[ccp4bb] CCP4 GUI problem
Dear colleagues, I am suddenly having a problem with starting the ccp4 Interface. Logged on as a normal user (username, group users) the Interface window pops up but hangs almost immediately (the top bar says CCP4Interface 2.1.0, the only program tab shown is Coordinate Utilities and the tabs on the right side of the window stop after View Any File). There are no error messages and job has to be killed (Ctrl c). When I log on to the user account from which ccp4 was installed (software, group users), the GUI opens without any problems. The software account does not have admin rights, by the way. The system is SUSE SLES 11, and I had no problems with the ccp4 installation in the past. However, I have added a few libraries in the meantime, in particular zlib-devel from the SLE-11-SDK repository. It looks to me as if there is a problem with file access permissions at some point but I cannot work out where. In my desperation I even set the permissions to rwx for all users (ugo) for the entire ccp4 folder but the problem persists. The problem is the same for ccp4 6.1.13 and 6.2.0. Any help will be appreciated. Cheers, Uli --- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.de mailto:ulrich.goh...@mdc-berlin.de http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/ http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/
Re: [ccp4bb] CCP4 GUI
On Thu, May 10, 2007 at 02:46:44PM +0100, Kolstoe S.E. wrote: The most useful aspect of the ccp4i GUI is its automatic generation of com files. However, I would prefer the GUI to output a .com file into my working directory (rather than the obscure location they are saved to now) every time I run a program so that I can then tinker with it and add any extra keywords I want to. I often use the GUI to get a 'second opinion' about good default values and options for a given CCP4 program - especially if the documentation is a bit confusing. Kind of double-checking if I understood the documentation correctly. One thing I found very confusing though, is that the com-files created by the CCP4i will often have (nearly) all possible keywords set, even if I haven't changed any of the defaults in the gui. Often, a CCP4 program has defaults itself and only requires keywords if one wants to change things - which is nice, since it leads e.g. to a very short SCALA comand-file. I'm not always convinced that the settings done by the CCP4i interface (when keeping all edfaults) correspond to the defaults as implemented in the program itself. Maybe any parameter setting unchanged from the values in the $CCP4/ccp4i/tasks/*.def file should be internally flagged as being at the 'default value' - resulting in them _not_ being written to the com-file? This way any potential change in defaults inside the actual program would have immediate effect, even if the CCP4i hasn't been updated yet. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] CCP4 GUI
Hi Maybe any parameter setting unchanged from the values in the $CCP4/ccp4i/tasks/*.def file should be internally flagged as being at the 'default value' - resulting in them _not_ being written to the com-file? This way any potential change in defaults inside the actual program would have immediate effect, even if the CCP4i hasn't been updated yet. This is a _really_ good idea for another reason. There are programs which determine processing parameter values dyamically, based on what they have actually been presented with - UNLESS those values have been input by the user, who is assumed to know better. If an interface (e.g. ccp4i) sets the value to a default, the program really has no way of knowing that it was the interface and not a user who knows their data which has input the value. Just my two ha'porth... Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] CCP4 GUI
Clemens Vonrhein wrote: One thing I found very confusing though, is that the com-files created by the CCP4i will often have (nearly) all possible keywords set, even if I haven't changed any of the defaults in the gui. Often, a CCP4 program has defaults itself and only requires keywords if one wants to change things - which is nice, since it leads e.g. to a very short SCALA comand-file. I'm not always convinced that the settings done by the CCP4i interface (when keeping all edfaults) correspond to the defaults as implemented in the program itself. This of course depends on whether the program author wrote their best set of defaults into the GUI or the program, which in turn depends on whether the program author wrote the GUI or not. I tend to assume that everyone is running through the GUI these days, and make sure that the GUI defaults are the sensible ones (although I try and keep the program source in step). If someone asks me how best to run one of my programs, the answer is therefore to use the GUI to generate a command script and start from there. Kevin
Re: [ccp4bb] CCP4 GUI
I would agree with Clemens that the Scala GUI task generates far too many keyworded commands, for things which have sensible defaults in the program. One problem conundrum for the GUI (because it works by generating a script without actually running the program) is that the GUI has no way of knowing what defaults are set in the program (particularly if they are dynamic depending on the data). But this could be managed better than it is in all cases. Phil On 11 May 2007, at 08:31, Clemens Vonrhein wrote: On Thu, May 10, 2007 at 02:46:44PM +0100, Kolstoe S.E. wrote: The most useful aspect of the ccp4i GUI is its automatic generation of com files. However, I would prefer the GUI to output a .com file into my working directory (rather than the obscure location they are saved to now) every time I run a program so that I can then tinker with it and add any extra keywords I want