[ccp4bb] ccp4 update 009

[Charles Ballard - STFC UKRI]

Dear All

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

Brief description:

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

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


cbuccaneerNN - new model building program


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

refmac - update to cif handling and bug fixes

pandda (on osx and linux) - further python3 fixes

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


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

CCP4 Core Team



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] CCP4 update manager command line options?

[Oleg Kovalevskiy - UKRI STFC]

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 Laboratory
Harwell Campus
Didcot
OX11 0QX

On 13/12/2019, 13:54, "CCP4 bulletin board on behalf of Christoph Parthier" 
 wrote:

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 
would be the apropriate command line parameter(s)?

Or would this rather be a job for the CCP4 package manager (ccp4pm)? 
What would be the respective command line paramters?

Any other suggestion to do this task unattended (batch file)?

Thanks,
Christoph



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





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

[ccp4bb] CCP4 update manager command line options?

[Christoph Parthier]

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 
would be the apropriate command line parameter(s)?


Or would this rather be a job for the CCP4 package manager (ccp4pm)? 
What would be the respective command line paramters?


Any other suggestion to do this task unattended (batch file)?

Thanks,
Christoph



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

[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.

Re: [ccp4bb] CCP4 Update victim of own success

[Herman . Schreuder]

With a good script, James will have won already before Eugene has started up 
his GUI.
Herman


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jim 
Pflugrath
Sent: Thursday, April 11, 2013 6:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 Update victim of own success

I think James gets to 'fight' like in the old game of rogue by pressing the h, 
j, k, l keys on his keyboard (not a detachable one either).  While Eugene gets 
to use a modern game controller or a Wii.

Ooops, game is already over and James has 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 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 Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.ilmailto:mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Apr 11, 2013, at 18:46 , 
eugene.krissi...@stfc.ac.ukmailto: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.ukmailto: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 it is reserved in Windows, which caused 
lots of troubles. Now it will stay as is.

Eugene

On 11 Apr 2013, at 05:16, James Stroud wrote:


On Apr 10, 2013, at 9:30 PM, 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk
 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.ukmailto: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). I only figured out what information was 
trying to be communicated because of your message (see attachment).

James


um-what.png



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 has reached its final update?

James







--
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update victim of own success

[Harry Powell]

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
 the remote end and client on the local.
 
 www.nomachine.com
 
 Fred
 ***
 Fred Dyda, Ph.D.   Phone:301-402-4496
 Laboratory of Molecular BiologyFax: 301-496-0201
 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov  
 Bldg. 5. Room 303 
 Bethesda, MD 20892-0560  URGENT message e-mail: 2022476...@mms.att.net
 Google maps coords: 39.000597, -77.102102
 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
 ***

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

Re: [ccp4bb] CCP4 Update victim of own success

[James Holton]

Alright, alright,

I should thank Eugene for being such a good sport.  And I should also 
apologize for all the work I just created for him!


 I fully appreciate all the years and years of effort and struggle that 
has gone into making ccp4i and other crystallographic GUIs the 
accessible tools that they are today.  I think these efforts should 
continue, and we should all send Martin Noble one of those letters he needs.


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.  This is why my favorite command-line programs 
are things like xautomation, xse and a tcl extension called cwind 
that lets you send mouse clicks and keystrokes into a Windoze machine 
from a tcl script. Comes in really handy for those late-night dialog 
boxes that always seem to pop up at 4am and would otherwise generate a 
user-support call because X has stopped working.  Yes, I could SSH in, 
open a tunnel through my firewall to an NX server and launch a vncviewer 
within the NX session and then (eventually) click on the OK button.  
But I'd rather just sleep through all that.


-James Holton
MAD Scientist


On 4/11/2013 9:34 AM, Jim Pflugrath wrote:
I think James gets to 'fight' like in the old game of rogue by 
pressing the h, j, k, l keys on his keyboard (not a detachable one 
either).  While Eugene gets to use a modern game controller or a Wii.


Ooops, game is already over and James has 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 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 Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il mailto:mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Apr 11, 2013, at 18:46 , eugene.krissi...@stfc.ac.uk 
mailto: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 
mailto: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 it 
is reserved in Windows, which caused lots of troubles. Now it will 
stay as is.


Eugene

On 11 Apr 2013, at 05:16, James Stroud wrote:


On Apr 10, 2013, at 9:30 PM, eugene.krissi...@stfc.ac.uk 
mailto:eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
eugene.krissi...@stfc.ac.uk 
mailto:eugene.krissi...@stfc.ac.ukmailto: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). I only figured out 
what information was trying to be communicated because of your 
message (see attachment).


James


um-what.png



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 has 
reached its final update?


James









--
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update victim of own success

[Nat Echols]

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
 push each day.


This is a very defensible position with regards to your normal workflow (or
mine) - but beamline scientists (or software developers) are not very
representative of crystallographers as a group.  I've seen a lot of
reflexive anti-GUI mentality from users who don't fall into either
category, presumably because a senior postdoc or PI told them real
crystallographers use the command line, when in reality they'd be better
served by figuring out on their own what workflow is most efficient for
them.

-Nat

Re: [ccp4bb] CCP4 Update victim of own success

[James Holton]

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 Fri, Apr 12, 2013 at 10:27 AM, James Holton jmhol...@lbl.gov 
mailto: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 push each day.


This is a very defensible position with regards to your normal 
workflow (or mine) - but beamline scientists (or software developers) 
are not very representative of crystallographers as a group.  I've 
seen a lot of reflexive anti-GUI mentality from users who don't fall 
into either category, presumably because a senior postdoc or PI told 
them real crystallographers use the command line, when in reality 
they'd be better served by figuring out on their own what workflow is 
most efficient for them.


-Nat

Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

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-oriented these 
days, like it or not. Whether to fight the reality or try to use it for benefit 
is, certainly, every developer's own choice. I still remember payroll officers 
saying that hand calculators (and even their predecessors) were much more 
convenient and robust than modern software, but do not hear this for some 15 
years already ...

Eugene


On 12 Apr 2013, at 19:09, James Holton wrote:


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 Fri, Apr 12, 2013 at 10:27 AM, James Holton 
jmhol...@lbl.govmailto: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 push each day.

This is a very defensible position with regards to your normal workflow (or 
mine) - but beamline scientists (or software developers) are not very 
representative of crystallographers as a group.  I've seen a lot of reflexive 
anti-GUI mentality from users who don't fall into either category, presumably 
because a senior postdoc or PI told them real crystallographers use the 
command line, when in reality they'd be better served by figuring out on their 
own what workflow is most efficient for them.

-Nat



-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update victim of own success

[James Stroud]

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 
 training, and the reality is that people get more and more GUI-oriented these 
 days, like it or not. Whether to fight the reality or try to use it for 
 benefit is, certainly, every developer's own choice. I still remember payroll 
 officers saying that hand calculators (and even their predecessors) were much 
 more convenient and robust than modern software, but do not hear this for 
 some 15 years already ...
 
 Eugene


There is nothing intrinsically wrong with a GUI. The problem, for those who 
like to take advantage of automation, is that a GUI is a bottleneck if it can't 
be automated in some way. In my opinion, the best automation is based on an API 
(in my favorite scripting language, of course).

The original unix tools were built with automation in mind, using pipes, 
redirects, and file I/O to control the flow of information. This automation 
wasn't designed because the architects couldn't conceive of a GUI, but because 
it was and is efficient.

A utility can easily lock a user into a GUI. The usual cruel method is by 
spawning a dialog box the forces the user to acknowledge whatever triviality 
the program is trying to communicate (instead of sending the information to a 
log file where it belongs). If a program locks the user into a GUI, by whatever 
means, then the program can't be automated. And if it can't be automated it 
becomes a source of inefficiency. I think this is James Holton's point.

