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.
>
> ##
> ##
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> --
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[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.



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[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



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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



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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




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[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 
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[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

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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
>
> 
>
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>
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--
--
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



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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:
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>

-
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




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[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

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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 
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[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<https://www.synchrotron-soleil.fr/fr/venir-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

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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



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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.




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Re: [ccp4bb] Issues in new Mac version 10.15

[Charles Ballard - UKRI STFC]

Dear All

as has been pointed out, and as per usual, OS X updates seem to remove some of 
the setup for XQuartz, which will cause most X11 based apps to stop working.  
It is best to re-install XQuartz.  This will work for an updated system that 
had CCP4 previously installed on it.  We have had a few reports of issues when 
installing on a fresh  10.15 machine through the CCP4 downloads manager 
(tarball route still works).  We are investigating.

All the best

Charles

On 16 Oct 2019, at 17:42, Werther, Rachel A wrote:

Thanks to all who gave advice.  The reinstallation of XQuartz worked for me.  I 
was using the most updated version of XQuartz before I reinstalled it, but as 
Guillaume Gaullier told me:

“…macOS updates typically wipe out most files of your XQuartz installation 
(XQuartz.app will still be where it was originally installed, but unlike most 
Mac applications this one is not self-contained and has important files under 
/opt/X11 that get erased by a system update). And Coot requires XQuartz to 
display its window, so this is the most likely explanation for why it would not 
work after a system update.

Try reinstalling XQuartz from 
https://www.xquartz.org/,
 then log out and log back in (or reboot, that should do it too), and see if 
Coot starts up normally.”

Happy solving,
Rachel

Rachel Werther / Research Technician III / Stoddard Lab / Basic Sciences / Fred 
Hutchinson Cancer Research Center / 
rwert...@fredhutch.org / 206-667-4066

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of "Werther, Rachel A" 
mailto:rwert...@fredhutch.org>>
Reply-To: "Werther, Rachel A" 
mailto:rwert...@fredhutch.org>>
Date: Tuesday, October 15, 2019 at 5:01 PM
To: "CCP4BB@JISCMAIL.AC.UK" 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] Issues in new Mac version 10.15

Hello All,

I downloaded the latest Mac Update, 10.15 Catalina, and then Coot wouldn’t open 
on my computer.

Phenix opened as usual.  I use the GUI, and the button that says “Open in COOT” 
was not greyed out, but would not launch the window.  When I tried to open it 
directly from Finder, it also failed to open.  The cartoon coot appeared on my 
recently opened section of my bottom-of-screen toolbar, but nothing happened.

Next I downloaded the latest CCP4-7.0.077, and followed the instructions to 
remove the extended attributes:
ATTENTION: If you are planning to install CCP4 from a tarball on Mac OS X 
version 10.13 or later (10.12 was not tested), you will have to remove extended 
attributes from the tar-gz-file before unpacking it, otherwise the app icons 
will not be functional (and you will be able to launch the CCP4 apps including 
ccp4i and ccp4i2 from the command line only). The extended attributes can be 
removed from the file _file_ using the command "xattr -c _file_". For example: 
xattr -c ccp4-7.0.065-macosx64.tar.gz

But when I try to open CCP4, I get this message:
Ccp4 cannot be opened because of a problem.
Check with the developer to make sure ccp4 works with this version of macOS. 
You may need to reinstall the application. Be sure to install any available 
updates for the application and macOS.
Click Report to see more detailed information and send a report to Apple.

And when I try to open Coot from the Finder, I again just see the icon in my 
recently opened section of my bottom-of-screen toolbar, but it doesn’t open.

Any advice?

Many thanks,
Rachel

Rachel Werther / Research Technician III / Stoddard Lab / Basic Sciences / Fred 
Hutchinson Cancer Research Center / 
rwert...@fredhutch.org / 206-667-4066



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[ccp4bb] shelxe update

[Charles Ballard - UKRI STFC]

Dear All

Ccp4 update 067 has been released and contains the updated shelxe

All the best

Charles



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[ccp4bb] CCP4 Study Weekend Early Bird ending

[Charles Ballard - UKRI STFC]

Dear All

a heads up that the early bird registration, and closing date for student 
bursaries, is Sunday 18th November 2018 i.e. this Sunday!

For more info see http://www.cvent.com/d/sgq8q6/1K?cpc=N7N8SK89V8N

Regards

Karen McIntyre
Scientific Computing Department - CCP4



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[ccp4bb] U-M Center for Structural Biology Research Fellow position

[Charles Ballard - UKRI STFC]

On behalf of Ashley Schork, University of Michigan:

Good morning,

I am reaching out on behalf of Jeanne Stuckey from the University of Michigan 
Life Sciences Institute Center for Structural Biology.

The Center for Structural 
Biology,
 (CSB) at the University of Michigan Life Sciences Institute seeks a 
post-doctoral candidate with crystallography experience, who is interested in 
developing cutting edge purification and crystallization technologies for RNA 
and RNA-Protein complexes. The CSB acts as the structural biology core for the 
Center for HIV RNA Studies (CRNA), which is a large consortium of researchers 
across the nation focusing on the structures, dynamics, interactions, and 
mechanisms of action of the HIV-1 RNA during the late phase of viral 
replication. Funding for these studies is provided by the National Institutes 
of General Medical Sciences, National Institutes of Health.  The post-doctoral 
fellow will work under the direction of Jeanne A. Stuckey, Ph.D, Managing 
Director of CSB and Research Associate Professor, and work in collaboration 
with members of the CSB.

Link to job posting: http://careers.umich.edu/job_detail/163107/research_fellow

The posting will be extended until October 18th. Would you be able to post to 
the CCP4 bulletin to reach those who would be interested in applying? Please 
let us know if you have any questions.

Ashley Schork
Structural Biology Program Coordinator
University of Michigan Life Sciences Institute
210 Washtenaw Ave
Ann Arbor, MI 48109-2216
734-647-8098 | ashls...@umich.edu

[U-M Life Sciences Institute logo]




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[ccp4bb] forming a 3D bioinformatics community

[Charles Ballard - UKRI STFC]

Structural bioinformatics is shaping its Community 

Relevance of structural informatics 
Structural bioinformatics has a broad impact across the life sciences and 
provides tools to archive, visualise, analyse, annotate, and predict the 
structure of biological macromolecules. Furthermore, the science of structural 
bioinformatics is traditionally very strong in Europe offering many software 
tools, methodologies, and databases, as well as community-wide prediction 
challenges. Its applications cover research activities from structural biology 
to drug discovery and personalized medicine. We envision that establishing an 
ELIXIR Community will facilitate deeper integration of our broad range of tools 
and services.
The leading research groups and activities in structural bioinformatics in 
Europe are already well represented within the ELIXIR nodes (e.g SWISS-MODEL). 
Several ELIXIR core data resources belong to this field, some of them, such as 
PDBe and CATH are of fundamental importance. Some of the highly cited ELIXIR 
tools also belong to the field of structural bioinformatics.  The 3D-BioInfo 
Community is building on this strength and links to several other 
infrastructures and EC projects. Tools and resources established by the 
3D-BioInfo Community have users in the field of structural biology (Instruct, 
iNEXT), cheminformatics (OpenScreen), system biology (ISBE), and molecular 
simulations (BioExcel) and these will benefit from collaborative projects with 
3D-BioInfo. The 3D-Bioinfo initiative will undoubtedly broaden this scope.

ELIXIR and instruct-ERIC 
The  instruct-ERIC is a most important collaborator and the 3D-BioInfo 
Community will coordinate closely with experimental structural biologists. We 
expect our collaborative projects to help link structural bioinformatic tools 
with emerging structural techniques, to help relate function to structure. This 
will attract new users and support the recognition of both ELIXIR and 
instruct-ERIC services. We expect potential collaborations to involve all five 
ELIXIR platforms (interoperability, data, tools, compute, training).

Goals of the community
The long term goals of the community include: improving integration of 
structural information with data on protein function, genomic variants, disease 
links, and drug action; developing platform for sharing, and benchmarking 
software for protein structure prediction, modeling protein assemblies and 
complexes with various ligands; integrating resources and tools for protein 
structural and evolutionary analyses; development and integration of various 
structural biology enabling tools, in close collaboration with Instruct-ERIC.

How to join 
If you are interested in participating, come to the launch meeting in Basel, 
October 19, 2018, to find out more. You will have the opportunity to present a 
poster and give a flash talk presenting your tools and suggesting how you might 
contribute to community activities. This meeting will be critical for 
collecting ideas for community activities, which will be the basis for a formal 
application to the ELIXIR Heads of Nodes to become an approved community in 
ELIXIR. 
If you would like to give a flash talk (one slide) to advertise a poster at the 
meeting on a proposed ELIXIR activity (involving collaborations across two or 
more groups within an ELIXIR node and preferably involving two or more nodes) 
please send a summary (maximum one page) to c.ore...@ucl.ac.uk outlining the 
groups and ELIXIR nodes involved and the ELIXIR platforms this activity would 
relate to i.e. interoperability, data, tools, compute or training. The proposed 
activity can involve multiple platforms.

Registration site: https://swissmodel.expasy.org/25years/

For information on the timelines for forming an ELIXIR Community in Structural 
Bioinformatics please see: 
https://drive.google.com/file/d/10a5PTWA8b00i7jYeuyOQQ0OXdn-EUoUI/view?usp=sharing
For information on suggested major themes and activities of the 3D-BioInfo 
Community – please see link below. You are welcome to add comments on 
additional activities.
https://drive.google.com/file/d/10DYf1uMg9jaHFOGX7gvKsHIAVRRwqyx1/view?usp=sharing




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[ccp4bb] ccp4 release 7.0 update 061 - major update to monomer library!

[Charles Ballard - UKRI STFC]

Dear All

ccp4 release update 061 is now available for updating and downloading.  It 
contains

 * monomer library
 - major update
 - 7000  new monomers
 - 8000 updated monomers

 * refmac
 - updated for new monomer library

 * buccaneer
 - new EM reference structure

This is a recommended update for all CCP4 users.

All the best

Charles (on behalf of the CCP4 core team)

ps - coming soon, ccp4i2 updates for molprobity, and dials 1.10




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[ccp4bb] ccp4 release 7.0 update 061

[Charles Ballard - UKRI STFC]

Dear All

ccp4 update 061 to release 7.0 is now available.  It contains

* DIALS 1.10.4 and XIA2 0.5.582
 - release notes: https://github.com/dials/dials/releases/tag/v1.10.0

* molprobity 4.4
 - scripts molprobity.molprobity, molprobity.clashscore, molprobity.cablam, 
probe, reduce, etc
 - http://molprobity.biochem.duke.edu/
 - thank you to Jane Richardson, Nigel Moriarty, Randy Read

* lorestr
 - update to use bundled molprobity.

This is available as an update to current installations, and as a direct 
download from the ccp4 site.

Coming soon:
 
 * major update to monomer library
 * molprobity integration to ccp4i2
 * DIALS gui update
 * additional reference structures for buccaneer.

All the best

Charles 


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[ccp4bb] SPring-8/CCP4 workshop on data collection and structure solution

[Charles Ballard - UKRI STFC]

Dear All

10 days to the registration closure for the second CCP4/Spring-8 (RIKEN) 
workshop running from 1-6 October 2018.

This workshop will cover data collection, processing and structure solution.  
Details are available at
http://www.ccp4.ac.uk/schools/Japan-2018 , with more to follow.  Registration 
is on the same site.  Registration will
close on 24 August.

Topics will include XDS (Kay Diederichs), DIALS (Graeme Winter), the CCP4 suite 
(myself and others),
PDB_REDO (Robbie Joosten), COOT and others. The format will cover data 
collection, lectures, tutorials and
problem solving, so students are encourages to bring their own data to work on.

Charles and Kunio.



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Re: [ccp4bb] FW: [ccp4bb] Sulphate or phosphate?