to. I often use the GUI to get a 'second opinion' about good default values and options for a given CCP4 program - especially if the documentation is a bit confusing. Kind of double-checking if I understood the documentation correctly. One thing I found very confusing though, is that the com-files created by the CCP4i will often have (nearly) all possible keywords set, even if I haven't changed any of the defaults in the gui. Often, a CCP4 program has defaults itself and only requires keywords if one wants to change things - which is nice, since it leads e.g. to a very short SCALA comand-file. I'm not always convinced that the settings done by the CCP4i interface (when keeping all edfaults) correspond to the defaults as implemented in the program itself. Maybe any parameter setting unchanged from the values in the $CCP4/ccp4i/tasks/*.def file should be internally flagged as being at the 'default value' - resulting in them _not_ being written to the com-file? This way any potential change in defaults inside the actual program would have immediate effect, even if the CCP4i hasn't been updated yet. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
[ccp4bb] CCP4 GUI (was:RE: [ccp4bb] Refmac and B factors)
Hi Simon, Well, X-ray crystallography nowadays often, but certainly not always, amounts to running a set of programs with default settings with a few mouse clicks in the GUI. The fun part is knowing when you have to deviate from default, leave the well travelled paths etc. The GUI is excellent with the straightforward stuff, if this fails you actually have the option of editing the generated scripts (run and view com file option), or leave the GUI altogether and go to old fashioned command mode or your own scripts. Think of the GUI as a welcome addition, but not as a panacea for all your crystallography problems, and certainly train new crystallographers in such away that they at least have an idea what is going on in the black box Flip _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Kolstoe S.E. Sent: Thursday, May 10, 2007 11:09 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac and B factors Thanks very much for the replies, and especially for the link to the previous thread on this topic (Eva). Just a comment about the ccp4i GUI in general - pretty much all the students in my department are slowly becoming dependant on the GUI because it is so much easier to use for those brought up using MS windows. However, is it really fair to be distributing the GUI as a finished product when it has so many limitations, and in this particular case is just plain misleading? Although I applaud the idea of making crystallography more user friendly, is it not just asking for trouble (and bad science) when software is written that gives the illusion that things are more straight forward than they actually are? Simon _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Eva Kirchner Sent: 09 May 2007 17:37 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac and B factors Hi Simon, you can't stop it - I asked the same question (with some more questions) some weeks ago. You can find the original email and the tips I got for not-so-good resolution B-factor refinement here: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html Good luck, Eva 2007/5/9, Kolstoe S.E. [EMAIL PROTECTED]: Dear all, I have a structure at fairly low resolution that I am trying to refine with Refmac. I do not want to refine B factors so have arbitrarily set them all to 20 and then run refmac in the ccp4i GUI after deselecting the refine temperature factors box. However, when I look at the resulting pdb file my B factors vary from 2 to 90. Is Refmac just calculating my B factors or is it still refining them, and if the latter how can I stop it? Thanks, Simon
Re: [ccp4bb] CCP4 GUI (was:RE: [ccp4bb] Refmac and B factors)
Seems to be a general issue. Read the editorial in Nature 10 May 2007 Volume 447 Number 7141, pp116. Under the microscope - The use of 'black box' techniques carries risks. Colin -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Flip Hoedemaeker Sent: 10 May 2007 10:21 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] CCP4 GUI (was:RE: [ccp4bb] Refmac and B factors) Hi Simon, Well, X-ray crystallography nowadays often, but certainly not always, amounts to running a set of programs with default settings with a few mouse clicks in the GUI. The fun part is knowing when you have to deviate from default, leave the well travelled paths etc. The GUI is excellent with the straightforward stuff, if this fails you actually have the option of editing the generated scripts (run and view com file option), or leave the GUI altogether and go to old fashioned command mode or your own scripts. Think of the GUI as a welcome addition, but not as a panacea for all your crystallography problems, and certainly train new crystallographers in such away that they at least have an idea what is going on in the black box Flip From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Kolstoe S.E. Sent: Thursday, May 10, 2007 11:09 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac and B factors Thanks very much for the replies, and especially for the link to the previous thread on this topic (Eva). Just a comment about the ccp4i GUI in general - pretty much all the students in my department are slowly becoming dependant on the GUI because it is so much easier to use for those brought up using MS windows. However, is it really fair to be distributing the GUI as a finished product when it has so many limitations, and in this particular case is just plain misleading? Although I applaud the idea of making crystallography more user friendly, is it not just asking for trouble (and bad science) when software is written that gives the illusion