Most of CCP4 can be automated by using the utilities from the command line, 
taking advantage of pipes, redirects, and file I/O as envisioned by the unix 
architects. CCP4 can also be run via a GUI, which I take advantage of in 
certain situations. It's a great model for user interaction. Long may it live 
(and may modal dialog boxes die a horrible and quick death).

James



 
 On 12 Apr 2013, at 19:09, James Holton wrote:
 
 
 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 Fri, Apr 12, 2013 at 10:27 AM, James Holton 
 jmhol...@lbl.govmailto: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 push 
 each day.
 
 This is a very defensible position with regards to your normal workflow (or 
 mine) - but beamline scientists (or software developers) are not very 
 representative of crystallographers as a group.  I've seen a lot of reflexive 
 anti-GUI mentality from users who don't fall into either category, presumably 
 because a senior postdoc or PI told them real crystallographers use the 
 command line, when in reality they'd be better served by figuring out on 
 their own what workflow is most efficient for them.
 
 -Nat
 
 
 
 -- 
 Scanned by iCritical.
 

Re: [ccp4bb] CCP4 Update victim of own success

[Boaz Shaanan]

Hi Nat,


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 always do what you
 told them to do and not what you think you told them, which is why inspecting the log file helps. BTW, I find the GUI's (ccp4i or phenix) as great help in preparing the command file, certainly the skeleton which can then be modified and run via the command
 line if needed.


 Cheers,


   Boaz

Boaz Shaanan, Ph.D.

Dept. of Life Sciences 
Ben-Gurion University of the Negev 
Beer-Sheva 84105 
Israel 
 
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220Skype: boaz.shaanan 
Fax: 972-8-647-2992 or 972-8-646-1710










From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Nat Echols [nathaniel.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 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.





This is a very defensible position with regards to your normal workflow (or mine) - but beamline scientists (or software developers) are not very representative of crystallographers as a group. I've seen a lot of reflexive anti-GUI mentality from users
 who don't fall into either category, presumably because a senior postdoc or PI told them real crystallographers use the command line, when in reality they'd be better served by figuring out on their own what workflow is most efficient for them.


-Nat

Re: [ccp4bb] CCP4 Update victim of own success

[Nat Echols]

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 time ago
 that computers always do what you told them to do and not what you think
 you told them, which is why inspecting the log file helps.


I agree in principle - I would not advocate that anyone (*especially*
novices) run crystallography software as a black box.  However, whether
or not a program constitutes a black box has nothing to do whether it runs
in a GUI or not.  The one advantage a GUI has is the ability to convey
inherently graphical information (plots, etc.).  That it is still necessary
to inspect the log file(s) carefully reflects the design of the underlying
programs; ideally any and all essential feedback should also be displayed
in the GUI (if one exists).  Obviously there is still much work to be done
here.

-Nat

Re: [ccp4bb] CCP4 Update victim of own success

[Ed Pozharski]

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 end
of the run is doomed and bound to commit senseless errors. I was
taught a long time ago that computers always do what you told them
to do and not what you think you told them, which is why
inspecting the log file helps.


I agree in principle - I would not advocate that anyone (*especially* 
novices) run crystallography software as a black box.  However, 
whether or not a program constitutes a black box has nothing to do 
whether it runs in a GUI or not.  The one advantage a GUI has is the 
ability to convey inherently graphical information (plots, etc.).  
That it is still necessary to inspect the log file(s) carefully 
reflects the design of the underlying programs; ideally any and all 
essential feedback should also be displayed in the GUI (if one 
exists).  Obviously there is still much work to be done here.


-Nat


It is hard to blame novices for running crystallography software as a 
black box when the websites from which they download the said software 
use the word automated to describe it.  Because, at least according to 
wikipedia (another great resource that should be used with care), 
automation is the operation of machinery without human supervision.  
Checking the log-files or messages supplied by GUI seems to fall under 
human supervision, which automated programmes should not really 
require.  I am not advocating return to the stone age when naming a 
tutorial for a widely used model building software ... for morons was 
probably considered a joke (not a good one too).  I am just saying that 
it is perhaps quite predictable that with promise of automation comes 
the expectation of, well, automation.  Whether the true automation of 
crystallographic structure determination may become available in the 
future is perhaps debatable.  Whether it is already available probably 
isn't.


On a broader question of GUI versus command line, both obviously have 
their uses.  Mastering command line gives one flexibility and perhaps 
greater insight into what programmes actually do.  Do I prefer a little 
button that opens a file chooser dialog over sam-atom-in?  Absolutely.  
But I am glad that --pdb and --auto command line options are supplied, 
because I can then write a little bash pipeline to pass 50 expected 
protein-ligand complex datasets through simple refmac-coot cycle to 
quickly see which ones are interesting.  In that regard, both ccp4 and 
phenix are doing it the right way - gui is simply a gateway to the 
command-line controlled code. I can then choose the interface that fits 
particular situation.


As for the relatively new CCP4 update feature, it is absolutely awesome.

Cheers,

Ed.



--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs

Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

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, at 05:16, James Stroud wrote:


On Apr 10, 2013, at 9:30 PM, 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
eugene.krissi...@stfc.ac.ukmailto: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). I only figured out what information was 
trying to be communicated because of your message (see attachment).

James


um-what.png



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 has reached its final update?

James




-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update victim of own success

[James Holton]

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 it is reserved in Windows, which caused 
lots of troubles. Now it will stay as is.

Eugene

On 11 Apr 2013, at 05:16, James Stroud wrote:


On Apr 10, 2013, at 9:30 PM, 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
eugene.krissi...@stfc.ac.ukmailto: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). I only figured out what information was trying to 
be communicated because of your message (see attachment).

James


um-what.png



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 has reached its final update?

James

Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

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 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, at 05:16, James Stroud wrote:
 
 
 On Apr 10, 2013, at 9:30 PM, 
 eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
 eugene.krissi...@stfc.ac.ukmailto: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). I only figured out what information 
 was trying to be communicated because of your message (see attachment).
 
 James
 
 
 um-what.png
 
 
 
 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 has reached its final 
 update?
 
 James
 
 
 
 
 


-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update victim of own success

[Tim Wiegels]

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 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, at 05:16, James Stroud wrote:
 
 
 On Apr 10, 2013, at 9:30 PM, 
 eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
 eugene.krissi...@stfc.ac.ukmailto: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). I only figured out what information 
 was trying to be communicated because of your message (see attachment).
 
 James
 
 
 um-what.png
 
 
 
 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 has reached its final 
 update?
 
 James
 
 
 
 
 
 
 
 -- 
 Scanned by iCritical.
 

Re: [ccp4bb] CCP4 Update victim of own success

[Felix Frolow]

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 Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Apr 11, 2013, at 18:46 , 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 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, at 05:16, James Stroud wrote:
 
 
 On Apr 10, 2013, at 9:30 PM, 
 eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
 eugene.krissi...@stfc.ac.ukmailto: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). I only figured out what information 
 was trying to be communicated because of your message (see attachment).
 
 James
 
 
 um-what.png
 
 
 
 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 has reached its final 
 update?
 
 James
 
 
 
 
 
 
 
 -- 
 Scanned by iCritical.
 

Re: [ccp4bb] CCP4 Update victim of own success

[Jim Pflugrath]

I think James gets to 'fight' like in the old game of rogue by pressing the h, 
j, k, l keys on his keyboard (not a detachable one either).  While Eugene gets 
to use a modern game controller or a Wii.

Ooops, game is already over and James has 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 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 Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.ilmailto:mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Apr 11, 2013, at 18:46 , 
eugene.krissi...@stfc.ac.ukmailto: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.ukmailto: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 it is reserved in Windows, which caused 
lots of troubles. Now it will stay as is.

Eugene

On 11 Apr 2013, at 05:16, James Stroud wrote:


On Apr 10, 2013, at 9:30 PM, 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk
 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.ukmailto: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). I only figured out what information was 
trying to be communicated because of your message (see attachment).