[Charles Ballard - UKRI STFC]

[cid:a3a4faea-08e2-46af-88de-3bde456d9124@fed.cclrc.ac.uk]


Sorry for spamming you all on this, but these images keep on getting stripped 
for Armin and myself.

On 2 Aug 2018, at 16:51, Charles Ballard - UKRI STFC wrote:

> Begin forwarded message (on behalf of Armin Wagner)
> From: ahw78 mailto:armin.wag...@diamond.ac.uk>>
> Date: 2 August 2018 at 09:17:48 BST
> To: Eleanor Dodson 
> mailto:eleanor.dod...@york.ac.uk>>
> Cc: ccp4bb mailto:ccp4bb@jiscmail.ac.uk>>
> Subject: Re: [ccp4bb] Sulphate or phosphate?
> Dear Eleanor,
>
> We can tune the wavelength over a large range (lambda = 1.2 – 6 A). This 
> allows collecting data above and below the absorption edges of Ca, K, Cl, S 
> and even P. Crystal, solvent and loop absorption are of course a problem for 
> the longest wavelengths, but so far we have done quite a fair amount of 
> studies around these absorption edges with strong signal above the edge and 
> obviously no signal below. Resolution in our setup is limited to around 3.2 A 
> at 5 A wavelength, but for anomalous difference fourier maps this is 
> sufficient. I have attached an example for a disulphide bridge which should 
> illustrate it better.
>
> Best regards,
>
>Armin
>
>
>
> [cid:image001.png@01D42A41.AE0B8B60]
>
> From: Eleanor Dodson 
> mailto:eleanor.dod...@york.ac.uk>>
> Date: Wednesday, 1 August 2018 at 19:09
> To: Armin Wagner 
> mailto:armin.wag...@diamond.ac.uk>>
> Cc: "ccp4bb@jiscmail.ac.uk<mailto:ccp4bb@jiscmail.ac.uk>" 
> mailto:ccp4bb@jiscmail.ac.uk>>
> Subject: Re: [ccp4bb] Sulphate or phosphate?
>
> I am not sure if you gave your wave length but it is always worth doing an 
> anomalous map, and looking at relativr peak heights for your known S 
> positions and the putative sulphate or phosphate.
> There are small differences in the expected f" at most wavelengths.
>
> Chemical arguments are doubtless better of Course!
> Eleanor
>
> On 1 August 2018 at 16:54, 
> armin.wag...@diamond.ac.uk<mailto:armin.wag...@diamond.ac.uk> 
> mailto:armin.wag...@diamond.ac.uk>> wrote:
> Dear David,
>
> The long-wavelength beamline I23 at Diamond 
> (http://www.diamond.ac.uk/Instruments/Mx/I23.html) can go all way down to the 
> phosphorous edge. While data quality will be obviously compromised by 
> absorption effects (we are working on this), for a reasonably well 
> diffracting crystal like yours we should be able to get anomalous difference 
> fourier maps from data collected above and below the sulphur edge (lambda ~5 
> A) to answer your question.
>
> We’ve published some test crystal work around the sulphur edge a while ago, 
> you might want to have a look here:
> https://doi.org/10.1016/j.nimb.2016.12.005
>
> The beamline is currently in an advanced commissioning phase accepting a 
> limited number of projects. So, please get into touch if you are interested. 
> We are currently sorting out a few more hardware and software aspects before 
> we can run the beamline as a standard user facility, but we have made a lot 
> of progress over the past months. There will be more details here on the 
> bulletin board ahead of the next call for proposals in autumn.
>
> Best regards,
>
>Armin
>
>
> Postdoc position for long-wavelength crystallography:
> https://vacancies.diamond.ac.uk/vacancy/post-doctoral-research-associate-355285.html
>
>
>
>
> On 31/07/2018, 14:38, "CCP4 bulletin board on behalf of David Schuller" 
> mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
> schul...@cornell.edu<mailto:schul...@cornell.edu>> wrote:
>
>How can one distinguish between a sulphate or phosphate in an electron
>density map? Both are present in the mother liquor, and resolution is in
>the range of 1.75 - 2.25 A
>
>
>--
>===
>All Things Serve the Beam
>===
>David J. Schuller
>modern man in a post-modern world
>MacCHESS, Cornell University
>
> schul...@cornell.edu<mailto:schul...@cornell.edu>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> --
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you are

[ccp4bb] Fwd: [ccp4bb] Sulphate or phosphate? (Armin's figures)

[Charles Ballard - UKRI STFC]

Begin forwarded message:

[cid:image001.png@01D42A41.AE0B8B60]




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[ccp4bb] FW: [ccp4bb] Sulphate or phosphate?

[Charles Ballard - UKRI STFC]

Begin forwarded message (on behalf of Armin Wagner)
From: ahw78 mailto:armin.wag...@diamond.ac.uk>>
Date: 2 August 2018 at 09:17:48 BST
To: Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>>
Cc: ccp4bb mailto:ccp4bb@jiscmail.ac.uk>>
Subject: Re: [ccp4bb] Sulphate or phosphate?
Dear Eleanor,

We can tune the wavelength over a large range (lambda = 1.2 – 6 A). This allows 
collecting data above and below the absorption edges of Ca, K, Cl, S and even 
P. Crystal, solvent and loop absorption are of course a problem for the longest 
wavelengths, but so far we have done quite a fair amount of studies around 
these absorption edges with strong signal above the edge and obviously no 
signal below. Resolution in our setup is limited to around 3.2 A at 5 A 
wavelength, but for anomalous difference fourier maps this is sufficient. I 
have attached an example for a disulphide bridge which should illustrate it 
better.

Best regards,

Armin



[cid:image001.png@01D42A41.AE0B8B60]

From: Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>>
Date: Wednesday, 1 August 2018 at 19:09
To: Armin Wagner mailto:armin.wag...@diamond.ac.uk>>
Cc: "ccp4bb@jiscmail.ac.uk" 
mailto:ccp4bb@jiscmail.ac.uk>>
Subject: Re: [ccp4bb] Sulphate or phosphate?

I am not sure if you gave your wave length but it is always worth doing an 
anomalous map, and looking at relativr peak heights for your known S positions 
and the putative sulphate or phosphate.
There are small differences in the expected f" at most wavelengths.

Chemical arguments are doubtless better of Course!
Eleanor

On 1 August 2018 at 16:54, 
armin.wag...@diamond.ac.uk 
mailto:armin.wag...@diamond.ac.uk>> wrote:
Dear David,

The long-wavelength beamline I23 at Diamond 
(http://www.diamond.ac.uk/Instruments/Mx/I23.html) can go all way down to the 
phosphorous edge. While data quality will be obviously compromised by 
absorption effects (we are working on this), for a reasonably well diffracting 
crystal like yours we should be able to get anomalous difference fourier maps 
from data collected above and below the sulphur edge (lambda ~5 A) to answer 
your question.

We’ve published some test crystal work around the sulphur edge a while ago, you 
might want to have a look here:
https://doi.org/10.1016/j.nimb.2016.12.005

The beamline is currently in an advanced commissioning phase accepting a 
limited number of projects. So, please get into touch if you are interested. We 
are currently sorting out a few more hardware and software aspects before we 
can run the beamline as a standard user facility, but we have made a lot of 
progress over the past months. There will be more details here on the bulletin 
board ahead of the next call for proposals in autumn.

Best regards,

Armin


Postdoc position for long-wavelength crystallography:
https://vacancies.diamond.ac.uk/vacancy/post-doctoral-research-associate-355285.html




On 31/07/2018, 14:38, "CCP4 bulletin board on behalf of David Schuller" 
mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
schul...@cornell.edu> wrote:

How can one distinguish between a sulphate or phosphate in an electron
density map? Both are present in the mother liquor, and resolution is in
the range of 1.75 - 2.25 A


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

schul...@cornell.edu



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[ccp4bb] CCP4 workshop at CSIR-IMTech, Chandigarh, 22-26 October 2018

[Charles Ballard - UKRI STFC]

Dear All

I am pleased to announce a CCP4 Crystallography School and Workshop at 
CSIR-IMTech, Chandigarh, India running from October 22 to October 26.

The course is intended mainly for graduate students and postdoctoral 
researchers in the area of structural biology. In some cases, assistant 
-professor-level applicants can be accepted as well. The school is not meant as 
an introductory level course to protein crystallography. It is designed more 
for applicants with reasonable expertise in crystallography and experience with 
the CCP4 suite. The purpose of the school is to address specific problems that 
the applicants face while processing diffraction data and while solving and 
refining novel structures. Applicants with already collected data will be given 
strong consideration, although this not a mandatory requirement.
Note: for the tuturials and practicals there is a limit of 35 students, 
lectures are open to all.


Application to the workshop is free of charge, but a letter from the supervisor 
or the professor will be required.Travel expenses will be the responsibility of 
the participant, accommodation and meals will be provided. There accommodation 
at the CSIR guest house.

Tutors will include:

Eleanor Dodson, Harry Powell, Udupi Ramagopal, members of the CCP4 team and 
ARP/wARP EMBL team.

Further details are available at

http://www.ccp4.ac.uk/schools/India-2018

All the best

Charles and Karthik




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[ccp4bb] update 057 RECOMMENDED

[Charles Ballard]

Dear All

This is out, and contains a fix to the nasty truncate bug detailed earlier (hat 
tip to GPL), it is therefore
recommended that this be applied.

Also included are updates to 

* aimless
* ccp4i2
* ccp4i
* gesamt
* mrbump
* dials interface

plus some workarounds for changes to web certificate handling (in ccp4.setup-sh 
and ccp4.setup-csh).  This
will need checking on your local installations as local changes may be lost.

Known issue:

Unfortunately, the changes to the setup files have broken the integration 
between ARP/wARP and CCP4.  This
can be recreated by re-running BINARY.setup.  The next update will address this.

Charles

[ccp4bb] update on nasty truncate bug

[Charles Ballard]

Dear All

credit to the Global Phasing team who along with Phil Jeffrey spotted and 
supplied the fix for this nasty bug which was introduced in CCP4 7.0 update 039 
(May 2017).   

I am sorry to say this is one of the occasions when CCP4s internal testing has 
fallen well sort, and I apologise for the problems this will have caused.  It 
looks like amplitudes with a I/sigma-/sigma in the range 10-20 will have the 
wrong values. this will have made structure solution significantly more 
difficult.  The Global Phasing team have been investigating the effects further.

Thanks to Clemens Vonrhein who e-mailed on the 8th, a fix went out in update 
057 yesterday.

To clarify some questions I received in follow-up to my e-mail yesterday, this 
effects truncate, not ctruncate as used by default by ccp4i and ccp4i2.  
ctruncate is uneffected.

Charles

[ccp4bb] serious issue: truncate program

[Charles Ballard]

Dear All

we discovered a serious bug in TRUNCATE that results in incorrect sets
of amplitudes/sigmas. The problem was introduced at update 7.0.039.  
The effect is a complete lack of amplitudes with F/SIGF values within
(roughly) the 10-20 range. It can easily be detected by plotting a
histogram of F/SIGF values from any MTZ file.

A fix will be in the next update.

Charles

Re: [ccp4bb] CCP4 release 7.0 update 056

[Charles Ballard]

Dear All (particulary OS X users)

A heads up for mac users of DUI,  There seems to be a issue (but not every 
time, and not when we were testing :-) with an illegal access in boost_adaptbx. 
  As the output will testify setting BOOST_ADAPTBX_FPE_DEFAULT=1 allows 
continuation.

Thanks Graeme for spotting this (3 hr and 37 minutes after announcement to 
report).