that things are more straight forward than they actually are? Simon From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Eva Kirchner Sent: 09 May 2007 17:37 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac and B factors Hi Simon, you can't stop it - I asked the same question (with some more questions) some weeks ago. You can find the original email and the tips I got for not-so-good resolution B-factor refinement here: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html Good luck, Eva 2007/5/9, Kolstoe S.E. [EMAIL PROTECTED]: Dear all, I have a structure at fairly low resolution that I am trying to refine with Refmac. I do not want to refine B factors so have arbitrarily set them all to 20 and then run refmac in the ccp4i GUI after deselecting the refine temperature factors box. However, when I look at the resulting pdb file my B factors vary from 2 to 90. Is Refmac just calculating my B factors or is it still refining them, and if the latter how can I stop it? Thanks, Simon
Re: [ccp4bb] CCP4 GUI
I would add that I have found the CCP4 development team very receptive to being informed about specific improvements which could be made, and even more so to fixes implemented by users themselves. Perhaps an explicit list of the many limitations which need attention would be useful to the development team. Cheers, Charlie Flip Hoedemaeker wrote: Hi Simon, Well, X-ray crystallography nowadays often, but certainly not always, amounts to running a set of programs with default settings with a few mouse clicks in the GUI. The fun part is knowing when you have to deviate from default, leave the well travelled paths etc. The GUI is excellent with the straightforward stuff, if this fails you actually have the option of editing the generated scripts (run and view com file option), or leave the GUI altogether and go to old fashioned command mode or your own scripts. Think of the GUI as a welcome addition, but not as a panacea for all your crystallography problems, and certainly train new crystallographers in such away that they at least have an idea what is going on in the black box Flip *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Kolstoe S.E. *Sent:* Thursday, May 10, 2007 11:09 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Refmac and B factors Thanks very much for the replies, and especially for the link to the previous thread on this topic (Eva). Just a comment about the ccp4i GUI in general - pretty much all the students in my department are slowly becoming dependant on the GUI because it is so much easier to use for those brought up using MS windows. However, is it really fair to be distributing the GUI as a finished product when it has so many limitations, and in this particular case is just plain misleading? Although I applaud the idea of making crystallography more user friendly, is it not just asking for trouble (and bad science) when software is written that gives the illusion that things are more straight forward than they actually are? Simon *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Eva Kirchner *Sent:* 09 May 2007 17:37 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Refmac and B factors Hi Simon, you can't stop it - I asked the same question (with some more questions) some weeks ago. You can find the original email and the tips I got for not-so-good resolution B-factor refinement here: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html Good luck, Eva 2007/5/9, Kolstoe S.E. [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]: Dear all, I have a structure at fairly low resolution that I am trying to refine with Refmac. I do not want to refine B factors so have arbitrarily set them all to 20 and then run refmac in the ccp4i GUI after deselecting the refine temperature factors box. However, when I look at the resulting pdb file my B factors vary from 2 to 90. Is Refmac just calculating my B factors or is it still refining them, and if the latter how can I stop it? Thanks, Simon -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia [EMAIL PROTECTED] +61 8 6488 4406
Re: [ccp4bb] CCP4 GUI
... Forgot to say that Simon obviously is right in that the check box before refine B factors should not be there. Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Charlie Bond Sent: Thursday, May 10, 2007 11:40 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 GUI I would add that I have found the CCP4 development team very receptive to being informed about specific improvements which could be made, and even more so to fixes implemented by users themselves. Perhaps an explicit list of the many limitations which need attention would be useful to the development team. Cheers, Charlie Flip Hoedemaeker wrote: Hi Simon, Well, X-ray crystallography nowadays often, but certainly not always, amounts to running a set of programs with default settings with a few mouse clicks in the GUI. The fun part is knowing when you have to deviate from default, leave the well travelled paths etc. The GUI is excellent with the straightforward stuff, if this fails you actually have the option of editing the generated scripts (run and view com file option), or leave the GUI altogether and go to old fashioned command mode or your own scripts. Think of the GUI as a welcome addition, but not as a panacea for all your crystallography problems, and certainly train new crystallographers in such away that they at least have an idea what is going on in the black box Flip *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Kolstoe S.E. *Sent:* Thursday, May 10, 2007 11:09 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Refmac and B factors Thanks very much for the replies, and especially for the link to the previous thread on this topic (Eva). Just a comment about the ccp4i GUI in general - pretty much all the students in my department are slowly becoming dependant on the GUI because it is so much easier to use for those brought up using MS windows. However, is it really fair to be distributing the GUI as a finished product when it has so many limitations, and in this particular case is just plain misleading? Although I applaud the idea of making crystallography more user friendly, is it not just asking for trouble (and bad science) when software is written that gives the illusion that things are more straight forward than they actually are? Simon *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Eva Kirchner *Sent:* 09 May 2007 17:37 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Refmac and B factors Hi Simon, you can't stop it - I asked the same question (with some more questions) some weeks ago. You can find the original email and the tips I got for not-so-good resolution B-factor refinement here: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html Good luck, Eva 2007/5/9, Kolstoe S.E. [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]: Dear all, I have a structure at fairly low resolution that I am trying to refine with Refmac. I do not want to refine B factors so have arbitrarily set them all to 20 and then run refmac in the ccp4i GUI after deselecting the refine temperature factors box. However, when I look at the resulting pdb file my B factors vary from 2 to 90. Is Refmac just calculating my B factors or is it still refining them, and if the latter how can I stop it? Thanks, Simon -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia [EMAIL PROTECTED] +61 8 6488 4406
Re: [ccp4bb] CCP4 GUI
The level of detail in the GUI is a matter of constant debate. The underlying programs are far far richer, so the question is how much to expose in the GUI. We try to get a balance between ease-of-use and coverage, but it won't always work. BTW I don't think we ever claimed that ccp4i (or anything else in ccp4) is finished ;-) Having said that, we're always happy to hear about specific defects in the GUI. When reporting these to [EMAIL PROTECTED] please give as much information as possible, in particular knowing the context is always helpful. Cheers Martyn On Thu, 2007-05-10 at 17:39 +0800, Charlie Bond wrote: I would add that I have found the CCP4 development team very receptive to being informed about specific improvements which could be made, and even more so to fixes implemented by users themselves. Perhaps an explicit list of the many limitations which need attention would be useful to the development team. Cheers, Charlie Flip Hoedemaeker wrote: Hi Simon, Well, X-ray crystallography nowadays often, but certainly not always, amounts to running a set of programs with default settings with a few mouse clicks in the GUI. The fun part is knowing when you have to deviate from default, leave the well travelled paths etc. The GUI is excellent with the straightforward stuff, if this fails you actually have the option of editing the generated scripts (run and view com file option), or leave the GUI altogether and go to old fashioned command mode or your own scripts. Think of the GUI as a welcome addition, but not as a panacea for all your crystallography problems, and certainly train new crystallographers in such away that they at least have an idea what is going on in the black box Flip *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Kolstoe S.E. *Sent:* Thursday, May 10, 2007 11:09 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Refmac and B factors Thanks very much for the replies, and especially for the link to the previous thread on this topic (Eva). Just a comment about the ccp4i GUI in general - pretty much all the students in my department are slowly becoming dependant on the GUI because it is so much easier to use for those brought up using MS windows. However, is it really fair to be distributing the GUI as a finished product when it has so many limitations, and in this particular case is just plain misleading? Although I applaud the idea of making crystallography more user friendly, is it not just asking for trouble (and bad science) when software is written that gives the illusion that things are more straight forward than they actually are? Simon *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Eva Kirchner *Sent:* 09 May 2007 17:37 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Refmac and B factors Hi Simon, you can't stop it - I asked the same question (with some more questions) some weeks ago. You can find the original email and the tips I got for not-so-good resolution B-factor refinement here: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html Good luck, Eva 2007/5/9, Kolstoe S.E. [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]: Dear all, I have a structure at fairly low resolution that I am trying to refine with Refmac. I do not want to refine B factors so have arbitrarily set them all to 20 and then run refmac in the ccp4i GUI after deselecting the refine temperature factors box. However, when I look at the resulting pdb file my B factors vary from 2 to 90. Is Refmac just calculating my B factors or is it still refining them, and if the latter how can I stop it? Thanks, Simon
[ccp4bb] RE : [ccp4bb] CCP4 GUI suggestion
