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
Dear Christoph,
Unfortunately there is no command line option to install any earlier version;
Windows installer provides only latest CCP4 version.
All the best,
Oleg Kovalevskiy and Andrey Lebedev
--
Dr Oleg Kovalevskiy
CCP4 team
Science and Technology Facilities Council
Rutherford Appleton
Hi,
In context of an unattended installation/update of CCP4 for Windows 7/10
in a computer pool environment, is it possible to install CCP4 (from
scratch) via update manager (ccp4um) command line option to an earlier
version than the latest (e.g. 7.0.072 instead of 7.0.078)? If yes, what
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.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Felix Frolow
[mbfro...@post.tau.ac.il]
Sent: Thursday, April 11, 2013 11:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 Update victim of own success
I would serve as a second in this duel, but I
Hi
I'd second NX; you can install a free server for one or two (I think - I only
use one at a time ;-)) concurrent connections and a local client, then it's
almost like being there.
On 11 Apr 2013, at 22:54, Dyda wrote:
Or nx, which works very well, although the server has to be installed at
, 2013 11:25 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] CCP4 Update victim of own success
I would serve as a second in this duel, but I respect very much both
engaged is this duel…
Drop you pistols or swords !
:-)
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
On Fri, Apr 12, 2013 at 10:27 AM, James Holton jmhol...@lbl.gov wrote:
But, when it comes to GUIs, I have always found them counterproductive.
In my humble opinion, the purpose of computers and other machines is to DO
work for me, not create work for me, and I already have enough buttons to
I agree with Nat. There are good GUIs and bad GUIs, just like there are
good command-line programs and bad command-line programs. Bad programs
are easy to write and good ones are hard. Conservation of work I think.
-James Holton
MAD Scientist
On 4/12/2013 10:38 AM, Nat Echols wrote:
On
What, I'm afraid, people rarely realise these days, is that their desktops are,
essentially, GUIs to various OS features, so they obviously use GUI more
frequently than they think :) After all, this is all matter of habits and
training, and the reality is that people get more and more
On Apr 12, 2013, at 12:44 PM, eugene.krissi...@stfc.ac.uk wrote:
What, I'm afraid, people rarely realise these days, is that their desktops
are, essentially, GUIs to various OS features, so they obviously use GUI more
frequently than they think :) After all, this is all matter of habits and
]
Sent: Friday, April 12, 2013 8:38 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 Update victim of own success
On Fri, Apr 12, 2013 at 10:27 AM, James Holton jmhol...@lbl.gov wrote:
But, when it comes to GUIs, I have always found them counterproductive. In my humble opinion
On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan
bshaa...@exchange.bgu.ac.ilwrote:
Whichever way the input file for the run is prepared (via GUI or command
line), anybody who doesn't inspect the log file at the end of the run is
doomed and bound to commit senseless errors. I was taught a long
On 04/12/2013 06:03 PM, Nat Echols wrote:
On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan
bshaa...@exchange.bgu.ac.il mailto:bshaa...@exchange.bgu.ac.il wrote:
Whichever way the input file for the run is prepared (via GUI or
command line), anybody who doesn't inspect the log file at the
Sorry that this was unclear. We assume that updater is used primarily from
ccp4i, where nothing changed (and why it should be used from command line at
all ?:)). The name was changed because it is reserved in Windows, which caused
lots of troubles. Now it will stay as is.
Eugene
On 11 Apr
CCP4 has a GUI?
-James Holton
MAD Scientist
On 4/11/2013 5:17 AM, eugene.krissi...@stfc.ac.uk wrote:
Sorry that this was unclear. We assume that updater is used primarily from
ccp4i, where nothing changed (and why it should be used from command line at
all ?:)). The name was changed because
That's really hard. Duel?
Eugene
On 11 Apr 2013, at 16:32, James Holton wrote:
CCP4 has a GUI?
-James Holton
MAD Scientist
On 4/11/2013 5:17 AM, eugene.krissi...@stfc.ac.uk wrote:
Sorry that this was unclear. We assume that updater is used primarily from
ccp4i, where nothing
Fight Fight Fight!
On Apr 11, 2013, at 5:46 PM, eugene.krissi...@stfc.ac.uk wrote:
That's really hard. Duel?
Eugene
On 11 Apr 2013, at 16:32, James Holton wrote:
CCP4 has a GUI?
-James Holton
MAD Scientist
On 4/11/2013 5:17 AM, eugene.krissi...@stfc.ac.uk wrote:
Sorry that
I would serve as a second in this duel, but I respect very much both engaged is
this duel…
Drop you pistols or swords !
