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 bui
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 L
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
wou
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.
On 04/12/2013 06:03 PM, Nat Echols wrote:
On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan
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 end
of the run is doome
On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan
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 end of the run is
> doomed and bound to commit senseless errors. I was taught a long time ago
> that computers a
haniel.ech...@gmail.com]
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 counterproductiv
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 an
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 GUI-orient
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 F
On Fri, Apr 12, 2013 at 10:27 AM, James Holton 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
> push each day
half 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 is this duel…
Drop you pistols or swo
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
lost.
Jim
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 d
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 Mole
On 11 Apr 2013, at 13:53, David Schuller 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
> another buildin
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 thos
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 usefu
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"
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 Stop
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 mach
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 Oliver
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 promise for next release.
On 11 Apr 2013, at 18:16, James Stroud wrote:
On Apr 11, 2013, at 6:17 AM,
mailto:eugene.krissi...@stfc.ac.uk>>
mailto:eugene.krissi...@stfc.ac.uk>> wrote:
Sorry that this was unclear. We assume that updater is used primarily from
ccp4i, where nothing changed (an
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.
B
On Apr 11, 2013, at 6:17 AM,
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, at 10:34 AM, Jim Pflugrath wrote:
> I think James get
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 cryst
_
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 respect very much both
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 Crys
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 wr
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 noth
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 i
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 2013
On Apr 10, 2013, at 9:30 PM, 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
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 CCP
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
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
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 . ./ccp4.s
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 coordi
Apologies for everybody, the previous message was sent to BB by mistake, please
disregard.
Eugene Krissinel
Begin forwarded message:
Date: 16 March 2013 11:25:08 GMT
To: mailto:andrey.lebe...@stfc.ac.uk>>
Cc: mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] CCP4 Update 019
Sp
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 fol
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, int
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 m
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 adde
t;
>
>
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ville 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 Us
CP4BB@JISCMAIL.AC.UK] on behalf of Ville 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.
* Ai
Dear CCP4 Users
A CCP4 update has just been released, consisting of the following
changes.
* Ctruncate: Memory leak fixed.
* Aimless, Pointless, Ctruncate: Documentation updated following
previous changes.
If you do not currently receive updates, consider re-installing your
CCP4 setup us
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 upgr
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 software
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 upda
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 generati
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: ...
:/software/CCP4-6.3.0/ccp4-6.3.
-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
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 wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Ian,
>
> did you source the ccp4 input scr
-BEGIN PGP SIGNED MESSAGE-
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:
> Dea
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
shutil.copy2 ( fname,fname1 )
File "/software/python/python_v2.7.3_64/lib/python2.7/shuti
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,
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 & X
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
> Dear CCP4 maintainers,
>
> I've come to appreciate th
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 CCP
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 s
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 ph
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 $CCP
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 <> of alias
"programs:i386-ma
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 ou
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.
Ca
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,
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 harvesting
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?
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
Cell
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 redundant
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