Dear all, As somebody already thought about an user-personalized interface, eg. a CCP4 menu where people could drag drop their favorite (or mostly used) programs? Cheers, Stefan -Message d'origine- De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] De la part de Martyn Winn Envoyé : jeudi, 10. mai 2007 13:05 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] CCP4 GUI This is timely. We're in the process of a) trying to organise a major effort to tidy up the existing ccp4i classic (rather than fire-fighting problems), and b) thinking about designing the next generation. Not sure which this is. Option b) would be a project over several years. Can you elucidate further. As an expert user, would you want a less scary free text box (which is essentially what RunView Com File is), or actual widgets for every option. The latter could be done as a hidden folder, made visible according to an Expert switch in Preferences. As developers, we also have to think about long-term maintainability. Options, in particular little-used options, can soon become out-of-date. m On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I'm a well-known luddite as Eleanor says. However, I shamelessly confess that the CCP4 GUI is great. Not that I think this is necessary here, I'm sure most people agree with that. If I write now is because Martynn's e-mail have reminded me of something I thought once, but forgot to ask for to the ccp4i developpers: perhaps the GUI could have two faces/modes, a basic one and an expert/advanced one. I understand that they already exist, but the expert one is hidden under the RunView Com File, while I'm thinking on a real expert GUI-mode. Users should be able to choose one or the other in their defaults, or switch from one to the other on-the-fly. I don't have a particular problem in editing the scripts as it is done now, but I have found that students tend to get a bit nervous about doing it themselves ;-) Cheers, Miguel Martyn Winn escribió: The level of detail in the GUI is a matter of constant debate. The underlying programs are far far richer, so the question is how much to expose in the GUI. We try to get a balance between ease-of-use and coverage, but it won't always work. BTW I don't think we ever claimed that ccp4i (or anything else in ccp4) is finished ;-) Having said that, we're always happy to hear about specific defects in the GUI. When reporting these to [EMAIL PROTECTED] please give as much information as possible, in particular knowing the context is always helpful. Cheers Martyn
Re: [ccp4bb] CCP4 GUI
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Martyn, I was thinking in the less scary widgets-based interface for not-so-used options. If possible, I think that all options should be available to the interface. This would make the GUI more consistent, in a way. I know is a lot more work, but I think that this will be especially appreciated by people newly approaching CCP4 (students or not). Those of us who worked with these programs from scripts (and rtfm) know that there are more options than those exported to the GUI. Others find this situation confusing. The Expert switch in Preferences would be excellent. I'm not sure to have understood the maintainability issue... unless you mean that it can happen that options that become outdated disappear from the program, so there would be a risk of having their ghosts in the GUI. But normally programs complain when an option is not available, don't they? Cheers, Miguel Martyn Winn escribió: This is timely. We're in the process of a) trying to organise a major effort to tidy up the existing ccp4i classic (rather than fire-fighting problems), and b) thinking about designing the next generation. Not sure which this is. Option b) would be a project over several years. Can you elucidate further. As an expert user, would you want a less scary free text box (which is essentially what RunView Com File is), or actual widgets for every option. The latter could be done as a hidden folder, made visible according to an Expert switch in Preferences. As developers, we also have to think about long-term maintainability. Options, in particular little-used options, can soon become out-of-date. m On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I'm a well-known luddite as Eleanor says. However, I shamelessly confess that the CCP4 GUI is great. Not that I think this is necessary here, I'm sure most people agree with that. If I write now is because Martynn's e-mail have reminded me of something I thought once, but forgot to ask for to the ccp4i developpers: perhaps the GUI could have two faces/modes, a basic one and an expert/advanced one. I understand that they already exist, but the expert one is hidden under the RunView Com File, while I'm thinking on a real expert GUI-mode. Users should be able to choose one or the other in their defaults, or switch from one to the other on-the-fly. I don't have a particular problem in editing the scripts as it is done now, but I have found that students tend to get a bit nervous about doing it themselves ;-) Cheers, Miguel Martyn Winn escribió: The level of detail in the GUI is a matter of constant debate. The underlying programs are far far richer, so the question is how much to expose in the GUI. We try to get a balance between ease-of-use and coverage, but it won't always work. BTW I don't think we ever claimed that ccp4i (or anything else in ccp4) is finished ;-) Having said that, we're always happy to hear about specific defects in the GUI. When reporting these to [EMAIL PROTECTED] please give as much information as possible, in particular knowing the context is always helpful. Cheers Martyn - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFGQwV9F6oOrDvhbQIRAvgxAJ4jJXkpU4pandgQKIZJeFooO/0FtACgl+FL KnxYHozGPko/tOAkcxawNYI= =TiHW -END PGP SIGNATURE-
Re: [ccp4bb] CCP4 GUI
Miguel Ortiz Lombardia wrote: I was thinking in the less scary widgets-based interface for not-so-used options. If possible, I think that all options should be available to the interface. My programs at least have a load of options which I put in for the purposes of testing out ideas, which didn't work but may be useful at some point in the future. Generally these options are not error checked. They should not be made available to the user.
