Hi Michael, Thanks for your response. I was able to solve the problem by installing latest version of Ubundu 11.10. NESSY works fine on this version. I really appreciate your help.
Dhanas On Jan 15, 2012, at 3:22 PM, [email protected] wrote: > Send Nessy-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.gna.org/listinfo/nessy-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Nessy-users digest..." > > > Today's Topics: > > 1. Re: Nessy-users Digest, Vol 9, Issue 3 (Michael Bieri) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 16 Jan 2012 09:22:12 +1100 > From: Michael Bieri <[email protected]> > Subject: Re: [Nessy-users] Nessy-users Digest, Vol 9, Issue 3 > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi Dhanas > > This is a very strange error. Are you using the default theme of Ubuntu? > I am not sure if this is a NESSY problem, as NESSY uses the system font > of the operating system, and so far, there was no problem on Ubuntu, > Fedora, Windows or Mac with the font. Could you solve this problem? > > Cheers > Michael > > > Am 14.01.2012 06:50, schrieb Dhanasekaran Muthu: >> Hi Michael, >> >> Thanks for the information. I was able to get the plots the way I >> wanted. I wanted to try the NESSY on Ubuntu now. I have installed >> Ubuntu on my mac using virtual box. I downloaded the >> NESSY.11.12.1.Deb.32bit version. When I try to run the program by >> ./nessy command, I get the GUI interface but the fonts are looking not >> right. I have attached the screen shot for your reference. The error >> is (nessy:3900) Pango-Warning **: failed to choose a font, expect ugly >> output ...... It seems Pango is already in the Ubundu. Do you have any >> idea what is this and how to correct it? >> >> Thanks, >> >> Dhanas >> >> >> On Jan 11, 2012, at 9:44 PM, Michael Bieri wrote: >> >>> Hi Dhanas >>> >>> Each result is also saved in a csv file, which you can open is Excel. >>> If you are looking for the summary of your results, you can find them >>> in Exp_x_Model_selection.csv or Global_fit_Model_Selection.csv.. If >>> you are looking for a summary of R2eff per residue, you will have to >>> activate the creation of R2eff plots in the NESSY settings. >>> >>> Cheers >>> Michael >>> >>> >>> >>> Am 12.01.2012 10:37, schrieb Dhanasekaran Muthu: >>>> Hi Michael, >>>> >>>> Thanks for your reply. In fact I have repeated some of the >>>> experiments. I will try to run with that data. >>>> >>>> I have recently encountered another problem with Windows version. I >>>> get "an unhandled exception occured" message when I try to load the >>>> PDB file. It is not a problem in the Mac version. So I create the >>>> state file (.nessy) in mac version and use that in Windows version >>>> to do the calculation. >>>> >>>> Is it possible to export the summary of R2eff into a excel sheet or >>>> a text file? >>>> >>>> Thanks, >>>> >>>> Dhanas >>>> >>>> On Jan 10, 2012, at 5:58 PM, Michael Bieri wrote: >>>> >>>>> Hi Dhanas >>>>> >>>>> I have reanalyzed your data and got the same error. If I turn on >>>>> Global Fit in the models settings, it works fine. This seems to >>>>> have something to do with the error of your data. As far as I can >>>>> see, you have never repeated any experiment. For appropriate error >>>>> estimation of your NMR data, at least one experiment should be >>>>> recorded in doublicate. For any reason, individual fit mode has >>>>> some problem with this and the global fit mode does not. I have to >>>>> dig in this. For the moment, you can select the global fit mode, >>>>> but I did not get any statistically significant exchange in your >>>>> data. This might be as you have no error of your data set. I >>>>> strongly recommend to perform at least one duplicate and record is >>>>> also on another field. >>>>> >>>>> I hope this helped and feel free to ask any further question. >>>>> >>>>> Cheers >>>>> Michael >>>>> >>>>> >>>>> Am 11.01.2012 10:21, schrieb Dhanasekaran Muthu: >>>>>> Hi Michael, >>>>>> >>>>>> The program works fine on Windows 7. In fact I used nessy.save >>>>>> file created from the mac version to run the calculation. I got >>>>>> the results. The x-axis range of the plot is very narrow (-0.0010 >>>>>> to 0.0010) which is not correct. It should be 0 to 1000 Hz. I >>>>>> have attached an ensemble .svg file for your reference. I do not >>>>>> know how to correct it. I am not sure I am setting the experiment >>>>>> right. I have also attached the .nessy for your reference. Any >>>>>> help will be very useful. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Dhanas >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Jan 6, 2012 at 4:00 AM, <[email protected] >>>>>> <mailto:[email protected]>> wrote: >>>>>> >>>>>> Send Nessy-users mailing list submissions to >>>>>> [email protected] <mailto:[email protected]> >>>>>> >>>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>>> https://mail.gna.org/listinfo/nessy-users >>>>>> or, via email, send a message with subject or body 'help' to >>>>>> [email protected] <mailto:[email protected]> >>>>>> >>>>>> You can reach the person managing the list at >>>>>> [email protected] <mailto:[email protected]> >>>>>> >>>>>> When replying, please edit your Subject line so it is more >>>>>> specific >>>>>> than "Re: Contents of Nessy-users digest..." >>>>>> >>>>>> >>>>>> Today's Topics: >>>>>> >>>>>> 1. Re: NESSY problem with the mac machine (Dhanasekaran Muthu) >>>>>> >>>>>> >>>>>> ---------------------------------------------------------------------- >>>>>> >>>>>> Message: 1 >>>>>> Date: Thu, 5 Jan 2012 16:47:01 -0700 >>>>>> From: Dhanasekaran Muthu <[email protected] >>>>>> <mailto:[email protected]>> >>>>>> Subject: Re: [Nessy-users] NESSY problem with the mac machine >>>>>> To: Michael Bieri <[email protected] >>>>>> <mailto:[email protected]>> >>>>>> Cc: [email protected] <mailto:[email protected]> >>>>>> Message-ID: <[email protected] >>>>>> <mailto:[email protected]>> >>>>>> Content-Type: text/plain; charset="iso-8859-1" >>>>>> >>>>>> Hi Michael, >>>>>> >>>>>> The Synthesis data creator pops up, nothing happens when I >>>>>> click the create and program freezes. I need to kill by >>>>>> shutting down the terminal window. >>>>>> >>>>>> I will try to install Ubuntu using virtual box on my Mac. I >>>>>> will inform you once I finish installing everything. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Dhanas >>>>>> >>>>>> >>>>>> On Jan 5, 2012, at 4:12 PM, Michael Bieri wrote: >>>>>> >>>>>>> Hi Dhanas >>>>>>> >>>>>>> Does the program freeze when you are pressing a button of >>>>>> the toolbar as well. There are some issues with dialogs on >>>>>> Mac. Does the Synthetis data creator pop up or dies it freeze >>>>>> immediately? >>>>>>> >>>>>>> NESSY is intensively tested on Linux. If you want to make >>>>>> sure you get the full power of it, you can always install >>>>>> Linux (eg. Ubuntu and use the .deb version of NESSY) in a >>>>>> virtual box (https://www.virtualbox.org/) on your Mac. This >>>>>> will slow down the analysis slightly, but Python programs work >>>>>> best on Linux Machines. Otherwise have a go on Windows. >>>>>>> >>>>>>> But I realy would like to debug the Mac version. So any >>>>>> information will help. >>>>>>> >>>>>>> Cheers >>>>>>> Michael >>>>>>> >>>>>>> Am 06.01.2012 09:43, schrieb Dhanasekaran Muthu: >>>>>>>> >>>>>>>> Hi Michael, >>>>>>>> >>>>>>>> Thanks for lightening fast reply. I did not expect that! >>>>>>>> >>>>>>>> I think I used the binary method to install. I downloaded >>>>>> the zip file and just used the command ./nessy on the prompt. >>>>>> It opened the beautiful graphical interface. Then I loaded the >>>>>> peak intensity from Sparky data and run the experiment. The >>>>>> R2eff is calculated without any problem, but it does not >>>>>> proceed further, even if it is it hangs after the first residue. >>>>>>>> >>>>>>>> I do not know what is the version, because About button is >>>>>> not working i.e. it does not do