James


um-what.png



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 has reached its final update?

James







--
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update victim of own success

[Dale Tronrud]

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 crystallographic computations.  I much prefer to simply run ccp4um
from the command line.

   In fact, I would rather put it in cron and forget about it -- and
I expect that is what --check-silent is for.  The usage statement,
however, doesn't explicitly say that this installs the new updates it
finds.  I'll have to experiment a bit.

Dale Tronrud

On 04/11/2013 05:17 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 it is reserved in Windows, which caused 
lots of troubles. Now it will stay as is.

Eugene

On 11 Apr 2013, at 05:16, James Stroud wrote:


On Apr 10, 2013, at 9:30 PM, 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
eugene.krissi...@stfc.ac.ukmailto: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). I only figured out what information was trying to 
be communicated because of your message (see attachment).

James


um-what.png



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 has reached its final update?

James

Re: [ccp4bb] CCP4 Update victim of own success

[James Stroud]

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, at 10:34 AM, Jim Pflugrath wrote:
 I think James gets to 'fight' like in the old game of rogue by pressing the 
 h, j, k, l keys on his keyboard (not a detachable one either).  While Eugene 
 gets to use a modern game controller or a Wii.
 
 Ooops, game is already over and James [Holton] has lost.


But he wrote the game.

James

Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

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 regards,

Eugene


On 11 Apr 2013, at 18:10, Dale Tronrud wrote:

 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 crystallographic computations.  I much prefer to simply run ccp4um
 from the command line.
 
   In fact, I would rather put it in cron and forget about it -- and
 I expect that is what --check-silent is for.  The usage statement,
 however, doesn't explicitly say that this installs the new updates it
 finds.  I'll have to experiment a bit.
 
 Dale Tronrud
 
 On 04/11/2013 05:17 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 it is reserved in Windows, which 
 caused lots of troubles. Now it will stay as is.
 
 Eugene
 
 On 11 Apr 2013, at 05:16, James Stroud wrote:
 
 
 On Apr 10, 2013, at 9:30 PM, 
 eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
 eugene.krissi...@stfc.ac.ukmailto: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). I only figured out what information 
 was trying to be communicated because of your message (see attachment).
 
 James
 
 
 um-what.png
 
 
 
 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 has reached its final 
 update?
 
 James
 
 
 
 


-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

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 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 gets to 'fight' like in the old game of rogue by pressing the h, 
j, k, l keys on his keyboard (not a detachable one either).  While Eugene gets 
to use a modern game controller or a Wii.

Ooops, game is already over and James [Holton] has lost.


But he wrote the game.

James



-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update victim of own success

[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 
eugene.krissi...@stfc.ac.uk wrote:

 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 regards,
 
 Eugene
 
 
 On 11 Apr 2013, at 18:10, Dale Tronrud wrote:
 
 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 crystallographic computations.  I much prefer to simply run ccp4um
 from the command line.
 
  In fact, I would rather put it in cron and forget about it -- and
 I expect that is what --check-silent is for.  The usage statement,
 however, doesn't explicitly say that this installs the new updates it
 finds.  I'll have to experiment a bit.
 
 Dale Tronrud
 
 On 04/11/2013 05:17 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 it is reserved in Windows, which 
 caused lots of troubles. Now it will stay as is.
 
 Eugene
 
 On 11 Apr 2013, at 05:16, James Stroud wrote:
 
 
 On Apr 10, 2013, at 9:30 PM, 
 eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
 eugene.krissi...@stfc.ac.ukmailto: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). I only figured out what information 
 was trying to be communicated because of your message (see attachment).
 
 James
 
 
 um-what.png
 
 
 
 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 has reached its final 
 update?
 
 James
 
 
 -- 
 Scanned by iCritical.
 

Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

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 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. 
 
 Many thanks. 
 
 Tony. 
 
 Sent from my iPhone
 
 On 11 Apr 2013, at 18:19, eugene.krissi...@stfc.ac.uk 
 eugene.krissi...@stfc.ac.uk wrote:
 
 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 regards,
 
 Eugene
 
 
 On 11 Apr 2013, at 18:10, Dale Tronrud wrote:
 
 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 crystallographic computations.  I much prefer to simply run ccp4um
 from the command line.
 
 In fact, I would rather put it in cron and forget about it -- and
 I expect that is what --check-silent is for.  The usage statement,
 however, doesn't explicitly say that this installs the new updates it
 finds.  I'll have to experiment a bit.
 
 Dale Tronrud
 
 On 04/11/2013 05:17 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 it is reserved in Windows, which 
 caused lots of troubles. Now it will stay as is.
 
 Eugene
 
 On 11 Apr 2013, at 05:16, James Stroud wrote:
 
 
 On Apr 10, 2013, at 9:30 PM, 
 eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
 eugene.krissi...@stfc.ac.ukmailto: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). I only figured out what information 
 was trying to be communicated because of your message (see attachment).
 
 James
 
 
 um-what.png
 
 
 
 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 has reached its final 
 update?
 
 James
 
 
 -- 
 Scanned by iCritical.
 


-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update victim of own success

[Ethan Merritt]

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 machines in the same network is to install a single 
master copy of ccp4 on one machine exported to the others via NFS, and have all 
the 
machines run it from there.  Then you only need to update one copy.
Works fine for me.

Ethan



 
 Many thanks. 
 
 Tony. 
 
 Sent from my iPhone
 
 On 11 Apr 2013, at 18:19, eugene.krissi...@stfc.ac.uk 
 eugene.krissi...@stfc.ac.uk wrote:
 
  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 regards,
  
  Eugene
  
  
  On 11 Apr 2013, at 18:10, Dale Tronrud wrote:
  
  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 crystallographic computations.  I much prefer to simply run ccp4um
  from the command line.
  
   In fact, I would rather put it in cron and forget about it -- and
  I expect that is what --check-silent is for.  The usage statement,
  however, doesn't explicitly say that this installs the new updates it
  finds.  I'll have to experiment a bit.
  
  Dale Tronrud
  
  On 04/11/2013 05:17 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 it is reserved in Windows, 
  which caused lots of troubles. Now it will stay as is.
  
  Eugene
  
  On 11 Apr 2013, at 05:16, James Stroud wrote:
  
  
  On Apr 10, 2013, at 9:30 PM, 
  eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
  eugene.krissi...@stfc.ac.ukmailto: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). I only figured out what 
  information was trying to be communicated because of your message (see 
  attachment).
  
  James
  
  
  um-what.png
  
  
  
  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 has reached its final 
  update?
  
  James
  
  
 

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Re: [ccp4bb] CCP4 Update victim of own success

[Richard Gildea]

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 64R0121
Berkeley
CA 94720-8118


On 11 April 2013 05:17, 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 it is reserved in Windows, which
 caused lots of troubles. Now it will stay as is.

 Eugene

 On 11 Apr 2013, at 05:16, James Stroud wrote:


 On Apr 10, 2013, at 9:30 PM, eugene.krissi...@stfc.ac.ukmailto:
 eugene.krissi...@stfc.ac.uk eugene.krissi...@stfc.ac.ukmailto:
 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). I only figured out what information
 was trying to be communicated because of your message (see attachment).

 James


 um-what.png



 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 has reached its final
 update?

 James




 --
 Scanned by iCritical.

Re: [ccp4bb] CCP4 Update victim of own success

[Roger Rowlett]

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 merr...@u.washington.edu 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 useful.

 Another option for a set of machines in the same network is to install a
 single
 master copy of ccp4 on one machine exported to the others via NFS, and
 have all the
 machines run it from there.  Then you only need to update one copy.
 Works fine for me.

 Ethan



 
  Many thanks.
 
  Tony.
 