Re: [ccp4bb] CCP4 GUI
Hi Martyn, I want to second Miguel: a switch between a basic GUI (could be with even less options) and an advanced and expert GUI that allows access to most and all options that can be used in scripts would be absolutely great! It would allow novice users to do a good job on standard problems, and gives experienced users the freedom to use any option of a program in more difficult cases. A similar idea is implemented in the SUSHI GUI of SHARP, where such a switch allows you to change less or more phase refinement and improvement parameters. Best regards, Dirk. Miguel Ortiz Lombardia wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Martyn, I was thinking in the less scary widgets-based interface for not-so-used options. If possible, I think that all options should be available to the interface. This would make the GUI more consistent, in a way. I know is a lot more work, but I think that this will be especially appreciated by people newly approaching CCP4 (students or not). Those of us who worked with these programs from scripts (and rtfm) know that there are more options than those exported to the GUI. Others find this situation confusing. The Expert switch in Preferences would be excellent. I'm not sure to have understood the maintainability issue... unless you mean that it can happen that options that become outdated disappear from the program, so there would be a risk of having their ghosts in the GUI. But normally programs complain when an option is not available, don't they? Cheers, Miguel Martyn Winn escribió: This is timely. We're in the process of a) trying to organise a major effort to tidy up the existing ccp4i classic (rather than fire-fighting problems), and b) thinking about designing the next generation. Not sure which this is. Option b) would be a project over several years. Can you elucidate further. As an expert user, would you want a less scary free text box (which is essentially what RunView Com File is), or actual widgets for every option. The latter could be done as a hidden folder, made visible according to an Expert switch in Preferences. As developers, we also have to think about long-term maintainability. Options, in particular little-used options, can soon become out-of-date. m On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I'm a well-known luddite as Eleanor says. However, I shamelessly confess that the CCP4 GUI is great. Not that I think this is necessary here, I'm sure most people agree with that. If I write now is because Martynn's e-mail have reminded me of something I thought once, but forgot to ask for to the ccp4i developpers: perhaps the GUI could have two faces/modes, a basic one and an expert/advanced one. I understand that they already exist, but the expert one is hidden under the RunView Com File, while I'm thinking on a real expert GUI-mode. Users should be able to choose one or the other in their defaults, or switch from one to the other on-the-fly. I don't have a particular problem in editing the scripts as it is done now, but I have found that students tend to get a bit nervous about doing it themselves ;-) Cheers, Miguel Martyn Winn escribió: The level of detail in the GUI is a matter of constant debate. The underlying programs are far far richer, so the question is how much to expose in the GUI. We try to get a balance between ease-of-use and coverage, but it won't always work. BTW I don't think we ever claimed that ccp4i (or anything else in ccp4) is finished ;-) Having said that, we're always happy to hear about specific defects in the GUI. When reporting these to [EMAIL PROTECTED] please give as much information as possible, in particular knowing the context is always helpful. Cheers Martyn - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFGQwV9F6oOrDvhbQIRAvgxAJ4jJXkpU4pandgQKIZJeFooO/0FtACgl+FL KnxYHozGPko/tOAkcxawNYI= =TiHW -END PGP SIGNATURE- -- Dirk Kostrewa Paul Scherrer Institut Biomolecular Research, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: [EMAIL PROTECTED] http://sb.web.psi.ch
Re: [ccp4bb] CCP4 GUI
I always liked Kevin's comments on little-used options in the DM documentation Don't use these unless you really know what you are doing. In which case you'd better have a better idea of what you are doing than I do. Phil On 10 May 2007, at 13:07, Kevin Cowtan wrote: Miguel Ortiz Lombardia wrote: I was thinking in the less scary widgets-based interface for not-so-used options. If possible, I think that all options should be available to the interface. My programs at least have a load of options which I put in for the purposes of testing out ideas, which didn't work but may be useful at some point in the future. Generally these options are not error checked. They should not be made available to the user.
Re: [ccp4bb] CCP4 GUI
The level of detail in the GUI is a matter of constant debate. The underlying programs are far far richer, so the question is how much to expose in the GUI. How about the simple and elegant way it is done in Refmac? Tacked under Developers Options is specify an external keyword script file for Refmac. I frequently use this and always wished that *all* CCP4i GUIs had this. Sounds like something that lets user enjoy the simplicity GUI yet allowing flexibility of using complete functionality of the programs. This should be very easy to implement. Dima
Re: [ccp4bb] CCP4 GUI
Hi Martyn, how about option c: in each gui window at the lower left corner have a button called Display script, or call it Expert Mode if people feel better as Experts :-) , before running of course. Then people who would like to edit their stuff could do so before running the script. I think it would be scary to many if the Expert Mode actually would display all other options available for that particular program - for this you have the RTFM* I tend to use the GUI only for standard stuff and keep migrating my scripts from directories to directories, which if you run a search on say e.g. refmac. spits out a ton of handcrafted scripts for each project - maybe also not the best thing to do, but that's how it is. Juergen * Fine of course, what else ! Martyn Winn wrote: This is timely. We're in the process of a) trying to organise a major effort to tidy up the existing ccp4i classic (rather than fire-fighting problems), and b) thinking about designing the next generation. Not sure which this is. Option b) would be a project over several years. Can you elucidate further. As an expert user, would you want a less scary free text box (which is essentially what RunView Com File is), or actual widgets for every