more) issues in the main CCP4 Python3 
folder/subfolders at
/ccp4/ccp4-8.0/lib/python3.7/site-packages/

Since my OS (openSuSE Leap 15.4) still comes with both Python version 2.7 and 
3.6 and CCP4 now comes (to my knowledge) with 3.7 I am confused what I have to 
correct/change to use the Pandda tools. By my error tracking I'm pretty sure 
that PATH and PYTHONPATH are directing to the CCP4 folders, but may be I'm 
wrong ...

And/or what was changed to the Pandda tools in the 8.0.005 CCP4 patch? 
Obviously, they are not working at my site ... :-(
For instance, all Pandda scripts are still coming with a Python3 obsolete 
program option "-Q" ?!?!
Was my 8.0.005 patch not properly executed? CCP4i teils me nothing.

It is a shame but my Python knowledge is more than limited. Therefore I ran 
2to3 for all Pandda scripts but then main CCP4 Python tools/scripts showed up, 
again with some syntax errors (= missing version 2/3 conversion ??) in the 
code. After also correcting these first 2-3 issues there were - by executing 
"pandemic.adp" - still more and more Python issues appearing...

Now I asked my self, what is wrong with my CCP4 installation? According to 
patch 8.0.005 these tools should run !!

And why are there version 3 issues beyond the CCP4 python3.7 folder ??  I'm 
confused. Any help is highly appreciated.

Best,
Michael




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



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/

[ccp4bb] Jiscmail message on disruption

[Charles Ballard - STFC UKRI]

https://www.jiscmail.ac.uk/20230111-ServiceDisruption.html

"On Thursday, 05 January 2023, we received notification that one of the email 
servers used by JiscMail was listed on a global spam "blacklist", causing 
recipient mail servers to start rejecting JiscMail posts.

We reported the issue to the operators of that email server, and worked with 
them to ensure that the server was removed from the list. By 09:00hrs on Friday 
(06 January) it was confirmed that the server had been removed from the 
blacklist, and that normal service had resumed.

Unfortunately, later that day, the server was re-added to the blacklist, 
causing recipient servers to start rejecting messages once more.

Due to the way in which the software underpinning the JiscMail service works, 
after several bounced or rejected messages to an individual email address, the 
software assumes that the address no longer exists and removes it from any 
subscribed groups. This had the effect of removing around 50,000 subscriptions 
to just short of 500 JiscMail lists.

We are pleased to inform you that, as of 14:00hrs on Wednesday, 11 January 
2023, we believe the root cause of the issue (the blacklisting) to have been 
resolved, and are in the process of resubscribing all affected users. We expect 
this to be completed by no later than 17:00hrs on Wednesday, 11 January 2023.

Despite these issues having been addressed, subscribers and list owners may 
continue to recieve error messages that have been "queued" by mail servers 
outside of our direct control. These are expected to have fully cleared by 
Friday, 13 January 2023.



This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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/

[ccp4bb] issues

[Charles Ballard - STFC UKRI]

Dear All

Jisc, who we use to run the ccp4bb have been having issues delivering to some 
(a lot) of e-mail addresses.  So far 1400 addresses have been unsubscribed, and 
another 2000 are being monitored.  I have turned for automatic removal (I 
think) and asked that the status of the list be returned to that Saturday's 
members lists.

All the best

Charles

This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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] Jenkins?

[Charles Ballard - STFC UKRI]

Can solve the mystery of Jenkins, it is our build system.

Charles

On 25/09/2022, 19:36, "CCP4 bulletin board"  wrote:
Hello David,

maybe a binary in $CBIN with the same name as a system command?
(try, e.g. 'apropos truncate'
truncate (1) - shrink or extend the size of a file to the
specified size
)

there used to be a switch to place $CBIN at the end of the $PATH -
maybe this helps?

Cheers,
Tim


On Sun, 25 Sep 2022 14:37:38 +
"David J. Schuller" mailto:schul...@cornell.edu>> wrote:

> CCP4 8.0.004
> Scientific Linux 7, kernel 3.10.0-1160.76.1.el7.x86_64
> mate-desktop-1.16.2-1.el7.x86_64
>
> This morning I updated my Nvidia graphics driver, then rebooted. When
> I logged in again, my desktop (Mate) was all messed up, no
> applications menus, etc. I perused the log files and found many lines
> similar to these in /var/log/messages:
>
> Sep 25 09:45:32 titan mate-session[1718]: WARNING: Could not connect
> to Systemd: Failed to connect to socket
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
> No such file or directorySep 25 09:45:34 titan journal: Error
> connecting to system bus: Failed to connect to socket
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
> No such file or directory Sep 25 10:12:35 titan pulseaudio[22894]:
> [alsa-sink-ALC887-VD Analog] core-util.c: Failed to connect to system
> bus: Failed to connect to socket
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
> No such file or directory Sep 25 10:12:40 titan pulseaudio[23162]:
> [pulseaudio] core-util.c: Failed to connect to system bus: Failed to
> connect to socket
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
> No such file or directory Sep 25 10:12:40 titan pulseaudio[23162]:
> [pulseaudio] core-util.c: Failed to connect to system bus: Failed to
> connect to socket
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
> No such file or directory
>
> I do not have, and have never had, a user "jenkins" on my system.
> Note that the CCP4 workspace is implicated.
>
> I took the CCP4 startup stuff out of my .cshrc login script and
> restarted, and everything appeared to be normal. # source
> /usr/local/xtal/ccp4/bin/ccp4.setup-csh  >& /dev/null
>
> Why is jenkins mucking about with  my desktop settings, and how do I
> keep him from doing so?
>
>
> ===
>  All Things Serve the Beam
>  ===
>  David J. Schuller
>  modern man in a post-modern world
>  MacCHESS, Cornell University
>  
> schul...@cornell.edu
>
> 
>
> 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/



