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
[ccp4bb] CCP4 Update victim of own success
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
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
