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From: Edward d'A. <ed...@nm...> - 2019-03-13 10:57:41
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Hi Stefano, I'll continue the bug #12 (https://sourceforge.net/p/nmr-relax/tickets/12/) discussions here on the relax users mailing list. It is preferable to have discussions on the mailing lists rather than in the ticket systems. Please see below: On Wed, 13 Mar 2019 at 10:48, Stefano Ciurli <ste...@us...> wrote: > > Edward, thank you, I think I overcame this hurdle and loaded the spins and the heteronuclear NOE Dynamics Center file with no problem. Did you have to rename the file to remove the '#' character? The code in the relax repository will now catch this in the structure.read_pdb user function and block that character with a RelaxError. It might be a month before I can release relax 4.1.2 with the fixes though, as I am about to go on a 3 week holiday. > However, when I try to repeat the procedure using the T1 DC file, the software (4.1.1) hangs up. In particular, a clock icon appears, in place of the arrow, upon me clicking on the “next” button, and nothing else happens. This might require a new bug report. I'm not exactly sure what this could be. Does the relax GUI stay in this state indefinitely? The clock icon is shown when relax is busy doing something. > As a follow up, IMHO it is not clear, in the GUI, when one has to click on “apply” or “next”. For example, upon loading the spins from the PDB file, after selecting the “load spin from PDB option” and indicating the filename of the PDB file (without the # symbol, thanks), if I click on “apply” and then on “next”, I load the same molecule twice. Maybe it would be more logical to have the “apply” button only when it is needed (for example upon loading the different types of nuclei, @N and @H, for example) but hide it or make it inactive when only the “next” option should be used. The "Apply" button was added as there are cases where users will load multiple PDB files, one after the other. From the details in the bug #12 report, I guess this is in the spin loading wizard. So one user case here is that the user will want the atomic position data structure for the spin to be a list of positions, one for each of a set of models. If the structural models are in separate files, which can sometimes be the case, then they would select the first file, click 'Apply', select the second file, click 'Apply', and so forth. This cannot be used in a model-free analysis, but it is used in the N-state or ensemble analyses and frame order analyses (which can actually be run from the GUI, despite it being not obvious). Catching the same file being loaded twice is also not an option, as this is also a valid operation in relax. This is often used to generate a distribution or ensemble of structures. You load the same structure X times and then execute user functions that will modify each structure individually. Maybe something that could help would be to improve the tooltips for these buttons. I see that the current wizard tooltips are not very informative: - Back: "Return to the previous page". - Apply: "Apply the operation". - Skip: "Skip the operation". - Next: "Move to the next page" - OK: "Accept the operation". - Finish: "Accept the operation" - Cancel: "Abort the operation" Note this text is to cover both individual user function windows and wizards. And for wizards, it covers both user function wizard pages and custom wizard pages (e.g. the first page of the spin loading wizard). Maybe these could be improved: - Back (multiple page wizard): "Return to the previous page". - Apply (single page wizard): "Apply the operation and leave the window open". - Apply (multiple page wizard): "Apply the operation and stay on the current page". - Skip (multiple page wizard): "Skip the operation and move to the next page". - Next (multiple page wizard): "Apply the operation and move to the next page" - OK (single page wizard): "Apply the operation and close the window". - Finish (multiple page wizard): "Apply the operation and close the wizard" - Cancel (single page wizard): "Abort the operation and close the window" - Cancel (multiple page wizard): "Abort the operation and close the wizard" I don't see another way to do this without removing useful functionality from relax. Regards, Edward On Wed, 13 Mar 2019 at 10:48, Stefano Ciurli <ste...@us...> wrote: > > Edward, thank you, I think I overcame this hurdle and loaded the spins and the heteronuclear NOE Dynamics Center file with no problem. > > However, when I try to repeat the procedure using the T1 DC file, the software (4.1.1) hangs up. In particular, a clock icon appears, in place of the arrow, upon me clicking on the “next” button, and nothing else happens. > > As a follow up, IMHO it is not clear, in the GUI, when one has to click on “apply” or “next”. For example, upon loading the spins from the PDB file, after selecting the “load spin from PDB option” and indicating the filename of the PDB file (without the # symbol, thanks), if I click on “apply” and then on “next”, I load the same molecule twice. Maybe it would be more logical to have the “apply” button only when it is needed (for example upon loading the different types of nuclei, @N and @H, for example) but hide it or make it inactive when only the “next” option should be used. > > Best, > Stefano > > On 13 Mar 2019, at 09:55, Edward d'Auvergne <eda...@us...<mailto:eda...@us...>> wrote: > > > Note that you can simply name your molecule differently via the structure.read_pdb user function. > > ________________________________ > > [tickets:#12]<https://sourceforge.net/p/nmr-relax/tickets/12/> Error message upon loading PDB file - NEW > > Status: open > Created: Fri Mar 08, 2019 02:59 PM UTC by Stefano Ciurli > Last Updated: Wed Mar 13, 2019 08:55 AM UTC > Owner: Edward d'Auvergne > Attachments: > > * NewRelaxBug.jpg<https://sourceforge.net/p/nmr-relax/tickets/12/attachment/NewRelaxBug.jpg> (90.9 kB; image/jpeg) > > Hello, it seems that the problem of loading the spins from a PDB file has not been fully resolved. Please help. > SC > > ________________________________ > > Sent from sourceforge.net<http://sourceforge.net> because you indicated interest in https://sourceforge.net/p/nmr-relax/tickets/12/ > > To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/ > > > > > --- > > ** [tickets:#12] Error message upon loading PDB file - NEW** > > **Status:** fixed > **Labels:** structure > **Created:** Fri Mar 08, 2019 02:59 PM UTC by Stefano Ciurli > **Last Updated:** Wed Mar 13, 2019 09:47 AM UTC > **Owner:** Edward d'Auvergne > **Attachments:** > > - [NewRelaxBug.jpg](https://sourceforge.net/p/nmr-relax/tickets/12/attachment/NewRelaxBug.jpg) (90.9 kB; image/jpeg) > > > Hello, it seems that the problem of loading the spins from a PDB file has not been fully resolved. Please help. > SC > > > --- > > Sent from sourceforge.net because you indicated interest in <https://sourceforge.net/p/nmr-relax/tickets/12/> > > > > To unsubscribe from further messages, please visit <https://sourceforge.net/auth/subscriptions/> |
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