--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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/


This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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] CCP4i under M1Pro

[Charles Ballard - STFC UKRI]

That openmp is not functioning is an issue that I will investigate.  It should 
be, so something is wrong.  Mostly I find that Sophos is sitting there using 2 
cores, and much of my IO.

Charles

From: CCP4 bulletin board  on behalf of Randy John Read 

Date: Tuesday, 28 June 2022 at 20:16
To: ccp4bb 
Subject: Re: [ccp4bb] CCP4i under M1Pro
We don’t have any computers with Apple silicon in our group yet to test Phaser 
on ourselves. When preparing the Phenix distribution, Billy Poon has run tests 
and when Phaser is compiled for Intel and run through Rosetta 2, it’s generally 
faster than on a recent Intel Mac. However, there have been reports from Phenix 
users of severe slowdowns, and we don’t understand what the special 
circumstances are that cause it to slow down on specific jobs.

The best performance is when it’s compiled natively for the M1 processor, and I 
believe both Phenix and CCP4 are aiming to distribute natively-compiled 
software as soon as technical complications are worked out. So hopefully this 
is just temporary!

I hadn’t realised that the OpenMP wasn’t enabled on CCP4. In Phenix, there were 
issues preventing the use of OpenMP with Python2, but those should go away when 
the Python3 version is ready to deploy.

Best wishes,

Randy Read

> On 28 Jun 2022, at 16:45, Lau Kelvin 
> <5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hello
>
> I have noticed running normal programs like Phaser MR on a MacBook Pro 
> (M1Pro) that jobs are extremely slow compared to my older computers.
>
> It doesn’t seem to be running over multiple CPUs anymore.
>
> Has this also been seen by others?
>
> Best
>
> Kelvin
>
>
> --
> 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: +41 21 69 34494
>
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building   Fax: +44 1223 336827
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk




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/

This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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/

[ccp4bb] CCP4/CCP-EM workshop at ECM33

[Charles Ballard - STFC UKRI]

Dear All

There will be a CCP4/CCP-EM workshop on the two days prior to the ECM33  
meeting at Soleil.   Details and registration are at

https://www.ecm33.fr/ccp4andccpemworkshops

Accommodation will be provided at the Soleil guest house during the workshop 
(individual’s responsibility to pay, but booked by ourselves).
The CCP4 day will introduce attendees to the CCP4cloud, in particular the use 
of AF2 models.

All the best

Charles

This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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/

[ccp4bb] CCP4/CCP-EM workshop at ECM33

[Charles Ballard - STFC UKRI]

Dear All

Following on for the CSD workshop e-mail there will be a joint CCP4/CCP-EM 
event at ECM33

https://www.ecm33.fr/copie-de-mechanical-properties


Date : 21 & 22 August 2022

Venue : Synchrotron SOLEIL

Organizer : Charles BALLARD

Description

​

The CCP4/CCP-EM workshop will focus on theory and practice in computational 
approaches in bio-crystallography and Cryo-EM single particle analysis This 
will be an in-person event taking place at Synchrotron SOLEIL - CNRS - Cea 
Paris-Saclay.



The CCP4 Workshop will focus on demonstrating the use of CCP4 Cloud for 
determining macromolecular structures from X-ray diffraction data. We will 
cover all steps from diffraction image processing to finalising refinement and 
model building.



To get the most value from the workshop, participants are encouraged to 
download and install the latest version of the CCP4 suite as well as register 
an account with CCP4 Cloud.


All the best

Charles

This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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] Security blockage: CCP4 installation on macOS Big Sur

[Charles Ballard - STFC UKRI]

Hi Yong

What I normally do is

sudo xattr –rc /Applications/ccp4-7.1

getting rid of the extended attributes seems to fix

Charles

From: CCP4 bulletin board  On Behalf Of Yong Tang
Sent: 29 September 2021 22:17
To: ccp4bb 
Subject: [ccp4bb] Security blockage: CCP4 installation on macOS Big Sur

Dear all,

I downloaded the latest mac version of CCP4 suite for installation on a new Mac 
(macOS Big Sur Version 11.5.2). The package was downloaded using Chrome. After 
unpacking and moving the folder to its destination /Applications/ccp4-7.1, the 
set up using

./BINARY.setup

gives error messages that the app was downloaded via Chrome and that "macOS 
cannot verify that this app is free from malware".

I tried using "sudo" but that didn't help.

Do you have a quick pointer for me?

Many thanks, -yong



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

This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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/