  Sent from my iPhone
 
  On 11 Apr 2013, at 18:19, eugene.krissi...@stfc.ac.uk 
 eugene.krissi...@stfc.ac.uk wrote:
 
   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 regards,
  
   Eugene
  
  
   On 11 Apr 2013, at 18:10, Dale Tronrud wrote:
  
   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 crystallographic computations.  I much prefer to simply run ccp4um
   from the command line.
  
In fact, I would rather put it in cron and forget about it -- and
   I expect that is what --check-silent is for.  The usage statement,
   however, doesn't explicitly say that this installs the new updates it
   finds.  I'll have to experiment a bit.
  
   Dale Tronrud
  
   On 04/11/2013 05:17 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 it is reserved in
 Windows, which caused lots of troubles. Now it will stay as is.
  
   Eugene
  
   On 11 Apr 2013, at 05:16, James Stroud wrote:
  
  
   On Apr 10, 2013, at 9:30 PM, eugene.krissi...@stfc.ac.ukmailto:
 eugene.krissi...@stfc.ac.uk eugene.krissi...@stfc.ac.ukmailto:
 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). I only figured out what
 information was trying to be communicated because of your message (see
 attachment).
  
   James
  
  
   um-what.png
  
  
  
   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 has reached its
 final update?
  
   James
  
  
 

 --
 Ethan A Merritt
 Biomolecular Structure Center,  K-428 Health Sciences Bldg
 University of Washington, Seattle 98195-7742

Re: [ccp4bb] CCP4 Update victim of own success

[David Schuller]

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 useful.

Another option for a set of machines in the same network is to install a single
master copy of ccp4 on one machine exported to the others via NFS, and have all 
the
machines run it from there.  Then you only need to update one copy.
Works fine for me.

Ethan

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 building. Even with gigabit, running X remotely is 
rather slow and bothersome.


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

Re: [ccp4bb] CCP4 Update victim of own success

[Ethan Merritt]

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 machines remotely. The 
  command line version of CCP4um will be very useful.
  Another option for a set of machines in the same network is to install a 
  single
  master copy of ccp4 on one machine exported to the others via NFS, and have 
  all the
  machines run it from there.  Then you only need to update one copy.
  Works fine for me.
 
  Ethan
 
 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 building. Even with gigabit, running X remotely is 
 rather slow and bothersome.

You may misunderstand - the executables live on a shared NFS directory
but there is no remote X connection involved.

Having said that, I routinely connect to the lab machines from home via ssh.
In that case the X connection is remote, but I find that the performance of
the ccp4i GUI is adequate even across the WAN.

Ethan  



 
 

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Re: [ccp4bb] CCP4 Update victim of own success

[Johan Hattne]

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 
 another building. Even with gigabit, running X remotely is rather slow and 
 bothersome.

In some cases I've found that compressing the ssh-traffic (i.e. ssh -C 
user@host) is enough to transform an unusably slow session to a workable one.

// Johan

Re: [ccp4bb] CCP4 Update victim of own success

[Dyda]

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
***
Fred Dyda, Ph.D.   Phone:301-402-4496
Laboratory of Molecular BiologyFax: 301-496-0201
DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov  
Bldg. 5. Room 303 
Bethesda, MD 20892-0560  URGENT message e-mail: 2022476...@mms.att.net
Google maps coords: 39.000597, -77.102102
http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
***

[ccp4bb] CCP4 Update victim of own success

[James Stroud]

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

Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

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 has reached its final 
 update?
 
 James


-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update victim of own success

[James Stroud]

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). I only figured out what information was trying to be communicated because of your message (see attachment).JamesOn 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 has reached its final update?James

Re: [ccp4bb] CCP4 Update 021

[Tim Gruene]

-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.setup-sh in $CBIN/ccp4um
resolved the problem.

I am sending a copy to the ccp4bb in case others come across this problem.

Thanks a lot for your help,
Tim


On 04/06/2013 12:25 PM, andrey.lebe...@stfc.ac.uk wrote:
 
 Hi Tim,
 
 Command line: ccp4um
 
 Please check permissions and ownerships of the following files and
 directories: $CCP4 $CCP4/libexec $CCP4/libexec/ccp4um
 
 I can imagine problems if you have different read-write access to
 these files.
 
 Another problem that we have already encountered occurs when update
 is used with the ccp4 installation from source. In this case you
 will not have ccp4.setup-sh in $CCP4/bin If this is the case or you
 does not have this file for any other reasons, please remove the
 following line . ./ccp4.setup-sh from the file $CCP4/bin/ccp4um
 
 
 Andrey
 
 
 On 5 Apr 2013, at 06:09, Tim Gruene wrote:
 
 Dear Andrey,
 
 when I click on 'Manage Updates' in ccp4i (is I usually do to
 update ccp4), the info line changes from '1 new updates available'
 to 'checking for new updates' and then back to '1 new updates
 available', but the actual update window does not pop up.
 
 What's the command to start the updater directly?
 
 Best wishes, Tim
 
 
 
 On 04/04/2013 10:13 PM, Andrey Lebedev wrote:
 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
 packages, which now have the CCP4 Update Manager (ccp4um)
 integrated.
 
 Note that auto-updates will work correctly only with CCP4
 release 6.3.0, therefore upgrade if necessary. Please report
 any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk
 
 Many thanks for using CCP4
 
 Andrey Lebedev
 
 
 
 

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFRYATuUxlJ7aRr7hoRAvpNAKCz/e8kgotpIqiFv2Y8si5vcGauqwCfXLcq
38X/B2VBonCVVWwgBHW4AMo=
=P9dg
-END PGP SIGNATURE-

[ccp4bb] CCP4 Update 021

[Andrey Lebedev]

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 packages, which now have the CCP4 Update 
Manager (ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk

Many thanks for using CCP4

Andrey Lebedev


-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update 019

[Andrey Lebedev]

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 coordinates);
   better presentation in QtRView result viewer
* Refmac, ProSmart: Results of superposition analysis and external restraints 
are now accessible through QtRView report

If you do not currently receive updates, consider re-installing your
CCP4 setup using the latest binary packages, which now have the CCP4 Update 
Manager (ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk

Many thanks for using CCP4

Andrey Lebedev




-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update 019

[eugene . krissinel]

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 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
Simply call it with path to the log file as the only parameter
 * QtRView: Cosmetic improvements and changes for Logview
 * Gesamt: Now prints superposition matrices also in fractional coordinates
 * Superpose: Now prints superposition matrices also in fractional coordinates
 
 If you do not currently receive updates, consider re-installing your
 CCP4 setup using the latest binary packages, which now have the CCP4 Update 
 Manager (ccp4um) integrated.
 
 Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
 therefore upgrade if necessary. Please report any bugs to 
 c...@stfc.ac.ukmailto:c...@stfc.ac.uk
 
 Many thanks for using CCP4
 
 Andrey Lebedev
 
 
 -- 
 Scanned by iCritical.
 


-- 
Scanned by iCritical.

[ccp4bb] Fwd: [ccp4bb] CCP4 Update 019

[eugene . krissinel]

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: andrey.lebe...@stfc.ac.ukmailto:andrey.lebe...@stfc.ac.uk
Cc: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [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, 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
  Simply call it with path to the log file as the only parameter
* QtRView: Cosmetic improvements and changes for Logview
* Gesamt: Now prints superposition matrices also in fractional coordinates
* Superpose: Now prints superposition matrices also in fractional coordinates

If you do not currently receive updates, consider re-installing your
CCP4 setup using the latest binary packages, which now have the CCP4 Update 
Manager (ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk

Many thanks for using CCP4

Andrey Lebedev


--
Scanned by iCritical.




-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update 019

[Andrey Lebedev]

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
Simply call it with path to the log file as the only parameter
* QtRView: Cosmetic improvements and changes for Logview
* Gesamt: Now prints superposition matrices also in fractional coordinates
* Superpose: Now prints superposition matrices also in fractional coordinates

If you do not currently receive updates, consider re-installing your
CCP4 setup using the latest binary packages, which now have the CCP4 Update 
Manager (ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk

Many thanks for using CCP4

Andrey Lebedev


-- 
Scanned by iCritical.