option. The latter could be done as a hidden folder, made visible according to an Expert switch in Preferences. As developers, we also have to think about long-term maintainability. Options, in particular little-used options, can soon become out-of-date. m On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I'm a well-known luddite as Eleanor says. However, I shamelessly confess that the CCP4 GUI is great. Not that I think this is necessary here, I'm sure most people agree with that. If I write now is because Martynn's e-mail have reminded me of something I thought once, but forgot to ask for to the ccp4i developpers: perhaps the GUI could have two faces/modes, a basic one and an expert/advanced one. I understand that they already exist, but the expert one is hidden under the RunView Com File, while I'm thinking on a real expert GUI-mode. Users should be able to choose one or the other in their defaults, or switch from one to the other on-the-fly. I don't have a particular problem in editing the scripts as it is done now, but I have found that students tend to get a bit nervous about doing it themselves ;-) Cheers, Miguel Martyn Winn escribió: The level of detail in the GUI is a matter of constant debate. The underlying programs are far far richer, so the question is how much to expose in the GUI. We try to get a balance between ease-of-use and coverage, but it won't always work. BTW I don't think we ever claimed that ccp4i (or anything else in ccp4) is finished ;-) Having said that, we're always happy to hear about specific defects in the GUI. When reporting these to [EMAIL PROTECTED] please give as much information as possible, in particular knowing the context is always helpful. Cheers Martyn -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002
Re: [ccp4bb] CCP4 GUI
I think a tweak script button or option (before running) would be an excellent idea. Cheers, ___ Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Juergen Bosch Sent: Thursday, May 10, 2007 10:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 GUI Hi Martyn, how about option c: in each gui window at the lower left corner have a button called Display script, or call it Expert Mode if people feel better as Experts :-) , before running of course. Then people who would like to edit their stuff could do so before running the script. I think it would be scary to many if the Expert Mode actually would display all other options available for that particular program - for this you have the RTFM* I tend to use the GUI only for standard stuff and keep migrating my scripts from directories to directories, which if you run a search on say e.g. refmac. spits out a ton of handcrafted scripts for each project - maybe also not the best thing to do, but that's how it is. Juergen * Fine of course, what else ! Martyn Winn wrote: This is timely. We're in the process of a) trying to organise a major effort to tidy up the existing ccp4i classic (rather than fire-fighting problems), and b) thinking about designing the next generation. Not sure which this is. Option b) would be a project over several years. Can you elucidate further. As an expert user, would you want a less scary free text box (which is essentially what RunView Com File is), or actual widgets for every option. The latter could be done as a hidden folder, made visible according to an Expert switch in Preferences. As developers, we also have to think about long-term maintainability. Options, in particular little-used options, can soon become out-of-date. m On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I'm a well-known luddite as Eleanor says. However, I shamelessly confess that the CCP4 GUI is great. Not that I think this is necessary here, I'm sure most people agree with that. If I write now is because Martynn's e-mail have reminded me of something I thought once, but forgot to ask for to the ccp4i developpers: perhaps the GUI could have two faces/modes, a basic one and an expert/advanced one. I understand that they already exist, but the expert one is hidden under the RunView Com File, while I'm thinking on a real expert GUI-mode. Users should be able to choose one or the other in their defaults, or switch from one to the other on-the-fly. I don't have a particular problem in editing the scripts as it is done now, but I have found that students tend to get a bit nervous about doing it themselves ;-) Cheers, Miguel Martyn Winn escribió: The level of detail in the GUI is a matter of constant debate. The underlying programs are far far richer, so the question is how much to expose in the GUI. We try to get a balance between ease-of-use and coverage, but it won't always work. BTW I don't think we ever claimed that ccp4i (or anything else in ccp4) is finished ;-) Having said that, we're always happy to hear about specific defects in the GUI. When reporting these to [EMAIL PROTECTED] please give as much information as possible, in particular knowing the context is always helpful. Cheers Martyn -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002
Re: [ccp4bb] CCP4 GUI
As long as I have been using the ccp4i (which has been a couple of years now), this magic button has been there, and it has even been in the 'lower left corner': When you hold your mouse button on the Run button, a submenu appears, the second item of which is saying RunView com file. This opens an editable window with the script used to run the ccp4-program. This, by the way, is very handy for setting the matrix weight in Refmac5 to 'auto', as recommended by the authors of ARP/wARP. Tim -Original Message- From: Roger Rowlett [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Date: Thu, 10 May 2007 10:44:13 -0400 Subject: Re: [ccp4bb] CCP4 GUI I think a tweak script button or option (before running) would be an excellent idea. Cheers, ___ Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Juergen Bosch Sent: Thursday, May 10, 2007 10:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 GUI Hi Martyn, how about option c: in each gui window at the lower left corner have a button called Display script, or call it Expert Mode if people feel better as Experts :-) , before running of course. Then people who would like to edit their stuff could do so before running the script. I think it would be scary to many if the Expert Mode actually would display all other options available for that particular program - for this you have the RTFM* I tend to use the GUI only for standard stuff and keep migrating my scripts from directories to directories, which if you run a search on say e.g. refmac. spits out a