Charles

On 27 Apr 2018, at 11:57, Charles Ballard wrote:

> Dear All
> 
> the latest update is available
> 
> * monomer library
> - fixes for ASN, etc
> 
> * dui (release under osx and linux, alpha under windows)
> - new interface for DIALS
> 
> * DIALS
> - 1.9.2
> 
> * XIA2
> - 0.5.542
> 
> * aimless
> - 0.7.1
> 
> * ccp4i2
> - minor interface fixes
> 
> * ccp4i
> - minor interface fixes
> 
> * phaser
> - minor changes
> 
> CCP4 Core team

[ccp4bb] CCP4 release 7.0 update 056

[Charles Ballard]

Dear All

the latest update is available

* monomer library
- fixes for ASN, etc

* dui (release under osx and linux, alpha under windows)
- new interface for DIALS

* DIALS
- 1.9.2

* XIA2
- 0.5.542

* aimless
- 0.7.1

* ccp4i2
- minor interface fixes

* ccp4i
- minor interface fixes

* phaser
- minor changes

CCP4 Core team

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Charles Ballard - UKRI STFC]

Update 055 should have reverted out ASP, and update 056 (coming real soon now) 
should fix the other issues.

Charles


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
"Weiergräber, Oliver H."
Sent: 26 April 2018 15:06
To: ccp4bb 
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Indeed, update 54 from Mar 29 seems to have messed up several monomer 
definitions and/or their handling in coot (the version distributed with ccp4):
- GLU and ASP contain lines referencing GLN and ASN, respectively, preventing 
coot from finding any chi angles.
- For GLN, chi angles appear twice in the coot torsion dialog.
- Many amino acid definitions now contain main chain torsion angles, which are 
erroneously listed as chi in coot.

The coot version available from Paul Emsleys website comes with its own version 
of the monomer library, which seems to work fine.

Best
Oliver


  PD Dr. Oliver H. Weiergräber
  Institute of Complex Systems
  ICS-6: Structural Biochemistry
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-9540





From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson 
[176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk]
Sent: Thursday, April 26, 2018 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Oops - oh dear - GLN labels should NOT appear in a list devoted to GLU!!


Well spotted..
Eleanor



On 26 April 2018 at 10:34, Chris Richardson 
> wrote:
Many thanks for explaining where it is going awry.

Looking at GLU.cif in the monomer library that is part of the CCP4 
distribution, it contains the following lines:

 GLN  chi1 N  CA CB CG   180.000   15.000   3
 GLN  chi2 CA CB CG CD   180.000   15.000   3
 GLN  chi3 CB CG CD OE10.000   30.000   2

In the monomer library you link, it has:

 GLU  chi1 N  CA CB CG   180.000   15.000   3
 GLU  chi2 CA CB CG CD   180.000   15.000   3
 GLU  chi3 CB CG CD OE20.000   30.000   2

Which makes more sense.

Thanks again,

Chris

From: CCP4 bulletin board > 
on behalf of Huw Jenkins >
Sent: 26 April 2018 09:47
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

> On 26 Apr 2018, at 09:19, Chris Richardson 
> > wrote:
>
> I've just compiled Coot on the same Mac using Fink, and the dialogue for this 
> version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the 
> same residue.

>From a quick look at the Fink coot.info it appears to get 
>the monomer library from here:

 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz

Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for CCP4 
distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG  and CG <--> CD of Glu 14 
A from the RNase tutorial model.



Huw

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten 
Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian 
M. Schmidt

[ccp4bb] ccp4 release 7.0 update 053

[Charles Ballard]

Dear All

a further update to the series 7.0 ccp4 release containing

* refmac5 - bug fixes and speedup

* crank2 - bug fixes

* arcimboldo

* morda

* fragon (linux and osx)

* buccaneer

* nautilus

* ccp4mg

All the best

Charles

ps - next update to contain shelxe and a monomer library update

[ccp4bb] ccp4 7.0 update 51

[Charles Ballard]

Dear All

just released is ccp4 7.0.051 containing

* phaser 2.8.2 

* dials 1.8.4

* ample 1.4.1

* simbad 0.10.1 (linux and osx)

* arcimboldo

Thanks to the authors of the software, and enjoy

CCP4 Core team

[ccp4bb] UKSR50, 50 Years of UK Synchrotron Radiation meeting

[Charles Ballard]

Dear All

Just a note that the deadline for Abstract Submission for UKSR50 is 31 January

50 Years of Synchrotron Radiation in the UK and its Global Impact
26-29 June 2018, University of Liverpool, UK
www.UKSR50.org
 
Charles 

On behalf of

Sue Waller
 
ASTeC Events Manager
Science and Technology Facilities Council,
Daresbury Laboratory,
Sci-Tech Daresbury
Daresbury
Warrington, Cheshire WA4 4AD.
Tel: 01925 603212 

Re: [ccp4bb] update ccp4 without network

[Charles Ballard]

Dear Wei

there are details at http://www.ccp4.ac.uk/updates/

"
 The tarballs linked to this page are for use with CCP4 updater (ccp4um) in 
off-line mode (e.g. without network connection). You do not need them if your 
CCP4 update works normally through the internet.

Follow instructions below if you do intend to use the CCP4 updater in off-line 
mode.

1. Download and un-compress the update directory:

Linux 32 bit
Linux 64 bit
Mac OS 64 bit
Windows 32 bit
Windows 64 bit

Then, EITHER

2a. use the command line:


ccp4um -uri path-to-update-directory

OR

2b. use the graphic mode:

Launch ccp4um available from CCP4 7.0 installation; answer "No" in the first 
dialog suggesting revision of proxy settings; press "OK" in the second dialog 
suggesting installation of updates from local update directory; navigate to the 
update directory in the file browser, select it and press "Choose". From this 
point on, ccp4um will operate as usual.

"

All the best

Charles

On 22 Jan 2018, at 02:18, Wei Ding wrote:

> Dear all, 
> There is a small cluster in my lab, all of them use the intranet, so we can 
> not update the ccp4 from internet.
> Are there any ways to download the  update packages and install them in my 
> cluster?
> Thank you for your time.
> Wei
> 
> 
> 
> 
> 
> 
> 
>  

[ccp4bb] study weekend live stream

[Charles Ballard]

Dear All

a little clunky, but here are the instructions.  Streaming starts for the 
what's new at 9am GMT tomorrow

Go to 
http://www.stfc.ac.uk/about-us/our-purpose-and-priorities/freedom-of-information/webinars/

And the select your device type.

 
 Charles

[ccp4bb] ccp4online webservices

[Charles Ballard]

Dear All

just a heads up that these will be unavailable from 3pm GMT on Friday 15th 
until the following Monday as we go through fixed line testing on the electrics.

Sorry for any inconvenience

Charles

[ccp4bb] ccp4 release 7.0 update 047

[Charles Ballard]

Dear All

update 047 is out and contains

* mmdb2
- fix for false duplicate sequence number error in case of short residue names

* panddas
- version 2.11.0

* edstats
- new version

* ccp4i2
- updates to molrep interface

* pointless
- 1.115, bug fix for multi-lattice data

* lorestr
- fix to ccp4i interface

* molrep
- fix in PFmod

* ccp4mg
- fix in MG/MrBUMP alignment
- update download from PDBe

* monomers
- add 0WD,2Q5,6G6,6ZL,79F,7K9,8LL,9Q8,FJI,OMZ,QUJ,QVE,RU2,YY9
- fix CPN,CPO,DEF,GCR,IMF,QPT
- replace UAP


CCP4 Core Team

Next update DIALS 1.8.1, auspex plus various bug fixes

[ccp4bb] CCP4 series 7.0 update 042

[Charles Ballard]

Dear All 

updates 042 has been release.  This contains

DIALS 1.6.0 (2017-06-02):
• dials/xia2: dynamic masking of diamond anvil cells for DLS I19-2 high 
pressure experiments
• JMP improvements to mosaic spread estimate (#342, #119)
xia2 0.5.319:
• xia2: new xia2.html
• xia2 fixed for I23 data with distance != 0; xia2/xia2#124 & friends

DIALS 1.6.1 includes xia2 0.5.325 (2017-06-14):
• dials.image_viewer: respect kernel_size parameter (#354)
• Rayonix TIFF format fixes (#370)
• xia2: XDS compatibility fixes (xia2/xia2#131)
• xia2: Trap non-fatal fatal error (xia2/xia2#115)
• xia2: respect batch_range parameter in resolution determination
• xia2: silence xtriage output

DIALS 1.6.2 includes xia2 0.5.328 (2017-06-20):
• cctbx algorithmic stability fixes (cctbx/cctbx_project#43)
• dials.export_mtz: improved error messages (#357)
• xia2: Generate .p4p files in small molecule mode (xia2/xia2#134)

plus associated changes to ccp4i2.

All the best

CCP4 Core team and DIALS developers.

[ccp4bb] ccp4 7.0 update 041

[Charles Ballard]

Dear All

update 041 contains

* rdkit 2017_03_02

* acedrg 
 - update for new rdkit

* ccp4i2
 - update for new rdkit and acedrg

* ccp4mg
 - update for new rdkit

* coot
 - update for new rdkit

Next up dials 1.6.1

All the best

CCP4 core team

[ccp4bb] DLS BAG training, 5th-6th July.

[Charles Ballard]

The Diamond Light Source Macromolecular Crystallography group would like to 
invite both our academic and industrial users to MX beamline training sessions 
on the 5th -6st July 2017.

The aim is to provide MX users with sufficient training to be able to operate 
any of the Diamond MX beamlines efficiently and to get the most benefit from 
their beam-time. The training will involve hands-on sessions on the suite of 
five operational MX beamlines (http://www.diamond.ac.uk/mx-home/) as well as 
offline software sessions.
 
Sessions include:

5th July afternoon session Hands on software: 
Two tutorial sessions:
CCP4
DIALS
6st July, MX beamlines and data room sessions:
MX software: automation in data analysis
Multi axis goniometry / SAD Anomalous data collection
Introduction to VMX-i
I24 new end station/ In-situ diffraction
Fragment screening – I04-1/Lab36
Experiment database: new  ISPyB
 
 
Registration is free-of-charge with lunch provided on the 5th and 6st July, and 
accommodation and dinner for the night of July 5th. Travelling expenses within 
the UK will also be provided. The training is targeted at all users, and is not 
limited to students and post docs. It is essential that each BAG sends at least 
one representative per calendar year.
 
Registration
Places are limited to twenty five participants. The registration deadline is on 
the June 25th 2017 at 11:59.
Registration is now open:
 
http://www.diamond.ac.uk/Home/Events/2017/MX-BAG-TrainingJuly2017.html
 
 
 
For more information please contact:
 
Dr. Pierpaolo Romano
 
Diamond light Source Ltd.
 
pierpaolo.rom...@diamond.ac.uk
 
Tel. 01235 778179

[ccp4bb] CCP4 7.0 update 040

[Charles Ballard]

Dear All, 

another update containing

* ccp4mg/mrbump 
 - improved sequence matching

* molrep
 - packing function improvement

* sfcheck
 - improved EM map handling

* ssm/mmdb
 - fix for bug in forced element name correction

* clipper
 - support for more non-standard spacegroup settings

* ctruncate
 - more stability in truncate procedure

available through ccp4i2, ccp4i and ccp4um on the command line

All the best

CCP4 core team

[ccp4bb] CCP4 release 7.0 update 39

[Charles Ballard]

Dear All

a further update to release 7.0

* crank2
  - update including bug fixes and prasa

* monomers
  - various corrections

* ccp4i2
 - updates to crank2 interface, fix for lidia on linux, fix for missing ccp4mg 
images

* acorn
 - fix for tolerance issues in cell check

* sfcheck
  - cell format correction

All the best

Charles 

[ccp4bb] ccp4 release 7.0 update 037

[Charles Ballard]

Dear All

new update containing

* DIALS 1.5.1

* XIA2 0.5.277

All the best

CCP4 Core team.