[ccp4bb] CCP4 Update 017

[eugene . krissinel]

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, interface and assembly details in plain 
text; eliminated Qt widget flashing

If you do not currently receive updates, consider re-installing your CCP4 setup 
using the latest binary packages, which now have the CCP4 Update Manager 
(ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk

Many thanks for using CCP4

Eugene Krissinel


-- 
Scanned by iCritical.

[ccp4bb] CCP4 Update 017

[Andrey Lebedev]

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 mp mode

If you do not currently receive updates, consider re-installing your
CCP4 setup using the latest binary packages, which now have the CCP4 Update 
Manager (ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk

Many thanks for using CCP4

Andrey Lebedev


-- 
Scanned by iCritical.

[ccp4bb] CCP4 Update 016

[ronan . keegan]

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 added to binary (Mac OSX and Linux)
*   Pdbcur: Execution permissions added to binary (Mac OSX and Linux)
*   Pisa: Execution permissions added to binary (Mac OSX and Linux)
*   INDEX.html: CCP4 documentation index updated to have link to Aimless 
program documentation

If you do not currently receive updates, consider re-installing your
CCP4 setup using the latest binary packages, which now have the CCP4 Update 
Manager (ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk

Many thanks for using CCP4.

Ronan Keegan

-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update 015

[eugene . krissinel]

Dear Boaz,

If that was not done, it's an oversight. Surely this is possible, will have a 
look into.

Thanks for reporting (but please use c...@stfc.ac.uk for future bug reports 
please),

Eugene



On 26 Jan 2013, at 14:00, Boaz Shaanan wrote:

 Dear Developers,
 
 As part of the wonderful work you're doing with development and upgrades, 
 would it be possible to also update the INDEX.html in the $CCP4/html 
 directory whenever a new program html is entered into this directory (e.g. 
 the latest aimless.html)? 
 
  Thanks,
 
Boaz
 
 
 Boaz Shaanan, Ph.D.
 Dept. of Life Sciences
 Ben-Gurion University of the Negev
 Beer-Sheva 84105
 Israel
 
 E-mail: bshaa...@bgu.ac.il
 Phone: 972-8-647-2220  Skype: boaz.shaanan
 Fax:   972-8-647-2992 or 972-8-646-1710
 
 
 
 
 
 
 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 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 using the latest binary packages, which now have the CCP4
 Update Manager (ccp4um) integrated.
 
 Note that auto-updates will work correctly only with CCP4 release 6.3.0,
 therefore upgrade if necessary. Please report any bugs to
 c...@stfc.ac.ukmailto:c...@stfc.ac.uk
 
 Many thanks for using CCP4.
 
 Ville Uski
 --
 Scanned by iCritical.


-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update 014

[Kay Diederichs]

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 update seems just adequate to me - but that's just a user's 
perspective, and probably this has been discussed somewhere although I'm not 
aware of it.

thanks for making this available, and the hard work to make it so perfect!

Kay

On Fri, 18 Jan 2013 19:04:37 +, Andrey Lebedev andrey.lebe...@stfc.ac.uk 
wrote:

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 generation of Remark 350 in no-complex 
 situations
 *   PDBCur: Finish gracefully, rather than terminate, when atom selection is 
 empty
 *   PDB_Merge: Various bug fixes
 *   Xia2: Correction to Ctruncate wrapper

Linux and Mac only: *)

 *   Aimless: Various bug fixes
 *   Pointless: Correction for XDS input
 *   Scala: Corrected output for CC(1/2)

 *)  Corresponding changes for Windows have been already included in update No 
 13

Windows only:

 *   Phaser.ensembler: Corrected path to syminfo.lib


If you do not currently receive updates, consider re-installing your CCP4 
setup using the latest binary packages, which now have CCP4 Update manager 
(ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk


Many thanks for using CCP4.

Andrey Lebedev


-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update 014

[Steiner, Roberto]

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.

Roberto

On 20 Jan 2013, at 11:32, Kay Diederichs kay.diederi...@uni-konstanz.de
 wrote:

 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 update seems just adequate to me - but that's just a user's 
 perspective, and probably this has been discussed somewhere although I'm not 
 aware of it.
 
 thanks for making this available, and the hard work to make it so perfect!
 
 Kay
 
 On Fri, 18 Jan 2013 19:04:37 +, Andrey Lebedev 
 andrey.lebe...@stfc.ac.uk wrote:
 
 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 generation of Remark 350 in no-complex 
 situations
 *   PDBCur: Finish gracefully, rather than terminate, when atom selection is 
 empty
 *   PDB_Merge: Various bug fixes
 *   Xia2: Correction to Ctruncate wrapper
 
 Linux and Mac only: *)
 
 *   Aimless: Various bug fixes
 *   Pointless: Correction for XDS input
 *   Scala: Corrected output for CC(1/2)
 
 *)  Corresponding changes for Windows have been already included in update 
 No 13
 
 Windows only:
 
 *   Phaser.ensembler: Corrected path to syminfo.lib
 
 
 If you do not currently receive updates, consider re-installing your CCP4 
 setup using the latest binary packages, which now have CCP4 Update manager 
 (ccp4um) integrated.
 
 Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
 therefore upgrade if necessary. Please report any bugs to 
 c...@stfc.ac.ukmailto:c...@stfc.ac.uk
 
 
 Many thanks for using CCP4.
 
 Andrey Lebedev
 
 
 -- 
 Scanned by iCritical.
 

Roberto A. Steiner
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London
roberto.stei...@kcl.ac.uk

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Phone 0044 20 78488216
Fax0044 20 78486435

Re: [ccp4bb] CCP4 Update 014

[eugene . krissinel]

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 upgrade is needed 
whenever we face the need for structural changes in the Suite, which cannot be 
easily accommodated by a mere update due to a considerable number of various 
dependencies to be followed.

At present, we still need full releases because:

1) currently we are doing a considerable work under the hood of the CCP4 
Suite, which is not reflected in what a general user would see. Some elements 
of that include better organised source repositories, synced with updates, 
completely new build mechanism, which would allow one to update installations 
compiled from sources, new test system and some others. From time to time, this 
results in structural changes in the backyard of CCP4 suite, which cannot be 
accommodated by update mechanism

2) sometimes we have new contributions which change really a lot. For example, 
when new GUI comes to release, it will change about everything

3) sometimes, new versions of various components result in changes far beyond 
their own scope. Usually (but not always), this relates to new versions of 
phaser, cctbx, refmac and some other programs 

4) incremental updates make the Suite asynchronous on component versions. For 
example, recent phaser update resulted in duplication of cctbx, which was 
necessary in order to keep other cctbx-related components running. With time, 
this results in higher complexity and lower manageability of the suite.

I am sure that this list is far from complete, hence one more reason

5) unpredictable things happen, when updater cannot manage something.

I hope that these reflections give some insight into maters and you will be 
less disappointed by having to upgrade to 6.3.1 fairly soon :)


Best regards,

Eugene



On 20 Jan 2013, at 11:32, Kay Diederichs wrote:

 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 update seems just adequate to me - but that's just a user's 
 perspective, and probably this has been discussed somewhere although I'm not 
 aware of it.
 
 thanks for making this available, and the hard work to make it so perfect!
 
 Kay
 
 On Fri, 18 Jan 2013 19:04:37 +, Andrey Lebedev 
 andrey.lebe...@stfc.ac.uk wrote:
 
 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 generation of Remark 350 in no-complex 
 situations
 *   PDBCur: Finish gracefully, rather than terminate, when atom selection is 
 empty
 *   PDB_Merge: Various bug fixes
 *   Xia2: Correction to Ctruncate wrapper
 
 Linux and Mac only: *)
 
 *   Aimless: Various bug fixes
 *   Pointless: Correction for XDS input
 *   Scala: Corrected output for CC(1/2)
 
 *)  Corresponding changes for Windows have been already included in update 
 No 13
 
 Windows only:
 
 *   Phaser.ensembler: Corrected path to syminfo.lib
 
 
 If you do not currently receive updates, consider re-installing your CCP4 
 setup using the latest binary packages, which now have CCP4 Update manager 
 (ccp4um) integrated.
 
 Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
 therefore upgrade if necessary. Please report any bugs to 
 c...@stfc.ac.ukmailto:c...@stfc.ac.uk
 
 
 Many thanks for using CCP4.
 
 Andrey Lebedev
 
 
 -- 
 Scanned by iCritical.


-- 
Scanned by iCritical.

[ccp4bb] CCP4 Update 014

[Andrey Lebedev]

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 generation of Remark 350 in no-complex 
situations
 *   PDBCur: Finish gracefully, rather than terminate, when atom selection is 
empty
 *   PDB_Merge: Various bug fixes
 *   Xia2: Correction to Ctruncate wrapper

Linux and Mac only: *)

 *   Aimless: Various bug fixes
 *   Pointless: Correction for XDS input
 *   Scala: Corrected output for CC(1/2)

 *)  Corresponding changes for Windows have been already included in update No 
13

Windows only:

 *   Phaser.ensembler: Corrected path to syminfo.lib


If you do not currently receive updates, consider re-installing your CCP4 setup 
using the latest binary packages, which now have CCP4 Update manager (ccp4um) 
integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk


Many thanks for using CCP4.

Andrey Lebedev


-- 
Scanned by iCritical.

Re: [ccp4bb] ccp4 update

[Ian Tickle]

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 /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line
128, in copy2
copyfile(src, dst)
  File /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line
82, in copyfile
with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: '/libexec/ccp4um'

Did I do something wrong?  Or is it just that there's nothing to update?

Cheers

-- Ian


On 16 January 2013 15:11, eugene.krissi...@stfc.ac.uk wrote:

 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,

 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 CCP4 from the command
 line without calling CCP4i?

 Thanks


 Andreas


 (from update.log:

 [Thu Jan 3 2013 11:00:21]
 Ready to make changes

   --- applying update 6.3.0-012
   --- update header read
   --- creating restore package, please wait ...
   --- done
 ... file '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed
 ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed
 ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update' removed
 ... directory '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed


 some more blah blah)


 --
  Andreas Förster, Research Associate
  Paul Freemont  Xiaodong Zhang Labs
 Department of Biochemistry, Imperial College London

 --
 Scanned by iCritical.

Re: [ccp4bb] ccp4 update

[Tim Gruene]

-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:
 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
 /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 
 128, in copy2 copyfile(src, dst) File
 /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 
 82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No
 such file or directory: '/libexec/ccp4um'
 
 Did I do something wrong?  Or is it just that there's nothing to
 update?
 
 Cheers
 
 -- Ian
 
 
 On 16 January 2013 15:11, eugene.krissi...@stfc.ac.uk wrote:
 
 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,
 
 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
 CCP4 from the command line without calling CCP4i?
 
 Thanks
 
 
 Andreas
 
 
 (from update.log:
 
 [Thu Jan 3 2013 11:00:21] Ready to make changes
 
 --- applying update 6.3.0-012 --- update header read --- creating
 restore package, please wait ... --- done ... file
 '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed ... file
 '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed ...
 file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update'
 removed ... directory
 '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed
 
 
 some more blah blah)
 
 
 -- Andreas Förster, Research Associate Paul Freemont  Xiaodong
 Zhang Labs Department of Biochemistry, Imperial College London
 
 -- Scanned by iCritical.
 
 
 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFQ9/O7UxlJ7aRr7hoRAhVVAJ4yomsoCO3CeOJ13XteKAt0B95yTgCgoqnq
8PgeNrjcFS3vLeuBk9cBjHM=
=IwT/
-END PGP SIGNATURE-

Re: [ccp4bb] ccp4 update

[Ian Tickle]

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 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:
  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
  /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line
  128, in copy2 copyfile(src, dst) File
  /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line
  82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No
  such file or directory: '/libexec/ccp4um'
 
  Did I do something wrong?  Or is it just that there's nothing to
  update?
 
  Cheers
 
  -- Ian
 
 
  On 16 January 2013 15:11, eugene.krissi...@stfc.ac.uk wrote:
 
  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,
 
  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
  CCP4 from the command line without calling CCP4i?
 
  Thanks
 
 
  Andreas
 
 
  (from update.log:
 
  [Thu Jan 3 2013 11:00:21] Ready to make changes
 
  --- applying update 6.3.0-012 --- update header read --- creating
  restore package, please wait ... --- done ... file
  '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed ... file
  '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed ...
  file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update'
  removed ... directory
  '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed
 
 
  some more blah blah)
 
 
  -- Andreas Förster, Research Associate Paul Freemont  Xiaodong
  Zhang Labs Department of Biochemistry, Imperial College London
 
  -- Scanned by iCritical.
 
 
 

 - --
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A

 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

 iD8DBQFQ9/O7UxlJ7aRr7hoRAhVVAJ4yomsoCO3CeOJ13XteKAt0B95yTgCgoqnq
 8PgeNrjcFS3vLeuBk9cBjHM=
 =IwT/
 -END PGP SIGNATURE-

Re: [ccp4bb] ccp4 update

[Tim Gruene]

-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 would result in the error you
receive.

Can you type 'which ccp4um' while being in
/software/CCP4-6.3.0/ccp4-6.3.0/bin and while being in some other
directory (e.g. $HOME)?

Does the error occur if you call 'ccp4um' from e.g. $HOME?

Tim

On 01/17/2013 01:44 PM, Ian Tickle wrote:
 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
 /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 
 128, in copy2 copyfile(src, dst) File
 /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 
 82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No
 such file or directory: '/libexec/ccp4um'
 
 Did I do something wrong?  Or is it just that there's nothing to
 update?
 
 Cheers
 
 -- Ian
 
 
 On 16 January 2013 15:11, eugene.krissi...@stfc.ac.uk wrote:
 
 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,
 
 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
 CCP4 from the command line without calling CCP4i?
 
 Thanks
 
 
 Andreas
 
 
 (from update.log:
 
 [Thu Jan 3 2013 11:00:21] Ready to make changes
 
 --- applying update 6.3.0-012 --- update header read --- creating
 restore package, please wait ... --- done ... file
 '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed ... file
 '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed ...
 file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update'
 removed ... directory
 '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed
 
 
 some more blah blah)
 
 
 -- Andreas Förster, Research Associate Paul Freemont  Xiaodong
 Zhang Labs Department of Biochemistry, Imperial College London
 
 -- Scanned by iCritical.
 
 
 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFQ9/vYUxlJ7aRr7hoRAqXlAJ9qkk3BBNTT6P8eR1HxP6ODEz2GfACgkkvR
hUlISdYdsr1v5dryb76tNLg=
=kESK
-END PGP SIGNATURE-

Re: [ccp4bb] ccp4 update

[Ian Tickle]

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/ccp4-6.3.0/share/dbccp4i/bin:/software/CCP4-6.3.0/ccp4-6.3.0/share/ccp4i/bin:/software/CCP4-6.3.0/ccp4-6.3.0/bin:/software/CCP4-6.3.0/ccp4-6.3.0/etc:/software/compilers/linux/intel_v11.7.256/composer_xe_2011_sp1.7.256/bin/ia32:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/software/CCP4-6.3.0/ccp4-6.3.0/share/xia2/xia2core/Test:/software/CCP4-6.3.0/ccp4-6.3.0/share/xia2/xia2/Applications

# CBIN is in the path, so we need to rehash after the update:

node066:~-62 rehash  

node066:~-63 which ccp4um
/software/CCP4-6.3.0/ccp4-6.3.0/bin/ccp4um

node066:~-64 ccp4um
WORKS!