:-)
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta
: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Felix Frolow
[mbfro...@post.tau.ac.il]
Sent: Thursday, April 11, 2013 11:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 Update victim of own success
I would serve as a second in this duel, but I respect very much both engaged
FYI
I have a small herd of computers here and find it cumbersome to ssh
to each and fire up ccp4i just to update the systems. ccp4i takes a
while to draw all those boxes (particularly over ssh) and leaves files
behind in my disk areas on computers that I'm not likely to, personally,
run
On Apr 11, 2013, at 6:17 AM, eugene.krissi...@stfc.ac.uk
eugene.krissi...@stfc.ac.uk wrote:
Sorry that this was unclear. We assume that updater is used primarily from
ccp4i, where nothing changed (and why it should be used from command line at
all ?:)).
Scriptability.
On Apr 11, 2013,
Dear Dale,
From next CCP4 release (due soon), ccp4um will be runnable from command line
in automatic, non-graphical mode, fully cronable. I hope that that will give
you what you want. --check-silent is a special option for ccp4i, it only
checks for new updates but do not install them.
Best
In promise for next release.
On 11 Apr 2013, at 18:16, James Stroud wrote:
On Apr 11, 2013, at 6:17 AM,
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk wrote:
Sorry that this was unclear. We assume that updater is
Eugene - that's great. I too run a small suite of Macs (12) and was trying to
find a practical way of updating all those machines remotely. The command line
version of CCP4um will be very useful.
Many thanks.
Tony.
Sent from my iPhone
On 11 Apr 2013, at 18:19, eugene.krissi...@stfc.ac.uk
In cases like this, a request at c...@stfc.ac.uk should be the way to go. CCP4
is a community resource and we are to listen and to do what's doable. We may
not do everything at once, but knowing what is required is vital for the
project.
Cheers,
Eugene
On 11 Apr 2013, at 18:22, Antony
On Thursday, April 11, 2013 10:22:59 am Antony Oliver wrote:
Eugene - that's great. I too run a small suite of Macs (12) and was trying to
find a practical way of updating all those machines remotely. The command
line version of CCP4um will be very useful.
Another option for a set of
Perhaps there needs to be a separate update manager to manage updates to
the update manager:
[image: Inline images 1]
(from http://xkcd.com/1197/)
Cheers,
Richard
--
Richard Gildea
Software Developer
Physical Biosciences Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
Mail
Yep. I put all specialty lab software tools on a file server and mount it
on all workstations as /usr/local/xtal, a suggestion I think I
learned...here. There are few programs that can't be served this way. I
only have to update the server.
Roger Rowlett
On Apr 11, 2013 1:42 PM, Ethan Merritt
On 04/11/13 13:36, Ethan Merritt wrote:
On Thursday, April 11, 2013 10:22:59 am Antony Oliver wrote:
Eugene - that's great. I too run a small suite of Macs (12) and was trying to
find a practical way of updating all those machines remotely. The command line
version of CCP4um will be very
On Thursday, April 11, 2013 01:53:16 pm David Schuller wrote:
On 04/11/13 13:36, Ethan Merritt wrote:
On Thursday, April 11, 2013 10:22:59 am Antony Oliver wrote:
Eugene - that's great. I too run a small suite of Macs (12) and was trying
to find a practical way of updating all those
On 11 Apr 2013, at 13:53, David Schuller dj...@cornell.edu wrote:
My method is to run the updater graphically on one machine, then spread it
around with rsync. Although being able to run it on the command line would
allow me to accomplish that from my own desk, without crossing campus to
Or nx, which works very well, although the server has to be installed at
the remote end and client on the local.
www.nomachine.com
Fred
[32m***
Fred Dyda, Ph.D. Phone:301-402-4496
Laboratory of
Hello All,
I downloaded a crispy new version of CCP4 and ran update until the update
update script disappeared. Is the reason that CCP4 has reached its final update?
James
No, it got renamed to ccp4um :) That should have been written in update
descriptions, was it not?
Eugene
On 11 Apr 2013, at 03:54, James Stroud wrote:
Hello All,
I downloaded a crispy new version of CCP4 and ran update until the update
update script disappeared. Is the reason that CCP4
On Apr 10, 2013, at 9:30 PM, eugene.krissi...@stfc.ac.uk eugene.krissi...@stfc.ac.uk wrote:No, it got renamed to ccp4um :) That should have been written in update descriptions, was it not?There was only one mention of "ccp4um" that I could find in all update descriptions that I found (6.3.0-020).
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Hello Andrey,
it was the second case - my original installation was from source.
Calling $CBIN/ccp4um directly showed that indeed
/xtal/Suites/CCP4/ccp4-6.3.0/bin/ccp4um: 4: .: Can't open ./ccp4.setup-sh
and commenting out the third line .