[ccp4bb] Structural Chemistry (Crystallography) position at UWA

[Charles Ballard]

Tenurable academic position (level B, C or D) at UWA in Structural Chemistry 
(single crystal X-ray diffraction)

Closing date Weds 17th May

We seek to appoint a high-calibre individual with an outstanding record, 
relative to opportunity, in the application of single crystal X-ray diffraction 
to innovative research problems in Chemistry as a joint appointment in the 
newly formed School of Molecular Sciences and the Centre for Microscopy, 
Characterisation and Analysis (CMCA) at the University of Western Australia.
http://external.jobs.uwa.edu.au/cw/en/job/498562/lecturer-senior-lecturer-associate-professor-of-structural-chemistry

-- 
Charlie Bond – http://bondxray.org/
Head, School of Molecular Sciences
The University of Western Australia
+61 8 6488 4699  - G.02 and 4.32 Bayliss Building

[ccp4bb] Phasing and Model Building satellite meeting in Hyderbad

[Charles Ballard]

Dear All

from http://www.iucr2017.org/program/satellite-meetings/

Phasing and Model Building

Satellite meeting in Hyderabad at CSIR-IICT on 20 – 21 August 2017

This one and half day satellite meeting on the CCP4/Phenix will provide an 
overview of Phasing with Anomalous Diffraction, Molecular Replacement, Model 
Building, Tutorials and Extreme Molecular Replacement.

This satellite meeting will be held in CSIR-Indian Institute of Chemical 
Technology, Hyderabad.

The program includes lectures and tutorials on
Phasing with Anomalous Diffraction – SAD phasing.
Molecular Replacement – Theory and performance.
Model Building in low-resolution and cryo-EM maps; with Coot and Buccaneer and 
with Polder maps.
Model Ligand-building with ARP/wARP.
Extreme Molecular Replacement.
Chairs:
Charles Ballard (STFC Rutherford Appleton Lab, UK; e-mail: 
charles.ball...@stfc.ac.uk)
Tom Terwilliger (Los Alamos National Laboratory, USA; e-mail: 
terwilli...@lanl.gov)
Li-Wei Hung (Los Alamos National Laboratory, USA; e-mail: lwh...@lanl.gov)
Dorothee Liebschner (Los Berkeley National Laboratory; e-mail: 
dcliebsch...@lbl.gov)

Local organizer:
Anthony Addlagatta (CSIR-Indian Institute of Chemical Technology, Hyderabad, 
India; e-mail: anth...@iict.res.in)
Dr. Mangayarkarasi Periasamy Nivaskumar (CSIR-Indian Institute of Chemical 
Technology, Hyderabad, India; e-mail:mangayarkara...@gmail.com)


All the best

Charles

[ccp4bb] CCP4 7.0 update 029

[Charles Ballard]

Dear All

another update to the 7.0 series.  This contains

 * pointless
 - Don't use alternative reindex operators which will fail cell tolerance test 
later. Make the just-reindex C2->I2 conversion more robust.

* pisa
 - Fixed a bug, which could cause disulphide bonds missing in PISA analysis

 * acedrg
 -  may updates including internal tables and algorithms

 * ccp4mg
 - Fix bug in Mg/MrBUMP whereby no atoms are shown. This is to cope with 
changes in multi-domain MrBUMP.

 * dimple
 - check the mtz unit cell against a list of known contaminants

 * ctruncate
 - relax data quality check for data to be used in statistics


Planned for update 030

 * DIALS 1.4.4
 * XIA2 0.5.179

All the best

CCP4 Core team

[ccp4bb] CCP4 study weekend 2017 talks

[Charles Ballard]

Dear All

for those of you who could not watch the live stream, Stuart and Laura have got 
the sessions up on 

https://sas.stfc.ac.uk/vportal/index.jsp

Under "CCP4 Study Weekend 2017"

Best wishes

Charles

[ccp4bb] CCP4 Study Weekend Link for CCP4 Stream

[Charles Ballard]

Dear All

Here is the link for CCP4 Study Weekend


https://sas.stfc.ac.uk/vportal/VideoPlayer.jsp?ccsid=C-5d13ead9-b217-4b5b-bceb-bb37e04bbefe:4#


Charles

[ccp4bb] CCP4 update 026

[Charles Ballard]

Dear All

contains updates to coot for linux 32/64-bit and OS X.  This re-corrects the 
auto-mutate problem on OS X, and various segv such as when using coot-mini-rsr.

Hopefully we now have a functional coot.  

Thank you for bearing with us

Charles on behalf of the CCP4 core team.

[ccp4bb] update 024

[Charles Ballard]

Dear All

hopefully this fixes the coot-0.8.7 issue on OS X and linux.

In this update

  * coot
   - new libcoot-coord-extra to address auto-mutate issue

  * crank2
   - update to 2.0.132

  * ccp4i2
   - gesamt chain selection
   - crank2

  * pointless
   - 1.10.28, fix for NaN with some centrosymmetric space groups

  * ccp4i
   - crank2 update

  * blend
   - 0.6.22

  * qtrview
  - fix for phaser log files
  
  * refmac
  - fix for atom name confusion when link involves monomers of same type

  * monomers
   - various additions and fixes.

All the best

Charles

Re: [ccp4bb] ccp4 release 7.0 update 023

[Charles Ballard]

Dear All

the current status is that we have a fix in testing.  The update has other 
elements in there that have too be tested too.  Hopefully not too long now

Charles 

On 23 Nov 2016, at 15:50, wtempel wrote:

> Hello,
> after installing updates 22 and 23 on an Ubuntu-14.04 (x86_64) box, I have 
> yet to successfully “mutate” any amino acid residue in COOT.
> (setup-mutate 1) is printed to the terminal, followed by a line confirming on 
> which atom I have clicked, but the residue type selection dialog does not 
> appear. Coot just hangs at this point. Has anyone else encountered this 
> problem?
> Regards.
> Wolfram
> 
> 
> On Wed, Nov 23, 2016 at 9:41 AM, Charles Ballard <charles.ball...@stfc.ac.uk> 
> wrote:
> Dear All
> 
> ccp4 update 23 has just been released.  It contains
> 
>   * coot:
>  - update to coot 0.8.7 on linux and os x
> 
>   * phaser:
> - Bug fixes: ccp4i and interaction with Arcimboldo
> - Update: Improved treatment of systematically weak data (e.g. severe 
> anisotropy)
> 
>   * ccp4i
>  - bug fix: phaser, updated defaults for phaser tasks
>  - bug fix: mrbump, updated defaults for phaser
> 
> All the best
> 
> Charles  Ballard on behalf of CCP4 core team
> 

Re: [ccp4bb] ccp4 release 7.0 update 023

[Charles Ballard]

Looking into this.  The automutate works if it is any help.

Charles

On 23 Nov 2016, at 15:50, wtempel wrote:

> Hello,
> after installing updates 22 and 23 on an Ubuntu-14.04 (x86_64) box, I have 
> yet to successfully “mutate” any amino acid residue in COOT.
> (setup-mutate 1) is printed to the terminal, followed by a line confirming on 
> which atom I have clicked, but the residue type selection dialog does not 
> appear. Coot just hangs at this point. Has anyone else encountered this 
> problem?
> Regards.
> Wolfram
> 
> 
> On Wed, Nov 23, 2016 at 9:41 AM, Charles Ballard <charles.ball...@stfc.ac.uk> 
> wrote:
> Dear All
> 
> ccp4 update 23 has just been released.  It contains
> 
>   * coot:
>  - update to coot 0.8.7 on linux and os x
> 
>   * phaser:
> - Bug fixes: ccp4i and interaction with Arcimboldo
> - Update: Improved treatment of systematically weak data (e.g. severe 
> anisotropy)
> 
>   * ccp4i
>  - bug fix: phaser, updated defaults for phaser tasks
>  - bug fix: mrbump, updated defaults for phaser
> 
> All the best
> 
> Charles  Ballard on behalf of CCP4 core team
> 

[ccp4bb] ccp4 release 7.0 update 023

[Charles Ballard]

Dear All

ccp4 update 23 has just been released.  It contains

  * coot: 
 - update to coot 0.8.7 on linux and os x

  * phaser:
- Bug fixes: ccp4i and interaction with Arcimboldo
- Update: Improved treatment of systematically weak data (e.g. severe 
anisotropy)

  * ccp4i
 - bug fix: phaser, updated defaults for phaser tasks
 - bug fix: mrbump, updated defaults for phaser

All the best

Charles  Ballard on behalf of CCP4 core team

[ccp4bb] CCP4/SPring-8 workshop

[Charles Ballard]

Dear All

just a reminder that there will be a CCP4 workshop at SPring-8, Japan, from 
23-27 January next year.  The workshop will cover the structure solution 
process, consisting of lectures, tutorials and problem solving sessions.  
Lectures include Garib Murshudov on refinement, Phil Evans on scaling using 
aimless and James Parkhurst from the DIALS team.  The deadline for application 
is the 10th of December.

More details, including how to apply, are on the CCP4 website.

http://www.ccp4.ac.uk/schools/Japan-2016/index.php

Best regards

Charles 

[ccp4bb] CCP4-6.5 Update 013

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.5 series has just been released, consisting
of the following changes

programs:

* seqwt
- sequence length limit increase

* zanuda
- update

* pointless
- update to 1.9.33

* amiless
- update to 0.5.12

libraries:

* clipper
- correction to setting of NaN on some systems
- fixes cbuccaneer issue on windows

* monomers
- various additions and corrections

interfaces:

* aimless task
* imosflm
- fix for issue with parallel processing in 7.2.0

documentation

* aimless, pointless, and various others


Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

[ccp4bb] Third CCP4-OIST workshop in Okinawa, third call

[Charles Ballard]

Dear Colleagues,

a reminder,  the third  CCP4 structure solution school at the Okinawa Institute 
of Science and Technology (OIST), Okinawa. All details can be found at 
http://www.ccp4.ac.uk/schools/OIST-2015 or contact ccp4_okin...@oist.jp

Title:
CCP4 school: From data processing to structure refinement and beyond
Dates: November 2 to 7, 2015
Site: Okinawa Institute of Science and Technology, Okinawa, Japan

The school content:

Software workshop: the workshop will be taught by authors and other experts, 
including Garib Murshudov (refmac), Victor Lamzin (arp/warp), Robbie Joosten 
(pdb_redo) and Phil Evans (aimless).  It will be organized in three Sections - 
lectures, tutorials and hands-on trouble-shooting.  We will also be covering 
the use of DIALS for data processing and the new ccp4 interface.

There will be model data sets available for tutorials but data, provided by 
participants, will have higher priority for the hands-on sessions.

Applicants:

Graduate students, postdoctoral researchers and young scientists at the 
assistant professor level are encouraged to apply. Only 25 applicants will be 
selected for participation. Participants of the workshop are strongly 
encouraged to bring their own problem data sets so the problems can be 
addressed during data collection workshop and/or hands-on sessions.

Application:

Application deadline is 22 August. Application form, the program, contact info 
and other details can be found at http://www.ccp4.ac.uk/schools/OIST-2015

Fees: 

There is no fee for the workshop. The students will be responsible for their 
transportation costs outside Okinawa.  Lodging will be provided at the OIST 
Guest House Seaside House.  The workshop will also cover the expenses for all 
meals and refreshments.

