Re: [ccp4bb] CCP4 update manager command line options?
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
Re: [ccp4bb] CCP4 Update victim of own success
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
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 [32m*** 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 ***[m 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Or nx, which works very well, although the server has to be installed at the remote end and client on the local. www.nomachine.com Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of 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 ***[m
Re: [ccp4bb] CCP4 Update victim of own success
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
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
-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-
Re: [ccp4bb] CCP4 Update 019
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
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
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.
Re: [ccp4bb] CCP4 Update 015
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
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
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
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.
Re: [ccp4bb] ccp4 update
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
-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
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
-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
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
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
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
Re: [ccp4bb] CCP4 update 6.3.0 006
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
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
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
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
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.
Re: [ccp4bb] CCP4 Update
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
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