So I just needed to rehash the PATH after the last update (or I could have
logged out  in).

Thanks to Tim  Eugene for suggestions.

Cheers

-- Ian


On 17 January 2013 13:25, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:

 -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 would result in the error you
 receive.

 Can you type 'which ccp4um' while being in
 /software/CCP4-6.3.0/ccp4-6.3.0/bin and while being in some other
 directory (e.g. $HOME)?

 Does the error occur if you call 'ccp4um' from e.g. $HOME?

 Tim

 On 01/17/2013 01:44 PM, Ian Tickle wrote:
  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
  /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line
  128, in copy2 copyfile(src, dst) File
  /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line
  82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No
  such file or directory: '/libexec/ccp4um'
 
  Did I do something wrong?  Or is it just that there's nothing to
  update?
 
  Cheers
 
  -- Ian
 
 
  On 16 January 2013 15:11, eugene.krissi...@stfc.ac.uk wrote:
 
  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,
 
  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
  CCP4 from the command line without calling CCP4i?
 
  Thanks
 
 
  Andreas
 
 
  (from update.log:
 
  [Thu Jan 3 2013 11:00:21] Ready to make changes
 
  --- applying update 6.3.0-012 --- update header read --- creating
  restore package, please wait ... --- done ... file
  '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed ... file
  '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed ...
  file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update'
  removed ... directory
  '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed
 
 
  some more blah blah)
 
 
  -- Andreas Förster, Research Associate Paul Freemont  Xiaodong
  Zhang Labs Department of Biochemistry, Imperial College London
 
  -- Scanned by iCritical.
 
 
 

 - --
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A

 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

 iD8DBQFQ9/vYUxlJ7aRr7hoRAqXlAJ9qkk3BBNTT6P8eR1HxP6ODEz2GfACgkkvR
 hUlISdYdsr1v5dryb76tNLg=
 =kESK
 -END PGP SIGNATURE-

Re: [ccp4bb] ccp4 update

[Qixu Cai]

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 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 CCP4 from the command
 line without calling CCP4i?

 Thanks


 Andreas


 (from update.log:

 [Thu Jan 3 2013 11:00:21]
 Ready to make changes

  --- applying update 6.3.0-012
  --- update header read
  --- creating restore package, please wait ...
  --- done
... file '/csb/soft/Linux64/share/ccp4-**6.3.0/bin/update' removed
... file '/csb/soft/Linux64/share/ccp4-**6.3.0/lib_exec/update' removed
... file '/csb/soft/Linux64/share/ccp4-**6.3.0/lib_exec/_update'
 removed
... directory '/csb/soft/Linux64/share/ccp4-**6.3.0/lib_exec' removed


 some more blah blah)


 --
 Andreas Förster, Research Associate
 Paul Freemont  Xiaodong Zhang Labs
 Department of Biochemistry, Imperial College London
 http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] ccp4 update

[Andreas Förster]

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  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] ccp4 update

[eugene . krissinel]

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,

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 CCP4 from the command
line without calling CCP4i?

Thanks


Andreas


(from update.log:

[Thu Jan 3 2013 11:00:21]
Ready to make changes

  --- applying update 6.3.0-012
  --- update header read
  --- creating restore package, please wait ...
  --- done
... file '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed
... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed
... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update' removed
... directory '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed


some more blah blah)


--
 Andreas Förster, Research Associate
 Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London

-- 
Scanned by iCritical.

[ccp4bb] ccp4 update

[Andreas Förster]

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 CCP4 from the command 
line without calling CCP4i?


Thanks


Andreas


(from update.log:

[Thu Jan 3 2013 11:00:21]
Ready to make changes

 --- applying update 6.3.0-012
 --- update header read
 --- creating restore package, please wait ...
 --- done
   ... file '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed
   ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed
   ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update' removed
   ... directory '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed


some more blah blah)


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] CCP4 Update 013

[eugene . krissinel]

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 strings are now automatically 
regularised
  *   QtRView: Improved performance on large log files, added inverse 
resolution scale in graphs, coot and ccp4mg configuration is now optionally 
imported from ccp4i settings

Linux only:

  *   Ensembler and Sculptor: Fixed file permissions in order to enable users 
other than root to use these applications

Windows only:

  *   Crank: Fix for preventing terminal windows from popping up
  *   CProdrg: HETATM notations synchronized with Refmac
  *   Pointless and Aimless: Now able to handle twice bigger datasets
  *   Scala: Corrections to plot titles
  *   Phaser: Added missing cctbx library files


If you do not currently receive updates, consider re-installing your CCP4 setup 
using the latest binary packages, which now have CCP4 Update manager (ccp4um) 
integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk


Many thanks for using CCP4.

Eugene Krissinel


-- 
Scanned by iCritical.

[ccp4bb] CCP4 update 6.3.0 008

[Andrey Lebedev]

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)
*  Pointless: fixed option Choose solution ... by Space group name for 
non-standard settings, e.g. P21 2 21 (all platforms)
*  Zanuda: fixed problem with MSE atoms defined as HETATM in pdb-files (all 
platforms)

The easiest way to obtain the update is to install the CCP4 update 
clienthttp://www.ccp4.ac.uk/download/update_manual.html, if you have not done 
so already. Note that autoupdates will work correctly only with CCP4 release 
6.3.0, therefore upgrade if necessary. Report bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4,

Andrey Lebedev


-- 
Scanned by iCritical.

[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



-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 update 6.3.0 006

[Dmitry Rodionov]

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 $CCP4 in launchd.conf Not sure if it's worth the effort.
The environment is probably set correctly (somewhere) on the machine that was 
used to install CCP4...
 
http://apple.stackexchange.com/questions/57385/where-are-system-environment-variables-set-in-mountain-lion
http://www.dowdandassociates.com/content/howto-set-environment-variable-mac-os-x-etclaunchdconf

Dmitry

On 2012-10-12, at 3:46 PM, Ben Eisenbraun wrote:

 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
 programs:i386-mac:ccp4:6.3.0:lib_exec:Update.app: into type Unicode text
 
 But I found an odd workaround. If I double-click the Update.app in Finder,
 I get the administrator password prompt, enter the credentials, and then
 the updater tells me that $CCP4 is unset, etc.
 
 I can then run 'open Update.app' from the shell, and it inherits $CCP4 and
 runs correctly.
 
 Any ideas? The workaround works, but since I don't really know why, I don't
 feel particularly good about it.
 
 Also, my installation is on NFS and is not owned by root, so it doesn't
 require administrator privileges to update. It would be nice if the
 application checked for write privileges before assuming it needs to be run
 with escalated privileges.
 
 -ben
 
 --
 | Ben Eisenbraun
 | SBGrid Consortium  | http://sbgrid.org   |
 | Harvard Medical School | http://hms.harvard.edu  |

Re: [ccp4bb] CCP4 update 6.3.0 006

[Ben Eisenbraun]

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
programs:i386-mac:ccp4:6.3.0:lib_exec:Update.app: into type Unicode text

But I found an odd workaround. If I double-click the Update.app in Finder,
I get the administrator password prompt, enter the credentials, and then
the updater tells me that $CCP4 is unset, etc.

I can then run 'open Update.app' from the shell, and it inherits $CCP4 and
runs correctly.

Any ideas? The workaround works, but since I don't really know why, I don't
feel particularly good about it.

Also, my installation is on NFS and is not owned by root, so it doesn't
require administrator privileges to update. It would be nice if the
application checked for write privileges before assuming it needs to be run
with escalated privileges.