Fadel Samatay, Charles Ballard

e-mail contact: 

ccp4_okin...@oist.jp

[ccp4bb] CCP4-6.5 Update 010

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.5 series has just been released, consisting
of the following changes

 * refmac5 (all platforms)
 - various bug fixes and new program header2matr

 * prosmart (all)
 - fixed issue with degenerate PDB files

* pointless (all)
 - 1.9.31, allow real-space reindex operators

* aimless (all)
 - 0.5.9 make ABSORPTION lmax work. Bug fix in RESTORE with TILES

* ctruncate (all)
 - fix for output column names issue

 * blend (all)
 - 0.6.7, Fixed a bug responsible for the deletion of any file whose name 
includes reference

 * 'libg  (all)
 - dps for stacking planes of DNA/RNA

 * examples  (all)
 - corrections python.exam, pyrogen.exam and gere.seq

 * documentation (all) 
 - update aimless and pointless documentation

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

[ccp4bb] Third CCP4-OIST workshop in Okinawa, second call

[Charles Ballard]

Dear Colleagues,

we are pleased to announce the third  CCP4 structure solution school at the 
Okinawa Institute of Science and Technology (OIST), Okinawa. All details can be 
found at http://www.ccp4.ac.uk/schools/OIST-2015

Title:
CCP4 school: From data processing to structure refinement and beyond
Dates: November 2 to 7, 2015
Site: Okinawa Institute of Science and Technology, Okinawa, Japan

The school content:

Software workshop: the workshop will be taught by authors and other experts, 
including Garib Murshudov (refmac), Victor Lamzin (arp/warp), Robbie Joosten 
(pdb_redo) and Phil Evans (aimless).  It will be organized in three Sections - 
lectures, tutorials and hands-on trouble-shooting.  We will also be covering 
the use of DIALS for data processing and the new ccp4 interface.

There will be model data sets available for tutorials but data, provided by 
participants, will have higher priority for the hands-on sessions.

Applicants:

Graduate students, postdoctoral researchers and young scientists at the 
assistant professor level are encouraged to apply. Only 25 applicants will be 
selected for participation. Participants of the workshop are strongly 
encouraged to bring their own problem data sets so the problems can be 
addressed during data collection workshop and/or hands-on sessions.

Application:

Application deadline is 22 August. Application form, the program, contact info 
and other details can be found at http://www.ccp4.ac.uk/schools/OIST-2015

Fees: 

There is no fee for the workshop. The students will be responsible for their 
transportation costs outside Okinawa.  Lodging will be provided at the OIST 
Guest House Seaside House.  The workshop will also cover the expenses for all 
meals and refreshments.

Fadel Samatay, Charles Ballard

[ccp4bb] CCP4-6.5 Update 009

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.5 series has just been released, consisting
of the following changes

* ARP/wARP (all platforms excluding windows)
 - activation of postinstall script for standalone arp/warp

* crank2 (all platforms)
 - several bugfixes
 - javascript output

* jsrview (all)
 - new javascript output

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

[ccp4bb] CCP4-6.5 Update 008

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.5 series has just been released, consisting
of the following changes

* ARP/wARP (all platforms excluding windows)
 - Solvent search run from ccp4i
 - The length of the file names in ligand search
 - Selection of MTZ column labels for protein model building

* Molrep (all platforms)
 - improve multi-copy search (nmr=4)

* aimless (all)
 - 0.5.8
 - bug fix for case SCALES CONSTANT BROTATION with one run
 - fixed bug when there are different resolution limits for different datasets

* ccp4i (all)
 - updated autosharp interface
 - updated blend interface/fix

* privateer
 - bug fixes

* clipper library (all)
 - fix bug reading anomalous data from cif file

* imosflm interface (all)
 - fix for atan issue

* dimple pipeline (all)
 - bug fixes

* ccp4 programs (all)
 - seqwt, update 
 - lsqkab, improve handling of nucleic acids and increased dimensions

* documentation (all)
 - updates

* acedrg (all)
 - fall back values of bonds added

* blend (all)
 -  0.6.6 01/04/2015
 - Added two columns in file CLUSTERS.txt which tell two datasets having 
current values of
LCV and aLCV (module blend1.R).
 - fixed bug for mode -g D. Now data sets at the bottom are printed correctly 
(module blend4.R).

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

[ccp4bb] CCP4-6.5 Update 006

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.5 series has just been released, consisting
of the following changes

* ccp4-progs
- rwcontents: support for strict NCS records, via pdb header/fix

* blend
- update to 0.6.3

* ccp4mg
- addition of pdbview (except windows)

* pointless
- Bug fixes
- update to 1.9.29

* prelyscar
- Bug fixes, documentation fixes

* 'imosflm
- fix for issue with 0 oscillation angle

* acedrg
- major update

* atoms_electron.lib
- Electron scattering terms for use in refmac (cyro-EM)


Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

Re: [ccp4bb] CCP4-6.5 Update 007

[Charles Ballard]

Dear All

for the record, this is, of course, Update 006

Charles

On 14 Mar 2015, at 10:51, Charles Ballard wrote:

 Dear CCP4 Users
 
 An update for the CCP4-6.5 series has just been released, consisting
 of the following changes
 
 * ccp4-progs
 - areaimol - bug fixes
 - r500 - update=
 - standard_geometry.cif - update
 
 * imosflm/mosflm
 - update to 7.1.3
 
 * Molrep
 - fix for bug in multi-copy search
 
 * aimless
 - 0.5.7, bug fixes
 
 * privateer
 - extended support for disaccharides
 - added support for external validation strings
 
 * prosmart
 - minor update to h-bond restaint generation
 
 * mmdb2
 - update to rwbrook interface
 
 * ccp4i'
 - updated autoSHARP interface
 
 Please report any bugs to c...@stfc.ac.uk.
 
 Many thanks for using CCP4.
 
 The CCP4 Core Team
 
 

[ccp4bb] Third CCP4-OIST workshop in Okinawa

[Charles Ballard]

Dear Colleagues,

we are pleased to announce the third  CCP4 structure solution school at the 
Okinawa Institute of Science and Technology (OIST), Okinawa. All details can be 
found at http://www.ccp4.ac.uk/schools/OIST-2015

Title:
CCP4 school: From data processing to structure refinement and beyond
Dates: November 2 to 7, 2015
Site: Okinawa Institute of Science and Technology, Okinawa, Japan

The school content:

Software workshop: the workshop will be taught by authors and other experts, 
including Garib Murshudov (refmac) and Phil Evans (aimless).  It will be 
organized in three Sections - lectures, tutorials and hands-on 
trouble-shooting.  We will also be covering the use of DIALS for data 
processing and the new ccp4 interface.
There will be model data sets available for tutorials but data, provided by 
participants, will have higher priority for the hands-on sessions.

Applicants:

Graduate students, postdoctoral researchers and young scientists at the 
assistant professor level are encouraged to apply. Only 25 applicants will be 
selected for participation. Participants of the workshop are strongly 
encouraged to bring their own problem data sets so the problems can be 
addressed during data collection workshop and/or hands-on sessions.

Application:

Application deadline is 22 August. Application form, the program, contact info 
and other details can be found at http://www.ccp4.ac.uk/schools/OIST-2015

Fees: 

There is no fee for the workshop. The students will be responsible for their 
transportation costs outside Okinawa.  Lodging will be provided at the OIST 
Guest House Seaside House.  The workshop will also cover the expenses for all 
meals and refreshments.

Fadel Samatay, Charles Ballard

[ccp4bb] CCP4-6.5 Update 006

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.5 series has just been released, consisting
of the following changes

* ccp4-progs
- areaimol - bug fixes
- r500 - update=
- standard_geometry.cif - update

* imosflm/mosflm
- update to 7.1.3

* Molrep
- fix for bug in multi-copy search

* aimless
- 0.5.7, bug fixes

* privateer
- extended support for disaccharides
- added support for external validation strings

* prosmart
- minor update to h-bond restaint generation

* mmdb2
- update to rwbrook interface

* ccp4i'
- updated autoSHARP interface

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

[ccp4bb] Fwd: CCP4-6.5 Update 005

[charles . ballard]

Dear CCP4 Users

An update for the CCP4-6.5 series has just been released, consisting
of the following changes

* ccp4mg (all platforms)
- update to 2.10.4.
- improved SMILES parser.
- Get monomer from library correctly bonds H atoms.
- Badly-named ligands no longer generate bad bonding schemes.
- Improvements to glyco-blocks representation.

* ccp4srs (all)
- update to descriptions and API.

* ccp4i(all)
- fix for shelxe4mr.
-  libg-related updates to the refmac gui.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

[ccp4bb] ccp4 offline updates

[Charles Ballard]

Dear All

update 004 included a new updater for use with off line updates.  This updater 
is available stand alone from http://www.ccp4.ac.uk/updates/, just follow the 
instructions.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

[ccp4bb] CCP4-6.5 Update 004

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.5 series has just been released, consisting
of the following changes

* ccp4 updater (all platforms)
- allows for offline updates
- details at http://www.ccp4.ac.uk/updates

* pointless (all)
- update to 1.9.27
- update for processing XDS INTEGRATE files

* aimless (all)
- update to 0.5.4
- bug fix update

* refmac5 (all)
- fix for bug in hydrogen generation

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

[ccp4bb] CCP4-6.5 Update 003

[charles . ballard]

Dear CCP4 Users

An update for the CCP4-6.5 series has just been released, consisting
of the following changes

 * refmac (all)
 - bug fix for occupancy refinement

 * imosflm/mosflm
 - update to 7.1.2
 - bug fix update

 * pointless (all platforms)
 - update to 1.9.25
 - Some fixes for Saint files. Fix to long-standing but rare bug in hash table
 - Improvements to analysis of 6-fold screws (though still needs further work), 
including avoiding an occasional crash

 * aimless (all)
 - update to 0.5.2
 - bug fix for already merged data

 * feckless (all)
 - update to 0.0.5
 - correction to hash

 * ctruncate (all)
 - update to 1.16.9
 - fix for sigma=0

 * molrep (all)
 - improved multi-copy search

 * sfcheck (all)
 - bug fixes

 * monomer library (all)
 - added missing components

 * ccp4i (all)
 - mrSHELXE renamed to shelxe4mr

 * ccp4.setup (linux, osx)
 - fixed setup scripts for MANPATH issues



Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

[ccp4bb] CCP4-6.5 Update 002

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.5 series has just been released, consisting
of the following changes

 * crank2 (all)
  - Several bug fixes, mainly related to the graphical interface and 
Crunch2/fix

* clipper-progs (all)
  - ctruncate: fix to issue with estimation of alpha in Murray-Rust plot/fix

* phaser (all)
  - version correction, 2.5.7

* blend (all)
 - Fixed a bug in keywords management; now accepting both uppercase and 
lowercase. Fixed a bug for the calculation of aLCV.

* privateer  (all)
  - Minor bugfix

* monomer  (all)
  - Several bug-fixes and addition of new compounds

* ccp4-progs  (all)
  - Zanuda: adjustments to changes in refmac output pdb-file; bypass for P1 
refinement failure

* ccp4  (all)
  - MrSHELXE: temporarily switched off pdb- and mtz-files crosscheck
  - Fix for handling Protein/DNA complex sequences in Matthews interface
/component

* documentation (all)
  - minor corrections and updates

* mrbump (all)
  - Fix for sftools path length problem and Mac fix for MAFFT


Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

[ccp4bb] CCP4 Study Weekend 2015

[Charles Ballard]

The CCP4 Study Weekend (7 - 9 January 2015)
East Midlands Conference Centre, University of Nottingham
 
Wednesday 7 - MX User Meeting
Thursday 8 / Friday 9 - CCP4 Study Weekend
 
Advances in Experimental Phasing
 
We cordially invite you to participate in this year's Study Weekend at the the 
East Midlands Conference Centre, University of Nottingham. The annual CCP4 
Study Weekend is a chance to shake off the post-New Year torpor, and work hard 
and play hard with your fellow crystallographers. Once again, we have put 
together an exciting scientific programme for the Thursday and Friday, either 
side of the traditional conference dinner. Please also check out the satellite 
meetings which may be of interest. The Study Weekend is a chance to catch up 
with old friends, but is also a chance to meet the CCP4 staff who will be there 
in force to demonstrate the latest software and to answer questions - please 
say hello!
 
This year, the topic for the Study Weekend is Advances in Experimental 
Phasing. In keeping with previous CCP4 meetings, the lectures will focus on 
the presentation and discussion of advanced methods and techniques developed 
and used by the leaders in the field.
 
