Hi，
As a new user of CcpNmr analysis (Version 3.0.2) on MacBook Pro, I am impressed by it`s ease of use and flexibility. I have been working through the tutorials, and while I am trying to open assign analysis in NMRbox I get a series of error messages:
==> Getting user preferences
==> Language set to `Chinese`
==> Creating new, empty project
INFO : Located at /var/folders/rw/hrghn4vs00gdf_y1cgc86_1c0000gn/T/CcpnProject_tk5n4r65.ccpn (Logging._info:109)
WARNING: text `Search Results` not in `Chinese` translation dictionary (Translation.translate:119)
WARNING: text `Load Data...` not in `Chinese` translation dictionary (Translation.translate:119)
WARNING: text `Nef File` not in `Chinese` translation dictionary (Translation.translate:119)
WARNING: text `NmrStar File` not in `Chinese` translation dictionary (Translation.translate:119)
WARNING: text `Save as...` not in `Chinese` translation dictionary (Translation.translate:119)
WARNING: text `Restore last` not in `Chinese` translation dictionary
I am able to uncompressed and launch the CcpNmrLauncher. I have uninstalled and reinstalled the software several times, but the problem has not been solved.
I would really appreciate any help or insight on this matter considering that I have been trying to figure this out for the past days. Please feel free to reach out to me if you need clarification on my question.
Cheers,
Junjie
Hi Junjie,
I think the problem may be that you have set the language to Chinese. We are hoping to add some translations to the software at some point, but haven`t been able to do this yet. I realise that the language drop-down in the Preferences suggests that we have done this, though. So perhaps try to set the language back to English and then see how you get on.
It sounds as though you are otherwise able to run the software in NMRbox.
As regards your MacBook. Are you running it with Catalina? Apple are making it hard and harder for people to run software that hasn`t been developed by an official Apple Developer. We are trying to sort this out, but things keep being stalled by our University Administration.
However, some people do seem to have managed to install the software with Catalina. Try the following these instructions carefully:
Please make sure you follow the instructions in the installer window. The first time you launch the App you will probably have to open it with right-click / Open in order to verify that you want to open an App from an unregistered Developer (in future we hope to gain official Apple Developer status, but as yet we don`t have this).
If you encounter any errors that the App `can`t be opened` or `is damaged`, please go to System Preferences / Security & Privacy / General and select `Allow apps downloaded from Anywhere`. If `Anywhere` is not an option, open a terminal window and enter sudo spctl --master-disable and then try opening the app again via right-click / Open.
Once you have opened the Launcher once this way, you should be okay and can set you security settings back to Allow apps downloaded from App Store or App Store and identified developers.
If you are still struggling with the Launcher you could otherwise try the command line download and see if that goes any better.
Best wishes,
Vicky
Thank you Vicky.
I can`t open the assign analysis in NMRbox so that I have no way to set the language back to English. I also have tried the command line download, however, it`s led to nothing. I tried again and again, but to no effect.
Hi Junjie, you can change the preferences externally from the JSON file in the hidden directory .ccpn which should be in your top home dir (/home/replaceWithuserName/.ccpn) . Open the v3settings.json file with a text editor and change the language entry, e.g. `language`: `English-UK`.
[attachment=28 Wrote:LucaM pid=`358` dateline=`1595416704`]Hi Junjie, you can change the preferences externally from the JSON file in the hidden directory .ccpn which should be in your top home dir (/home/replaceWithuserName/.ccpn) . Open the v3settings.json file with a text editor and change the language entry, e.g. `language`: `English-UK`.
Thank you Luca.
According to your suggestions, I found the defaultv3settings.json file. However, the language entry already is set to “English-UK” as shown in picture. So far, I`m still puzzled over this difficult problem.
,
I think you are looking to the wrong file. That is the default file which comes with the program. It is then copied inside your local machine in the top directory. If you are on a mac, try to open a Terminal window, use `cd` to change to the top dir, then do `open .ccpn` . This will show in finder the correct file.
(07-25-2020, 07:13 pm)LucaM Wrote: I think you are looking to the wrong file. That is the default file which comes with the program. It is then copied inside your local machine in the top directory. If you are on a mac, try to open a Terminal window, use `cd` to change to the top dir, then do `open .ccpn` . This will show in finder the correct file.
Dear Luca,
Thank you very much for your help.
I kept on checking all the folders of my mac, finally, I found the `.ccpn`folder which is hidden folder in the top directory. According your valuable advice, I open the v3settings.json file with a text editor and change the language entry.
Now I can open the assign again, however, I am faced with a new problem: I want to download the simulated HSQC data from the Biological Magnetic Resonance Data Bank. How can I open the formats of the backbone or all simulated shifts of the CSV/SPARKY by CCPN assign?
Hi Junjie,
rather than trying to read in the simulated Sparky peak list generated by the BMRB, simply read in the BMRB NMRStar file and simulate the HSQC peaks in Analysis during the import as shown here:
https://www.ccpn.ac.uk/manual/v3/BMRBImport.html
Best wishes,
Vicky
(07-27-2020, 08:04 am)VickyH Wrote: Hi Junjie,
rather than trying to read in the simulated Sparky peak list generated by the BMRB, simply read in the BMRB NMRStar file and simulate the HSQC peaks in Analysis during the import as shown here:
https://www.ccpn.ac.uk/manual/v3/BMRBImport.html
Best wishes,
Vicky
Dear Vicky,
It is appreciated for answering my question in your busy time.
I have download the NMRStar.str that contains the an assigned chemical shift list from BMRB. Follow the tutorial, I import the BMRM file to the CCPN assign and my project contain a new chemical shift list. I have some question: Whether the assigned chemical shift can only exist in the form of a list? Are there any ways that the assigned chemical shift could show in the HSQC spectrum？
(07-27-2020, 11:55 am)lanlaohu317 Wrote:Dear Vicky,(07-27-2020, 08:04 am)VickyH Wrote: Hi Junjie,
rather than trying to read in the simulated Sparky peak list generated by the BMRB, simply read in the BMRB NMRStar file and simulate the HSQC peaks in Analysis during the import as shown here:
https://www.ccpn.ac.uk/manual/v3/BMRBImport.html
Best wishes,
Vicky
Dear Vicky,
It is appreciated for answering my question in your busy time.
I have download the NMRStar.str that contains the an assigned chemical shift list from BMRB. Follow the tutorial, I import the BMRM file to the CCPN assign and my project contain a new chemical shift list. I have some question: Whether the assigned chemical shift can only exist in the form of a list? Are there any ways that the assigned chemical shift could show in the HSQC spectrum？
Thank you for your help.
I have read the tutorial carefully as shown here: https://www.ccpn.ac.uk/manual/v3/Transfe...ments.html , now I`ve already fixed the problem.
Best wishes,
Junjie