-ben

--
| Ben Eisenbraun
| SBGrid Consortium  | http://sbgrid.org   |
| Harvard Medical School | http://hms.harvard.edu  |

Re: [ccp4bb] CCP4 update 6.3.0 006

[William G. Scott]

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, at 11:20 AM, ronan.kee...@stfc.ac.uk wrote:

 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 parsing of output
 * DiffractionImage: corrections to reading of pilatus mini-cbf
 * ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA 
 launcher and bug fixes 
 * crank: bug fix (Windows only)
 
 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.
 
 Many thanks for using CCP4,
 
 -- Ronan Keegan
 
 
 
 -- 
 Scanned by iCritical.
 

Re: [ccp4bb] CCP4 update 6.3.0 006

[Andrew Sharff]

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.


Can I second that as well.

Thanks

Andrew


Many thanks in advance.

Bill



On Oct 8, 2012, at 11:20 AM, ronan.kee...@stfc.ac.uk wrote:


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 parsing of output
*   DiffractionImage: corrections to reading of pilatus mini-cbf
*   ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA 
launcher and bug fixes
*   crank: bug fix (Windows only)

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.

Many thanks for using CCP4,

-- Ronan Keegan



--
Scanned by iCritical.



--
--
*Dr. Andrew J. Sharff D.Phil**
*Research Scientist / Software Developer
Global Phasing Ltd
Sheraton House
Castle Park
Cambridge CB3 0AX
UK
Tel: +(0)1223 353033
Fax: +(0)1223 366889

Re: [ccp4bb] CCP4 update 6.3.0 006

[eugene . krissinel]

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 our efforts. CCP4 is currently 
in transitional state regarding its repository system and build mechanism, so 
that not everything is in due shape, and I apologise for any inconvenience this 
is causing to you.

Current source codes are available from FusionForge at

http://fg.oisin.rc-harwell.ac.uk

just choose Project-Project List-Project Name (e.g. sfcheck) - SCM and a 
checkout command will be on the screen. These are our new repositories, but we 
have not finished migration to them yet. Codes that you do not see on 
FusionForge, are still available from CVS:

http://www.ccp4.ac.uk/cvs

We do realise that checking out sources and building them on client's side may 
be a non-trivial task to do. In order to help that, we are developing a 
completely new build system, which allows one to automatically check out CCP4 
components and build them individually or all at once with a single command. 
This is meant to be our build system for next release (hopefully), and, in 
fact, Windows part of 6.3.0 was actually built with it. I would like to 
encourage you to have a look at

http://devtools.fg.oisin.rc-harwell.ac.uk

which is a not-so-long instruction on how to use the new system. It can be used 
right away to build current source codes, so that you do not have to browse the 
repositories.

We would be highly appreciative if you give it a try and communicate your 
feedback to us. As I mentioned, things are currently being shaped, and we are 
prepared to have any suggestions. Please do not put it away if it does not work 
for you for any reason, and speak to us instead.


Responsible people, who are to be contacted for feedback/clarification/help:

New build system: Marcin Wojdyr at  marcin.woj...@stfc.ac.uk

New repositories: Charles Ballard at charles.ball...@stfc.ac.uk and/or
 Ville Uski at ville.u...@stfc.ac.uk

I hope that this clarifies the issue, but let me know if it does not.

Best regards,

Eugene




On 9 Oct 2012, at 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.
 
 Many thanks in advance.
 
 Bill
 
 
 
 On Oct 8, 2012, at 11:20 AM, ronan.kee...@stfc.ac.uk wrote:
 
 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 parsing of output
 *DiffractionImage: corrections to reading of pilatus mini-cbf
 *ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA 
 launcher and bug fixes 
 *crank: bug fix (Windows only)
 
 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.
 
 Many thanks for using CCP4,
 
 -- Ronan Keegan
 
 
 
 -- 
 Scanned by iCritical.
 


-- 
Scanned by iCritical.

[ccp4bb] CCP4 update 6.3.0 006

[ronan . keegan]

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 parsing of output
*   DiffractionImage: corrections to reading of pilatus mini-cbf
*   ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA 
launcher and bug fixes 
*   crank: bug fix (Windows only)

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.

Many thanks for using CCP4,

-- Ronan Keegan



-- 
Scanned by iCritical.

[ccp4bb] CCP4 update

[David Waterman]

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

In addition to the above, on Windows:

   - *ccp4i*: added kill job functionality

The easiest way to obtain the update is to install the CCP4 update
clienthttp://www.ccp4.ac.uk/download/update_manual.html, if
you have not done so already. Note that autoupdates will work correctly
only with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs
to c...@stfc.ac.uk.

Many thanks for using CCP4,

-- David Waterman

Re: [ccp4bb] CCP4 Update

[Felix Frolow]

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
Cellular: 0547 459 608

On Sep 6, 2012, at 19:00 , eugene.krissi...@stfc.ac.uk wrote:

 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, while 
 delivering bug fixes and new features much more efficiently than before. 
 Please take a moment to install CCP4 update functionality as described below.
 
 While update mechanism will be integrated in all future CCP4 releases, it 
 needs to be installed manually in CCP4 6.3.0. When installed, the updater 
 checks for new updates automatically, and issues a message when new updates 
 are available. After that, updates can be installed in a few mouse clicks. 
 If, for some reason, you find a particular update undesirable, it can be 
 removed with auto-reverting your CCP4 setup to the pre-update state. Note 
 that the update mechanism cannot be used with CCP4 versions lower than 6.3.0, 
 therefore, please upgrade to the latest CCP4 release if you have not done it 
 so far. For upgrade, proceed to CCP4 download pages at 
 http://www.ccp4.ac.uk/download/ .
 
 Detail update installation instructions are given in
 
 http://www.ccp4.ac.uk/download/update_manual.html
 
 The document may seem to be lengthy, however, installation should not take 
 more than a few minutes:
 
 1) download update client (archived) using an appropriate link in the above 
 manual
 2) unpack the archive into the top of CCP4 directory ( C:/CCP4/6.3/ in 
 Windows, ccp4-6.3.0/ in Linux/Mac OSX)
 3) run the update client (update.exe/update/Update.app) _from CCP4 directory_ 
 by double-clicking on it in your file browser
 4) install 1st update
 5) (re-)start ccp4i, and see new Manage Updates button in the bottom-right 
 corner of ccp4i window.
 
 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.
 
 Thank you for using CCP4,
 
 Eugene Krissinel.
 
 
 
 -- 
 Scanned by iCritical.
 

Re: [ccp4bb] CCP4 Update

[William G. Scott]

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?

-- Bill Scott

[ccp4bb] CCP4 Update

[eugene . krissinel]

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, while delivering bug fixes and 
new features much more efficiently than before. Please take a moment to install 
CCP4 update functionality as described below.

While update mechanism will be integrated in all future CCP4 releases, it needs 
to be installed manually in CCP4 6.3.0. When installed, the updater checks for 
new updates automatically, and issues a message when new updates are available. 
After that, updates can be installed in a few mouse clicks. If, for some 
reason, you find a particular update undesirable, it can be removed with 
auto-reverting your CCP4 setup to the pre-update state. Note that the update 
mechanism cannot be used with CCP4 versions lower than 6.3.0, therefore, please 
upgrade to the latest CCP4 release if you have not done it so far. For upgrade, 
proceed to CCP4 download pages at http://www.ccp4.ac.uk/download/ .

Detail update installation instructions are given in

http://www.ccp4.ac.uk/download/update_manual.html

The document may seem to be lengthy, however, installation should not take more 
than a few minutes:

1) download update client (archived) using an appropriate link in the above 
manual
2) unpack the archive into the top of CCP4 directory ( C:/CCP4/6.3/ in Windows, 
ccp4-6.3.0/ in Linux/Mac OSX)
3) run the update client (update.exe/update/Update.app) _from CCP4 directory_ 
by double-clicking on it in your file browser
4) install 1st update
5) (re-)start ccp4i, and see new Manage Updates button in the bottom-right 
corner of ccp4i window.

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.

Thank you for using CCP4,

Eugene Krissinel.



-- 
Scanned by iCritical.