Scientific Organisers
Thomas Schneider - EMBL Hamburg (Germany)
Airlie McCoy - University of Cambridge (UK)

Further details of the program and the registration are at 
http://www.cse.scitech.ac.uk/events/CCP4_2015

Terms and Conditions apply.  Please read the cancellation policy before 
applying.


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[ccp4bb] CCP4 structure solution workshop at the Photon Factory - deadline 13th September

[Charles Ballard]

Dear Colleagues,

the deadline for the registration at the  CCP4 structure solution school at the 
Photon Factory, Tsukuba, is fast approaching on the 13th of September (if you 
want the cheap accommodation). All details can be found at 
http://www.ccp4.ac.uk/schools/Japan-2014

Title:
CCP4 school: From data processing to structure refinement and beyond
Dates: November 4 to 8, 2014
Site: The Photon Factory. Tsukuba, Japan

The school content:

Software workshop: The rest of the time after data collection will feature many 
modern crystallographic software packages taught by authors and other experts. 
It will be organized in three Sections - lectures, tutorials and hands-on 
trouble-shooting.
There will be model data sets available for tutorials but data, provided by 
participants, will have higher priority for the hands-on sessions.

Applicants:

Graduate students, postdoctoral researchers and young scientists at the 
assistant professor level are encouraged to apply. Only 20 applicants will be 
selected for participation. Participants of the workshop are strongly 
encouraged to bring their own problem data sets so the problems can be 
addressed during data collection workshop and/or hands-on sessions.

Application:

Application deadline is 13 September. Application form, the program, contact 
info and other details can be found at 
http://www.ccp4.ac.uk/schools/Japan-2014/index.php

Fees: 

There is no fee for the workshop, but the students will be responsible for 
their transportation and accommodation costs.  A limited number of places will 
be available in the KEK dormitory on a first come basis.

Naohiro Matsugaki, Charles Ballard
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[ccp4bb] CCP4-6.4.0 Update 021

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes

• monomer library:
   – corrected or added several entries

• ctruncate:
  – update to 1.15.10
  – correction for flat prior issue introduced in 1.15.6

• aimless:
   – update to 0.3.11
   – fix for nasty bug for XDS - pointless giving Assertion failed

• pointless:
 – update to 1.9.16
 – fix for when combining files in C2 and I2 or when I2 is favoured over C2

Note that auto-updates work only with CCP4 6.4.0 series, therefore
please upgrade if necessary.  The Update Manager is now included in the
package so you do not need to install it separately.  In addition, all
available updates will be installed automatically if you are using Setup
Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team--
Scanned by iCritical.

[ccp4bb] 3rd call, CCP4 structure solution workshop at the Photon Factory

[Charles Ballard]

Dear Colleagues,

we are pleased to announce the  CCP4 structure solution school at the Photon 
Factory, Tsukuba. All details can be found at 
http://www.ccp4.ac.uk/schools/Japan-2014

Title:
CCP4 school: From data processing to structure refinement and beyond
Dates: November 4 to 8, 2014
Site: The Photon Factory. Tsukuba, Japan

The school content:

Software workshop: The rest of the time after data collection will feature many 
modern crystallographic software packages taught by authors and other experts. 
It will be organized in three Sections - lectures, tutorials and hands-on 
trouble-shooting.
There will be model data sets available for tutorials but data, provided by 
participants, will have higher priority for the hands-on sessions.

Applicants:

Graduate students, postdoctoral researchers and young scientists at the 
assistant professor level are encouraged to apply. Only 20 applicants will be 
selected for participation. Participants of the workshop are strongly 
encouraged to bring their own problem data sets so the problems can be 
addressed during data collection workshop and/or hands-on sessions.

Application:

Application deadline is 13 September. Application form, the program, contact 
info and other details can be found at 
http://www.ccp4.ac.uk/schools/Japan-2014/index.php

Fees: 

There is no fee for the workshop, but the students will be responsible for 
their transportation and accommodation costs.  A limited number of places will 
be available in the KEK dormitory on a first come basis.

Naohiro Matsugaki, Charles Ballard
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[ccp4bb] 2nd call, CCP4 structure solution workshop at the Photon Factory

[Charles Ballard]

Dear Colleagues,

we are pleased to announce the  CCP4 structure solution school at the Photon 
Factory, Tsukuba. All details can be found at 
http://www.ccp4.ac.uk/schools/Japan-2014

Title:
CCP4 school: From data processing to structure refinement and beyond
Dates: November 4 to 8, 2014
Site: The Photon Factory. Tsukuba, Japan

The school content:

Software workshop: The rest of the time after data collection will feature many 
modern crystallographic software packages taught by authors and other experts. 
It will be organized in three Sections - lectures, tutorials and hands-on 
trouble-shooting.
There will be model data sets available for tutorials but data, provided by 
participants, will have higher priority for the hands-on sessions.

Applicants:

Graduate students, postdoctoral researchers and young scientists at the 
assistant professor level are encouraged to apply. Only 20 applicants will be 
selected for participation. Participants of the workshop are strongly 
encouraged to bring their own problem data sets so the problems can be 
addressed during data collection workshop and/or hands-on sessions.

Application:

Application deadline is 13 September. Application form, the program, contact 
info and other details can be found at 
http://www.ccp4.ac.uk/schools/Japan-2014/index.php

Fees: 

There is no fee for the workshop, but the students will be responsible for 
their transportation and accommodation costs.  A limited number of places will 
be available in the KEK dormitory on a first come basis.

Naohiro Matsugaki, Charles Ballard


-- 
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[ccp4bb] CCP4-6.4.0 Update 019

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes

• ctruncate (all platforms):
 – 1.15.5, fix to increase stability of normal calculation

• prodrg (all):
 – updated parameter file

• mrbump (all):
 – rebuild options including use of SHELXE (available separately from SHELX 
website
for phase improvement and C-alpha trace post MR
 – condor queue system support
 – HHpred support (command line only)

Note that auto-updates work only with CCP4 6.4.0 series, therefore
please upgrade if necessary.  The Update Manager is now included in the
package so you do not need to install it separately.  In addition, all
available updates will be installed automatically if you are using Setup
Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

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[ccp4bb] CCP4 structure solution workshop at the Photon Factory

[Charles Ballard]

Dear Colleagues,

we are pleased to announce the  CCP4 structure solution school at the Photon 
Factory, Tsukuba. All details can be found at 
http://www.ccp4.ac.uk/schools/Japan-2014

Title:
CCP4 school: From data processing to structure refinement and beyond
Dates: November 4 to 8, 2014
Site: The Photon Factory. Tsukuba, Japan

The school content:

Software workshop: The rest of the time after data collection will feature many 
modern crystallographic software packages taught by authors and other experts. 
It will be organized in three Sections - lectures, tutorials and hands-on 
trouble-shooting.
There will be model data sets available for tutorials but data, provided by 
participants, will have higher priority for the hands-on sessions.

Applicants:

Graduate students, postdoctoral researchers and young scientists at the 
assistant professor level are encouraged to apply. Only 20 applicants will be 
selected for participation. Participants of the workshop are strongly 
encouraged to bring their own problem data sets so the problems can be 
addressed during data collection workshop and/or hands-on sessions.

Application:

Application deadline is 13 September. Application form, the program, contact 
info and other details can be found at 
http://www.ccp4.ac.uk/schools/Japan-2014/index.php

Fees: 

There is no fee for the workshop, but the students will be responsible for 
their transportation and accommodation costs.  A limited number of places will 
be available in the KEK dormitory on a first come basis.

Naohiro Matsugaki, Charles Ballard
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[ccp4bb] CCP4-6.4.0 Update 016

[Charles Ballard]

Dear CCP4 users,

An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes:

* prelyscar: New program, predictor of lysine caboxylation
* CCP4i: prelyscar, new interface
* pdb2to3: fixed for new ccp4srs
* rapper: downgrade optimisation to workaround segv on OS X
* Xia2: workaround aimless ASSERT
* aimless: bug fixes, update to 0.3.5
* pdbse: copying chain ID into segment ID fields blocked for all PDB files 
except if marked for XPLOR use
* cparrot: bug fixes

Note that auto-updates work only with CCP4 6.4.0 series, therefore
please upgrade if necessary. The Update Manager is now included in the
package so you do not need to install it separately. In addition, all
available updates will be installed automatically if you are using
Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team
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[ccp4bb] CCP4-6.4.0 Update 014

[charles . ballard]

Dear CCP4 Users

An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes

* refmac5: 5.8.0071, fix for peptide planarity
* buccaneer: version 1.6 with new MR modes and user interface
* pointless: version 1.9.8, fixes for multilattice and output in qtrview
* aimiless: version 0.3.3, added option to analyse data against reference 
dataset
* ctruncate: version 1.15.4, ML target used in normalisation, bug fixes.
* viewhkl: Additional visual control to enhance weak reflections
* crank: fixes for mapro under os x/windows.

Note that auto-updates work only with CCP4 6.4.0 series, therefore
please upgrade if necessary.  The Update Manager is now included in the
package so you do not need to install it separately.  In addition, all
available updates will be installed automatically if you are using Setup
Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team


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[ccp4bb] CCP4-6.4.0 Update 013

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes

* qtpisa and pisa
 - New features
 + concentration dependence of predicted oligomeric states to aid the 
identification of biological units in protein's working conditions
 + multi-parameter interaction radar for more consistent discrimination 
between biologically-relevant interfaces and crystal contacts
 + help support (qtpisa only)

Note that auto-updates work only with CCP4 6.4.0 series, therefore
please upgrade if necessary.  The Update Manager is now included in the
package so you do not need to install it separately.  In addition, all
available updates will be installed automatically if you are using Setup
Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team--
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[ccp4bb] CCP4-6.4.0 Update 012

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes

* crank2
  - New SAD phasing pipeline

* monomer library
 - Corrections to OXY, PO4 and URE

* imosflm
 - Update to version 7.1.1

Note that auto-updates work only with CCP4 6.4.0 series, therefore
please upgrade if necessary.  The Update Manager is now included in the
package so you do not need to install it separately.  In addition, all
available updates will be installed automatically if you are using Setup
Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

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[ccp4bb] CCP4-6.4.0 Update 011

[Charles Ballard]

Dear CCP4 Users,

An update for the CCP4-6.4.0 series has just been released, consisting of the 
following changes

◆ ipmosflm(windows)
- update to 7.1.0

◆ imosflm(all platforms)
- fix for MOSFLM_EXEC not being set under csh
- fix for false missing ipmosflm error

Note that auto-updates work only with CCP4 6.4.0 series, therefore please 
upgrade if necessary.
The Update Manager is now included in the package so you do not need to install 
it separately.
In addition, all available updates will be installed automatically if you are 
using Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

the CCP4 core team.
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[ccp4bb] CCP4-6.4.0 Update 010

[Charles Ballard]

Dear CCP4 Users,

An update for the CCP4-6.4.0 series has just been released, consisting of the 
following changes

◆ ARP/wARP (Mac, Linux)
1. Fix in the use of free R flag in the ARP/wARP CCP4i interface for solvent 
building
2. Fix in the identification of non-crystallographic symmetry that in some 
cases led to zero target number of residues
3. Fix in recognition of secondary structural elements that in rare cases led 
to a 'bus error'
* Many thanks to Marcin Cymborowski, Carmelo Giacovazzo, Ulrich Gohlke and Vito 
Calderone for reporting these problem cases.