Dear CCP4 Users
A CCP4 update has just been released, consisting of the following changes.
* QtRView: corrected Prosmart result page; enabled incorporation of web-links
into citation section
If you do not currently receive updates, consider re-installing your
CCP4 setup using the latest binary
Dear CCP4 Users
A CCP4 update has just been released, consisting of the following changes.
* Update Manager (ccp4um), QtRView: Technical update in preparation for the
next release
* Gesamt, Superpose: Corrections to the previous update (Now print
superposition matrices also in fractional
Spasibo Andrey,
Ne znayu poka kak na Linuxe i vse ostal'noe, no na Mac superpose ne
proupdeitirovalas', matritsy ne pechataet. Poka ne znayu chto sluchilos'
Eugene
On 15 Mar 2013, at 23:51, Andrey Lebedev wrote:
Dear CCP4 Users
A CCP4 update has just been released, consisting of the
: [ccp4bb] CCP4 Update 019
Spasibo Andrey,
Ne znayu poka kak na Linuxe i vse ostal'noe, no na Mac superpose ne
proupdeitirovalas', matritsy ne pechataet. Poka ne znayu chto sluchilos'
Eugene
On 15 Mar 2013, at 23:51, Andrey Lebedev wrote:
Dear CCP4 Users
A CCP4 update has just been released
Dear CCP4 Users
A CCP4 update has just been released, consisting of the following changes.
* Aimless: Task interface fixed in part of input customisation section
* Molrep: Improvements to scoring system and bug fixes
* Logview: Command-prompt routine for viewing individual log files with QtRView
Dear CCP4 Users
A CCP4 update has just been released, consisting of the following changes:
* Aimless Bug fixing in task interface
* ccp4i Fixed long-standing issue on Linux and Mac: system Python was used
instead of the one distributed with CCP4
* QtPISA Added output of monomer,
Dear CCP4 Users
A CCP4 update has just been released, consisting of the following changes.
* Geomcalc: io bug fixing in residue numbering
* Pisa: fixes for handling back slashes on windows
* Aimless: fixes in Define Run section of the aimless task interface
* Ample/MrBUMP: now runs shelxd_mp in
Dear CCP4 Users
A CCP4 update has just been released, consisting of the following changes.
* Qtrview: Now uses runwincoot.bat script to start Wincoot on Windows
* MrBUMP: Assumes intensities rather than structure factor amplitudes when
calling SHELXE
* Pdb_merge: Execution permissions
Uski
[ville.u...@stfc.ac.uk]
Sent: Saturday, January 26, 2013 1:21 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4 Update 015
Dear CCP4 Users
A CCP4 update has just been released, consisting of the following
changes.
* Ctruncate: Memory leak fixed.
* Aimless, Pointless
Hi Andrey, Eugene and others -
it is time to say that this new system is extremely useful, and so easy to use
at the same time! Gone are the times when one had to worry about manually
updating parts of CCP4.
I just wonder why there should ever be a need for a CCP4 6.4.0 release; a
rolling
I can only echo Kay's comments. The CCP4 update system is just great.
Together with a few others I was one of the initial beta testers of the update
system. Beta-testing could not have not been easier. The thing just worked!
Congratulations on an brilliant and extremely useful piece of
Dear Kay,
Many thanks for nice words! We appreciate feedback from all our users.
Indeed, we expect that the update system will result in a lower frequency of
releases. Yet, full-scale releases will be needed. A good analogy here are the
update vs upgrade procedures in operating systems. An
Dear CCP4 Users
A CCP4 update has just been released, consisting of the following changes.
All systems:
* Ctruncate: Introduced DNA/RNA reference curve; uses flat prior on request,
or when have tNCS or twinning
* Othercell: Various bug fixes
* PISA, QtPISA: Stability fixes and
Dear Eugene
ccp4um doesn't work for me at all (update worked fine up until #012).
node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-45 ccp4um
Traceback (most recent call last):
File ccp4um, line 17, in module
shutil.copy2 ( fname,fname1 )
File
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Hash: SHA1
Dear Ian,
did you source the ccp4 input script so that variables like CCP4 are set?
IOError: [Errno 2] No such file or directory: '/libexec/ccp4um'
looks like CCP4 is an empty string.
Best,
Tim
On 01/17/2013 01:44 PM, Ian Tickle wrote:
Yes it's my .login so it's always set up:
node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-47 echo $CCP4
/software/CCP4-6.3.0/ccp4-6.3.0
Cheers
-- Ian
On 17 January 2013 12:51, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Ian,
did you source
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Ian,
I am not sure, but maybe the error is caused by $PWD being part of
your path variable so that when you call 'ccp4um' while your cwd is
/software/CCP4-6.3.0/ccp4-6.3.0/bin, python make 'sys.argv[0]' (line
10 in $CBIN/ccp4um) ./ccp4um. This
Tim Eugene
node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-58 which ccp4um
./ccp4um
node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-59 cd
node066:~-60 which ccp4um
ccp4um: Command not found.
node066:~-61 echo $PATH
/software/virtualenv/python2.7/64/cluster/bin: ...