anything if I click. I have >>>>>> attached the screen shot in this mail. The Synthetic Data >>>>>> generator does not seem to work. I run that nothing happens. I >>>>>> am not sure it takes very long time or not. >>>>>>>> >>>>>>>> BTW it is really a neat program. I really need this running >>>>>> and get some results. Is it fully tested on Windows machine? >>>>>> If so I can give a try. >>>>>>>> >>>>>>>> I also liked your Relax program. I have some questions >>>>>> regarding that also. I will ask about that in my next mail. >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Dhanas Muthu >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Jan 5, 2012, at 3:16 PM, Michael Bieri wrote: >>>>>>>> >>>>>>>>> Hi Dhanas >>>>>>>>> >>>>>>>>> I have not fully tested NESSY on Mac, as I don't have one. >>>>>> Can you tell me which version of NESSY you are using and if >>>>>> you are using the compiled binary or the source code? Did you >>>>>> try to only use the first 2 models? >>>>>>>>> >>>>>>>>> I will upload the Tutorial files shortly. In the mean >>>>>> time, you cane use the Synthetic Data generator (in Extras >>>>>> menu) to create a set of synthetic data in Sparky format. Then >>>>>> you can proceed as in the tutorial. >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Michael >>>>>>>>> >>>>>>>>> Am 06.01.2012 09:08, schrieb Dhanasekaran Muthu: >>>>>>>>>> I am just following the thread initiated by Michael >>>>>> Osborne. I recently installed NESSY in my Mac machine running >>>>>> Lion. When I try to run the calculations the program hangs >>>>>> after it starts the curve fitting. The R2eff values are >>>>>> calculated without any problem. For the fitting, I was trying >>>>>> to use only first 3 models. I am not sure Mike found any >>>>>> solution for his problem. I would greatly appreciate if you >>>>>> have any answer for that. >>>>>>>>>> >>>>>>>>>> Also, still the tutorial files are missing. Can you >>>>>> provide the tutorial files as you have published the paper on >>>>>> NESSY, which will be really useful to familiarize with this >>>>>> nice program. >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> >>>>>>>>>> Dhanas Muthu >>>>>>>>>> _______________________________________________ >>>>>>>>>> Nessy-users mailing list >>>>>>>>>> [email protected] <mailto:[email protected]> >>>>>>>>>> https://mail.gna.org/listinfo/nessy-users >>>>>>>> <Mail Attachment.png> >>>>>> >>>>>> -------------- next part -------------- >>>>>> An HTML attachment was scrubbed... >>>>>> URL: >>>>>> </public/nessy-users/attachments/20120105/33519382/attachment.htm> >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> _______________________________________________ >>>>>> Nessy-users mailing list >>>>>> [email protected] <mailto:[email protected]> >>>>>> https://mail.gna.org/listinfo/nessy-users >>>>>> >>>>>> >>>>>> End of Nessy-users Digest, Vol 9, Issue 3 >>>>>> ***************************************** >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Nessy-users mailing list >>>>>> [email protected] >>>>>> https://mail.gna.org/listinfo/nessy-users >>>> >> >> >> _______________________________________________ >> Nessy-users mailing list >> [email protected] >> https://mail.gna.org/listinfo/nessy-users > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: </public/nessy-users/attachments/20120116/a8e0fb71/attachment.htm> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: not available > Type: image/png > Size: 456049 bytes > Desc: not available > URL: </public/nessy-users/attachments/20120116/a8e0fb71/attachment.png> > > ------------------------------ > > _______________________________________________ > Nessy-users mailing list > [email protected] > https://mail.gna.org/listinfo/nessy-users > > > End of Nessy-users Digest, Vol 9, Issue 6 > ***************************************** _______________________________________________ Nessy-users mailing list [email protected] https://mail.gna.org/listinfo/nessy-users