◆ imosflm (update to 7.1.0 for all platforms)
- Multi-lattice implementation
- Parallel processing of wedges

◆ feckless (0.0.2, all)
- Fixes several major bugs

◆ pointless (1.9.2, all)
- General update for multi-lattice

◆ ctruncate (1.13.13, all)
- Fixes negative eigenvalue exit during anisotropy analysis

◆ cnautilus (0.4, all)
- Some basic output markup and numbering of output sequences

◆ refmac5 (5.8.006, all)
- Fixes for ARP/wARP and forthcoming release of Crank2




Note that auto-updates work only with CCP4 6.4.0 series, therefore please 
upgrade if necessary.
The Update Manager is now included in the package so you do not need to install 
it separately.
In addition, all available updates will be installed automatically if you are 
using Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

the CCP4 core team.
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Re: [ccp4bb] CCP4-6.4.0 Update 010

[Charles Ballard]

Dear CCP4 Users

as ever with life, a couple of errors have made it into the update

a. ipmosflm.exe 7.1.0 is missing from the windows update

b. a small change in ccp4i/src/imosflm means that MOSFLM_EXEC is not being set 
for csh users.

The suggested remedy is for windows users to hold off this update until we get 
the next update out.  csh shell users should temporarily add MOSFLM_EXEC 
ipmosflm to their environments.

Charles


On 7 Mar 2014, at 11:10, Charles Ballard wrote:

 Dear CCP4 Users,
 
 An update for the CCP4-6.4.0 series has just been released, consisting of the 
 following changes
 
 ◆ ARP/wARP (Mac, Linux)
 1. Fix in the use of free R flag in the ARP/wARP CCP4i interface for solvent 
 building
 2. Fix in the identification of non-crystallographic symmetry that in some 
 cases led to zero target number of residues
 3. Fix in recognition of secondary structural elements that in rare cases led 
 to a 'bus error'
 * Many thanks to Marcin Cymborowski, Carmelo Giacovazzo, Ulrich Gohlke and 
 Vito Calderone for reporting these problem cases.
 
 ◆ imosflm (update to 7.1.0 for all platforms)
 - Multi-lattice implementation
 - Parallel processing of wedges
 
 ◆ feckless (0.0.2, all)
 - Fixes several major bugs
 
 ◆ pointless (1.9.2, all)
 - General update for multi-lattice
 
 ◆ ctruncate (1.13.13, all)
 - Fixes negative eigenvalue exit during anisotropy analysis
 
 ◆ cnautilus (0.4, all)
 - Some basic output markup and numbering of output sequences
 
 ◆ refmac5 (5.8.006, all)
 - Fixes for ARP/wARP and forthcoming release of Crank2
 
 
 
 
 Note that auto-updates work only with CCP4 6.4.0 series, therefore please 
 upgrade if necessary.
 The Update Manager is now included in the package so you do not need to 
 install it separately.
 In addition, all available updates will be installed automatically if you are 
 using Setup Manager for CCP4 installation.
 
 Please report any bugs to c...@stfc.ac.uk.
 
 Many thanks for using CCP4.
 
 the CCP4 core team.
 
 -- 
 Scanned by iCritical.
 
 


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[ccp4bb] CCP4-6.4.0 Update 008

[Charles Ballard]

Dear CCP4 Users,

An update for the CCP4-6.4.0 series has just been released, consisting of the 
following changes:

 *   phaser
*   update to 2.5.6
 *   ccp4i
*   phaser_EP: corrected HySS output parsing

Note that auto-updates work only with CCP4 6.4.0 series, therefore please 
upgrade if necessary.
The Update Manager is now included in the package so you do not need to install 
it separately.
In addition, all available updates will be installed automatically if you are 
using Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4.

Charles

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[ccp4bb] CCP4 Study Weekend Live Stream

[Charles Ballard]

Dear All

the live stream of the CCP4 Study Weekend 2014 at Nottingham University on 
Complimentary Methods - a two way street should be available on 4-5 January 
at the following web address

http://www.stfc.ac.uk/webinars

Charles Ballard
CCP4

ps - link also available through our home page www.ccp4.ac.uk
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Re: [ccp4bb] CPRODRG segfault on Mac OS X 10.9,

[Charles Ballard]

Dear All

as Eugene says this will go into an update, but until then there is a probable 
fixed binary at

ftp://ftp.ccp4.ac.uk/ccp4/6.4.0/updates/osx/cprodrg

Charles Ballard

On 25 Nov 2013, at 14:03, Eugene Krissinel wrote:

 Dear All,
 
 CCP4 Core Group is aware of the issue and is looking into it. Once fixed, new 
 cprodrg will be put into update.
 
 Thank you,
 
 Eugene Krissinel
 
 On 25 Nov 2013, at 13:46, Oliver Clarke wrote:
 
 Hi all,
 
 I have recently been trying to use the LIDIA ligand-viewer of Coot, which 
 calls cprodrg.
 
 I am running CCP4 6.4.0 with all the latest updates on a Macbook Air 
 (mid-2012 model) with OS X 10.9 installed and the latest nightly build of 
 coot (r4833).
 
 Unfortunately, when I run cprodrg either via coot or from the command line, 
 it crashes with what appears to be a segmentation violation (stderr 
 reproduced below). Does anyone have any thoughts as to what may be causing 
 this or how to fix it?
 
 Many thanks,
 Oliver
 
 BFONT COLOR=#FF!--SUMMARY_BEGIN--
 html !-- CCP4 HTML LOGFILE --
 hr
 !--SUMMARY_END--/FONT/B
 BFONT COLOR=#FF!--SUMMARY_BEGIN--
 pre
 
 ###
 ###
 ###
 ### CCP4 6.4: PRODRGversion 2.5-AA0717 : ##
 ###
 User: olibclarke  Run date: 25/11/2013 Run time: 08:34:44
 
 
 Please reference: Collaborative Computational Project, Number 4. 1994.
 The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 
 760-763.
 as well as any specific reference in the program write-up.
 
 !--SUMMARY_END--/FONT/B
 forrtl: severe (180): SIGBUS, bus error occurred
 Image  PCRoutineLineSource
 cprodrg000113FC  Unknown   Unknown  Unknown
 cprodrg000111AC  Unknown   Unknown  Unknown
 cprodrg00011164  Unknown   Unknown  Unknown
 
 
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Re: [ccp4bb] Error with iMosflm 1.0.7 of CCP4 6.4.0 kit

[Charles Ballard]

Dear All

the soon to be released update (via the update mechanism)  will address this by 
applying the patch to imosflm.tcl. 

Charles Ballard
CCP4

On 23 Oct 2013, at 23:35, Andreas Förster wrote:

 Hi David,
 
 I've just renamed the ipmosflm in $CCP4/bin to ipmosflm_new and then defined
 
 MOSFLM_EXEC as /path/to/ccp4-6.3.0/bin/ipmosflm.
 
 CCP4 6.3 needs to be installed for this to work.
 
 
 Andreas
 
 
 
 On 23/10/2013 5:39, David Schuller wrote:
 iMosflm developers:
 
 I have installed CCP4 6.4.0, which includes iMosflm 1.0.7 and ipmosflm
 7.0.9.
 This is on Scientific Linux 6.x, 64 bit distribution.
 
 When I run iMosflm either from the command shell or from the ccp4i
 interface, I get an error just like this:
 http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27243.html
 
 iMosflm claims it cannot run without mosflm 7.0.9, followed by output
 indicating that mosflm 7.0.9 runs. (See attached screen capture of error
 message)
 Note the linked description is for the previous versions of imosflm amd
 mosflm, so this error seems to be a repeat.
 
 I downloaded the iMosflm and ipmosflm executables from the iMosflm web
 site, put ipmosflm in my executable directory, and this seems to fix the
 problem.
 
 You should get the CCP4 folks to investigate this and propagate a fix.
 
 Cheers,
 
 
 -- 
  Andreas Förster
 Crystallization and Xray Facility Manager
   Centre for Structural Biology
  Imperial College London

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Re: [ccp4bb] ctruncate bug?

[Charles Ballard]

To add to the discussion a plot of the acentric KW from -10 to 10 (normalised 
wrt sqrt(sigma) ).  ftp://ftp.ccp4.ac.uk/ccb/aZF2.pdf,
black dots are F/sqrt(sigma) while blue is corresponding plot for sigma

The value drops from 0.42 to 0.28 going from h = -4 to h = -10.

Note:  for this we are heading for F/sigF of ~1.92.


In ctruncate the norm is corrected (somewhat) for anisotropy, while for cases 
with twinning or NCS the default is to use a flat prior (in intensity).

Charles


On 19 Jun 2013, at 14:29, Kay Diederichs wrote:

 On Wed, 19 Jun 2013 14:19:19 +0100, Kay Diederichs 
 kay.diederi...@uni-konstanz.de wrote:
 
 I wonder if problem b) is why Evans and Murshudov  observe little 
 contribution of reflections in shells with CC1/2 below 0.27 in one of their 
 test cases, which had very anisotropic data.
 
 sorry, forgot the reference. The paper is How good are my data and what is 
 the resolution? by PR Evans and GN Murshudov (2013) ActaD 69, 1204-1214, 
 accessible at http://journals.iucr.org/d/issues/2013/07/00/ba5190/index.html
 
 Kay

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[ccp4bb] The Second CCP4/OIST School on computational macromolecular crystallography

[Charles Ballard]

Dear Colleagues,

we are pleased to announce the second  CCP4 structure solution school at the 
Okinawa Institute of Science and Technology (OIST), Okinawa. All details can be 
found at http://www.ccp4.ac.uk/schools/OIST-2013/index.php

Title:
CCP4 school: From data processing to structure refinement and beyond
Dates: November 4 to 8, 2013
Site: Okinawa Institute of Science and Technology, Okinawa, Japan

The school content:

Software workshop: The rest of the time after data collection will feature many 
modern crystallographic software packages taught by authors and other experts. 
It will be organized in three Sections - lectures, tutorials and hands-on 
trouble-shooting.
There will be model data sets available for tutorials but data, provided by 
participants, will have higher priority for the hands-on sessions.

Applicants:

Graduate students, postdoctoral researchers and young scientists at the 
assistant professor level are encouraged to apply. Only 20 applicants will be 
selected for participation. Participants of the workshop are strongly 
encouraged to bring their own problem data sets so the problems can be 
addressed during data collection workshop and/or hands-on sessions.

Application:

Application deadline is 7 September. Application form, the program, contact 
info and other details can be found at 
http://www.ccp4.ac.uk/schools/OIST-2013/index.php

Fees: 

There is no fee for the workshop. The students will be responsible for their 
transportation costs outside Okinawa.  Lodging will be provided at the OIST 
Guest House Seaside House.  The workshop will also cover the expenses for all 
meals and refreshments.

Fadel Samatay, Charles Ballard, Matthais Wolf
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[ccp4bb] archive of talks from 2013 study weekend

[charles . ballard]

Dear All

some people have asked if the talks will be archived.

We will make the majority of the talks available as sessions on this site

http://87.83.31.218/tcs/#page:recordingListpageNumber:1

Unfortunately some of the talks contain sensitive material, so we will not be 
archiving those talks.

The sessions will be accessible for about 1 week before we remove them.

Charles Ballard
CCP4

ps - for none windows users VLC will work as per the last e-mail I sent


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[ccp4bb] streaming of the 2013 CCP3 Study Weekend

[Charles Ballard]

Dear All

it is the time of year again when we will be (attempting) to stream the Study 
Weekend live from Nottingham on the 4th and 5th of January.  This time round we 
have a different method for you to access the stream

The link for watching the Live Event is:  87.83.31.218/stfc
 
Open Internet Explorer or VLC media player 
http://vlc-media-player.en.softonic.com/ and copy and paste the link into the 
address bar.
This should open Windows media or VLC player (whichever is loaded on your Pc) 
and you will see the Live event.
 
The link will be the same for all sessions. You will have to shut down the 
media player (Windows/VLC) at the end of the session and start the process 
again. If you just refresh the webpage with the media player still open it may 
be looking for a previous session and show errors.


Charles Ballard
CCP4



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Re: [ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?