ton of handcrafted scripts for each project - maybe also not the best thing to do, but that's how it is. Juergen * Fine of course, what else ! Martyn Winn wrote: This is timely. We're in the process of a) trying to organise a major effort to tidy up the existing ccp4i classic (rather than fire-fighting problems), and b) thinking about designing the next generation. Not sure which this is. Option b) would be a project over several years. Can you elucidate further. As an expert user, would you want a less scary free text box (which is essentially what RunView Com File is), or actual widgets for every option. The latter could be done as a hidden folder, made visible according to an Expert switch in Preferences. As developers, we also have to think about long-term maintainability. Options, in particular little-used options, can soon become out-of-date. m On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I'm a well-known luddite as Eleanor says. However, I shamelessly confess that the CCP4 GUI is great. Not that I think this is necessary here, I'm sure most people agree with that. If I write now is because Martynn's e-mail have reminded me of something I thought once, but forgot to ask for to the ccp4i developpers: perhaps the GUI could have two faces/modes, a basic one and an expert/advanced one. I understand that they already exist, but the expert one is hidden under the RunView Com File, while I'm thinking on a real expert GUI-mode. Users should be able to choose one or the other in their defaults, or switch from one to the other on-the-fly. I don't have a particular problem in editing the scripts as it is done now, but I have found that students tend to get a bit nervous about doing it themselves ;-) Cheers, Miguel Martyn Winn escribió: The level of detail in the GUI is a matter of constant debate. The underlying programs are far far richer, so the question is how much to expose in the GUI. We try to get a balance between ease-of-use and coverage, but it won't always work. BTW I don't think we ever claimed that ccp4i (or anything else in ccp4) is finished ;-) Having said that, we're always happy to hear about specific defects in the GUI. When reporting these to [EMAIL PROTECTED] please give as much information as possible, in particular knowing the context is always helpful. Cheers Martyn -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX:+1-206-685-7002
Re: [ccp4bb] CCP4 GUI
Hi Martyn: I never use the GUI and it scares me, so I probably should just STFU, but that sort of thing has never kept me from pontificating. I often get emails from people asking how to do something with the GUI and they don't believe me, because I've developed a reputation as something of a Mac OS X shill. The Mac OS X GUI (and newer Linux desktops like Xfce) are nice because they are unobtrusive. The CCP4 GUI, at least back when I decided to try it, seemed to always fight me and try to make me do stuff I don't want to do, and I already have a wife. The worst GUI I have seen is the one with Phenix. Which is odd, because it has the best command-line experience. I think the file parsing and IO is part of the open-source portion of the project (CCTBX) and since that is already an optional distribution with CCP4, may I humbly suggest tighter integration with the existing CCP4 suit? If that happens, a parsing editor for the def file is really all you would probably need for a GUI. Bill On Thu, 10 May 2007, Martyn Winn wrote: This is timely. We're in the process of a) trying to organise a major effort to tidy up the existing ccp4i classic (rather than fire-fighting problems), and b) thinking about designing the next generation. Not sure which this is. Option b) would be a project over several years. Can you elucidate further. As an expert user, would you want a less scary free text box (which is essentially what RunView Com File is), or actual widgets for every option. The latter could be done as a hidden folder, made visible according to an Expert switch in Preferences. As developers, we also have to think about long-term maintainability. Options, in particular little-used options, can soon become out-of-date. m On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I'm a well-known luddite as Eleanor says. However, I shamelessly confess that the CCP4 GUI is great. Not that I think this is necessary here, I'm sure most people agree with that. If I write now is because Martynn's e-mail have reminded me of something I thought once, but forgot to ask for to the ccp4i developpers: perhaps the GUI could have two faces/modes, a basic one and an expert/advanced one. I understand that they already exist, but the expert one is hidden under the RunView Com File, while I'm thinking on a real expert GUI-mode. Users should be able to choose one or the other in their defaults, or switch from one to the other on-the-fly. I don't have a particular problem in editing the scripts as it is done now, but I have found that students tend to get a bit nervous about doing it themselves ;-) Cheers, Miguel Martyn Winn escribió: The level of detail in the GUI is a matter of constant debate. The underlying programs are far far richer, so the question is how much to expose in the GUI. We try to get a balance between ease-of-use and coverage, but it won't always work. BTW I don't think we ever claimed that ccp4i (or anything else in ccp4) is finished ;-) Having said that, we're always happy to hear about specific defects in the GUI. When reporting these to [EMAIL PROTECTED] please give as much information as possible, in particular knowing the context is always helpful. Cheers Martyn
Re: [ccp4bb] CCP4 GUI
Hopefully my offhand remark wasn't taken as a criticism of ccp4i (it wasn't meant as such); but seeing as I don't use it, it's not a place where I could tell someone how to find an option. As developers, we also have to think about long-term maintainability. Options, in particular little-used options, can soon become out-of-date. This is might be a bad idea*, but I'll throw it out there anyhow: What about the storing program keywords in a grammer file (something along the lines of yacc/lex), reading gui options from the grammer, and generating a parser subroutine from the grammer for the data-processing programs? This would mean changes to the parser library (and to a large number of existing programs which already work), but would eliminate the issue of keeping the gui options in sync with the program options. Pete *specifically, bad idea type #2 - probably more trouble than it's worth Pete Meyer Fu Lab BMCB grad student Cornell University