Dear Andreas Förster,
You can use ccp4um (ccp4 update manage) to update CCP4 from command line.
Best wishes,
Q. Cai
Qixu Cai
Email: caiq...@gmail.com
School of Life Sciences,
Xiamen University, Fujian, China
2013/1/14 Andreas Förster docandr...@gmail.com
Dear CCP4 maintainers,
I've come
Ah, I see. This was part of update 10. Thank you.
Andreas
On 16/01/2013 2:51, Qixu Cai wrote:
Dear Andreas Förster,
You can use ccp4um (ccp4 update manage) to update CCP4 from command line.
Best wishes,
Q. Cai
--
Andreas Förster, Research Associate
Paul Freemont
Dear Andreas,
Sorry for late response to your post and confusion with the updater. For
technical reasons (Windows does not like names containing update :)), the
updater was renamed into ccp4um (ccp4 update manager) and is found in $CCP4/bin.
I hope this helps,
Eugene
Dear CCP4 maintainers,
Dear CCP4 maintainers,
I've come to appreciate the CCP4 update functionality, which, in our
multiuser network (RHEL 6.2), I used to invoke by calling $CCP4/bin/update.
Update 012 removed that script with no immediately obvious replacement.
Was that on purpose? Is there a way of updating
Dear CCP4 Users,
A CCP4 update has just been released, consisting of the following changes:
All systems:
* molrep: Significantly more accurate packing function implemented
* pisa: Now reports on monomeric properties ina no-complex situations
* JLigand: Compounds derived from smile
Dear CCP4 Users,
A CCP4 update has just been released, consisting of the following changes:
* Arp/Warp: fixes problem with overwriting modules.def file by other
updates; enables Arp/Warp tasks in ccp4i (OS X and Linux)
* Phaser: added DLL files missing in the previous update (Windows)
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
Hi Ben,
Applications launched from Finder and Spotlight get environment variables from
~/.MacOSX/environment.plist (before 10.8) their own Info.plist (10.8) and
launchd (system-wide) and not .tcshrc etc.
Sounds like to get the updater to work from Finder for all users you have to
set your
On Mon, Oct 08, 2012 at 06:20:59PM +, Ronan Keegan wrote:
Dear CCP4 Users,
A CCP4 update has just been released, consisting of the following changes:
Hi Ronan et al,
The update client on OS X doesn't seem to like our installation and dies
with:
Can't make class cfol of alias
Dear Ronan et al:
I apologize if I have missed it, but is there a simple way to obtain the
corresponding changes in the source code for those of us who compile ccp4
ourselves?
I looked on the web site and the ftp site but can't seem to find it.
Many thanks in advance.
Bill
On Oct 8, 2012,
On 09/10/12 15:09, William G. Scott wrote:
Dear Ronan et al:
I apologize if I have missed it, but is there a simple way to obtain the
corresponding changes in the source code for those of us who compile ccp4
ourselves?
I looked on the web site and the ftp site but can't seem to find it.
Dear Bill,
You have not missed anything, we do not have a mechanism for delivering source
code *updates* in automatic fashion as yet. Our statistics shows that source
code distributions make only 2-3% of binary downloads, therefore, I hope that
you would understand that we have to prioritise
Dear CCP4 Users,
A CCP4 update has just been released, consisting of the following changes:
* MrBUMP: model building options added
* PISA: new QT interface
* AMPLE: bug fixes and expanded interface (Linux and MAC only)
* tlsextract: correction of output format which broke
Dear CCP4 Users,
A CCP4 update has just been released, consisting of the following changes.
For Linux and Mac:
- *areaimol*: fixed segmentation fault due to a bug in dynamic memory
allocation
- *cprodrg*: HETATM notations synchronised with refmac
- *ccp4i*: fixes in refmac
EXCELLENT !!!
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
On Sep 6, 2012, at 9:00 AM, eugene.krissi...@stfc.ac.uk wrote:
If this does not work for you for any reason, please (re-)read update manual
for details. If that does not help as well, please write to us.
Dear Eugene:
Will there be a way to get the corresponding changes to the source-code?
Dear CCP4 Users,
Following the release of ccp4 6.3.0, CCP4 core team sets up an update mechanism
for moderate modifications of Suite's components between the releases. It is
expected that updates will be essential for CCP4 maintenance and will make
patch releases less frequent or even
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