[Charles Ballard]

To add to the general list (and future class action).  I have just had the 
battery expansion on one  for the second time.  Added to the number of them I 
have bricked by letting the charge run down to low by unplugging them.  
Interestingly apple agreed to replace the bricked batteries free of charge, for 
their US customers.  But, us foreigners had to pay for the pleasure...

Charles

On 18 Nov 2012, at 17:30, Bosch, Juergen wrote:

 Bill I think that's crap.
 I had issues on a 2005 MacBook Pro with inflating battery and it was replaced 
 (after about 6 months). There were troubles with those batteries and 
 impurities but mine still had apple care at that time and the batteries were 
 exchangeable. 
 I have not heard of the build in batteries to have problems but yours sure 
 did. Send Tim Cook an email with the picture. This should not have happened 
 and also keeping the power cord on leading to this problem should not have 
 happened. For what did they introduce the trickling charging ? If you can't 
 leave the coord plugged in how many nice wooden US households gave caught 
 fire due to Apple products ?
 
 Jürgen 
 ..
 Jürgen Bosch
 Johns Hopkins Bloomberg School of Public Health
 Department of Biochemistry  Molecular Biology
 Johns Hopkins Malaria Research Institute
 615 North Wolfe Street, W8708
 Baltimore, MD 21205
 Phone: +1-410-614-4742
 Lab:  +1-410-614-4894
 Fax:  +1-410-955-3655
 http://lupo.jhsph.edu
 
 On Nov 17, 2012, at 16:28, William G. Scott wgsc...@ucsc.edu wrote:
 
 Hi folks:
 
 I'm trying to get a sense for how frequently this sort of thing occurs:
 
 CIMG4451.jpeg
 
 That was a macbook air that served me well for four years, but then 
 self-destructed. (I took it to the Apple store.  They generously offered to 
 repair it for $800 or to sell me a new one, and suggested this was normal if 
 you leave the power cord attached after the battery charges, even while 
 giving a lecture or seminar.)  It strikes me as a bit dangerous.
 
 --Bill Scott
 
 
 
 
 
 William G. Scott
 Professor
 Department of Chemistry and Biochemistry
 and The Center for the Molecular Biology of RNA
 228 Sinsheimer Laboratories
 University of California at Santa Cruz
 Santa Cruz, California 95064
 USA
 
 
 

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[ccp4bb] CCP4 Study Weekend, early bird deadline

[Charles Ballard]

Dear All,

A quick reminder to you all about this coming January's CCP4 Study Weekend 
entitled Molecular Replacements (January 3rd-5th 2010). As the title 
suggests, the meeting will be all about the latest developments in molecular 
replacement with many leading crystallographers and software developers giving 
presentations on the subject. The deadline for the first round of registrations 
will be the 23rd of November after which the registration price will increase 
from £210 to £260. So please get your registration in before then. 

After a few years in Warwick, the meeting will be returning to the East 
Midlands Conference Centre at Nottingham University in the UK. For more details 
and to register please see the Study Weekend website at:

http://www.cse.scitech.ac.uk/events/CCP4_2013/

We hope to see you there.

Best wishes

Charles

Organisers: Helen Walden, Pietro Roversi, along with Airlie McCoy
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[ccp4bb] CCP4 update 007

[Charles Ballard]

Dear CCP4 Users,

A CCP4 update has just been released, consisting of the following changes:

*   PHASER: update to 2.5.2
*   ctruncate: correction to twinning tests for H3
*   DiffractionImage: further corrections to displaying of pilatus mini-cbf 
(Linux and Mac)
*   ccp4i: New phaser.ensembler (Linux and Mac)  interface.

The easiest way to obtain the update is to install the CCP4 update client, if 
you have not done so already. Note that auto-updates will work correctly only 
with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to 
c...@stfc.ac.uk.

Source code for this update, combined with the previous changes to the core 
suite is available from
ftp://ftp.ccp4.ac.uk/ccp4/6.3.0/updates/source/ccp4-6.3.0-updates-combined-007.tgz

Many thanks for using CCP4,

CCP4 team



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[ccp4bb] Postdoctoral Fellow - University of Oklahoma

[Charles Ballard]

Postdoctoral Fellow – Protein CrystallographyUniversity of Oklahoma Health Sciences Center, USAA postdoctoral position is available immediately in the laboratory of Dr. Marie Hanigan for a highly motivated, creative individual with strong interest in the structure and function of enzymes relevant to redox stress and inflammation.The successful candidate will investigate the structure, catalytic mechanism and inhibition of the human gamma-glutamyl transpeptidase family of enzymes using macromolecular X-ray crystallography. This position is funded through a new NIH-sponsored Center of Biomedical Research Excellence in Structural Biology (OCSB) at The University of Oklahoma and the University of Oklahoma Health Sciences Center. The Center is directed by Dr. Ann West and is well equipped with state-of-the-art equipment for molecular biology, protein biochemistry, and crystallography, including a new protein production core facility, crystallization robot, and upgraded X-ray generator. The successful candidate will be actively involved in the Center including interaction and potential collaboration with all members of the OCSB.Candidates should have a Ph.D. in a field relevant to structural biology and a strong background in X-ray crystallography. The candidate should be familiar with the methods of determining protein X-ray structures including indexing/scaling of data, structure determination through molecular replacement and other techniques, refinement, and analysis of the resulting structure. Experience with molecular docking and/or modeling is advantageous. The candidate must have clear communication skills and fluency in the English language. Applicants should send a cover letter, a CV, a list of publications, a detailed summary of research experience and interests as well as the names and contact information of three references. The information should be sent via e-mail to marie-hani...@ouhsc.edu.the University of Oklahoma is an Equal Opportunity/Affirmative Action Employer.Marie Hanigan Marie H. Hanigan, Ph.D.Professor of Cell BiologyUniversity of Oklahoma Health Sciences CenterBiomedical Research Center, Room 264975 N.E. 10th StreetOklahoma City, Oklahoma 73104Phone: 405-271-3832FAX: 405-271-3758
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Postdoc Ad.docx
Description: application/vnd.openxmlformats-officedocument.wordprocessingml.document

[ccp4bb] CCP4 Study Weekend 2012

[Charles Ballard]

The CCP4 Study Weekend (3 - 5 January 2013)
East Midlands Conference Centre, University of Nottingham
 
Thursday 3 - MX User Meeting
Friday 4 / Saturday 5 - CCP4 Study Weekend
 
Molecular Replacements
 
We cordially invite you to participate in this year's Study Weekend at the the 
East Midlands Conference Centre, University of Nottingham. The annual CCP4 
Study Weekend is a chance to shake off the post-New Year torpor, and work hard 
and play hard with your fellow crystallographers. Once again, we have put 
together an exciting scientific programme for Friday and Saturday, either side 
of the traditional conference dinner. Please also check out the satellite 
meetings which may be of interest. The Study Weekend is a chance to catch up 
with old friends, but is also a chance to meet the CCP4 staff who will be there 
in force to demonstrate the latest software and to answer questions - please 
say hello!
 
This year, the topic for the Study Weekend is Molecular Replacements. In 
keeping with previous CCP4 meetings, the lectures will focus on the 
presentation and discussion of advanced methods and techniques developed and 
used by the leaders in the field.
 
Scientific Organisers
Helen Walden - Cancer Research (UK)
Pietro Roversi - University of Oxford (UK)

Further details of the program and the registration are at 
http://www.cse.scitech.ac.uk/events/CCP4_2013/

Terms and Conditions apply.  Please read the cancellation policy before 
applying.
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[ccp4bb] CCP4 Fukuoka workshop 29 Oct - 2 Nov 2012

[Charles Ballard]

Dear All,
 
We are pleased to announce the CCP4 Fukuoka Workshop. All details can be found 
at http://www.ccp4.ac.uk/schools/Japan-2012/
 
Title:
CCP4 Fukuoka school: From data processing to structure refinement and beyond
Dates: October 29 to November 2.
Site: Biomedical Research Station, Kyushu University, Kyushu, Japan.
 
The school content:
Software workshop: The workshop will feature many modern crystallographic 
software packages taught by authors and other experts. It will be organized in 
three Sections – lectures, tutorials and hands-on trouble-shooting. There will 
be model data sets available for tutorials but data, provided by participants, 
will have higher priority for the hands-on sessions.
 
Applicants:
Graduate students, postdoctoral researchers and young scientists at the 
assistant professor level are encouraged to apply. Only 20 applicants will be 
selected for participation. Participants of the workshop are strongly 
encouraged to bring their own problem data sets so the problems can be 
addressed during the hands-on sessions.
 
Application:
Application deadline is October 1. The application form, the program, contact 
info and other details can be found at http://www.ccp4.ac.uk/schools/Japan-2012/
 
Fees: 
There is no fee for the workshop, but students are responsible for their travel 
and accommodation costs.
 
Charles Ballard, Daisuke Kohda, Garib Murshudov
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Re: [ccp4bb] ctruncate and anistropy correction

[Charles Ballard]

Hi Frank

this means that the anisotropy corrected data is used to calculate the twinning 
statistics, moments etc.  The corrected data is not used in the truncate 
procedure.

Charles

On 1 May 2012, at 19:28, Frank von Delft wrote:

 Hello, a colleague just pointed me to an innocuous sentence in the ctruncate:
 
CTRUNCATE looks for anisotropy in the data and performs anisotropy 
 correction.
 
 What exactly does that involve...?
 
 phx.

[ccp4bb] Postdoc position in structural biology

[Charles Ballard]

Posted on behalf of Sylvie Nessler (CNRS):

Postdoctoral Fellowship in Structural Biology: Bacterial tyrosine kinases and 
signalisation networks.

A post-doctoral position is available for highly motivated candidates to join 
the research group of Prof. Sylvie Nessler at University Paris-sud 11. We are 
concerned by the increase in drug-resistant bacteria and the need for new 
antibiotics. Our research focuses on the characterization of atypical bacterial 
protein kinases considered as potential therapeutic targets. The post-doctoral 
project consists in the resolution of the crystal structure of cytoplasmic 
tyrosine kinases in complex with their cognate protein substrates and 
activators.

Applicants should hold a PhD degree and have significant experience in protein 
production and X-ray crystallography. Additional background in molecular 
cloning is considered as a plus but not essential.

As one of the major research universities in France, University Paris-sod 11 
houses well-equipped crystallization facilities. The synchrotron Soleil is 
located at only 5 km from the laboratory and Paris centre is at 30 min by 
train. Such an environment allows one to have a good balance of life and 
science.

The expected starting date is September 2012. Interested applicants should send 
a curriculum vitae, a summary of past research experience and accomplishments, 
and contact information of two or three references to sylvie.ness...@u-psud.fr

[ccp4bb] postdoctoral position in structural biology and epigenetics

[Charles Ballard]

A post-doctoral position is available for highly motivated candidates to join a 
research group interested in investigating molecular mechanisms underlying 
epigenetic regulation and inheritance, and the broad area of chromatin biology. 
Projects will involve structure determination of macromolecular complexes by 
X-ray crystallography and/or NMR spectroscopy, and related biochemical 
characterizations. Applicants should hold a PhD degree and have significant 
experience in molecular cloning, protein production and X-ray crystallography. 
Additional background in NMR spectroscopy and enzymatic assay is considered a 
plus but not essential. The expected starting date is September 1st, 2012 or 
sooner. Interested applicants should send curriculum vitae, a summary of past 
research experience and accomplishments, and contact information of two or 
three references to Jikui Song, Ph.D. Department of Biochemistry, University of 
California, Riverside, CA 92521 (Email: songlab...@gmail.edu).
 
As one of the major research univerisities in California, UCR houses well 
equipped structural biology facilities. Riverside is located near to big cities 
such as Los Angeles, San Diego and Las Vegas. Such an environment allows one to 
have a good balance of life and science here.
 
More information can be found in 
http://biochemistry.ucr.edu/faculty/song/song.html.
 
Jikui Song, PhD
Assistant Professor
Department of Biochemistry
University of California, Riverside