Hello!
I was following the `BMRB Import` tutorial and I keep getting an error message. The following is what is displayed in the terminal:
==> Getting user preferences
==> Language set to `English-UK`
==> Creating new, empty project
INFO : Located at /tmp/CcpnProject_qsmdyroj.ccpn (Logging._info:109)
==> Done, AnalysisAssign is starting
==> Loading NMR-STAR NMRStar project `/home/dkhago/Desktop/RING_domain.str`
INFO : Closing /tmp/CcpnProject_qsmdyroj.ccpn/default (Logging._info:109)
==> Creating new, empty project
INFO : Located at /tmp/CcpnProject_rncdxpv5.ccpn (Logging._info:109)
WARNING: Error loading NMRStar file: `nef_nmr_meta_data` (ContextManagers.catchExceptions:466)
I just want to import assignments to my existing spectra but seem to continue having problems. This was a problem I had last year when I first starting using V3 and I know that it was still being worked on. I checked to make sure that there were no outstanding updating. Any suggestions? Thanks again for all the help!
Hi,
could you perhaps send us (ccpnmr3 (at) gmail.com) the BMRB file you are trying to import, so we can take a look at it?
Thanks,
Vicky
Hi Domarin,
thanks for sending the file.
I wonder how you are trying to load it. If I drag the file into either an empty or an existing project everything is fine for me. Similarly if I do BI or Project / Import / NmrStar file. In all cases a new Chemical Shift list and NmrChain are added to the project.
I can basically only recreate your error message if I use the Project/Load Data menu item (or shortcut LD).
Vicky
Hi Vicky!
So when I drag the file into the empty project window, I get a warning message that reads `Error lading NMRStar file: `nef_nmr_meta_data.`` I can not try and import it any other way. I click on the `Project` menu and do not see anything option to import besides the `NEF` submenu. I checked again to make sure I was not missing an update. Is there another beta version available that I need to install? I guess I should mention that I am on b5.
Hi Domarin,
using beta5 will be the problem, then. Try using the 3.0.0 version:
https://www.ccpn.ac.uk/v3-software/downl...-downloads
It probably won`t be long before there will then a 3.0.1 version which you will have to download and install from the website, too. But after that, the upgrades to newer versions will work via the update server (but we have to update the update mechanism first!).
Vicky
Hi Vicky!
I installed version 3.0.0 and that helps with importing the peak list. Thanks so much!
Domarin
The BMRB import makes problems for me, too. I tried to import e.g. BMRB 6457, and neither the version in NMRSTAR 2.1 nor in 3.0 format works here. Is there any solution? I tried going via CCPN v2 (Format Converter), and export NMRSTAR from there, but this did not solve anything either; the output from there is not even recognized by CCPN3. The BMRB file in NMRSTAR 2.1 format is not recognized either, there is not even an error message in CCPN3 when I try to import the NMRSTAR 2.1 file.
Is there any solution to this? Is there a CCPN3 version which can import the chemical shift assignments of BMRB entry 6457?
In addition to my previous message: there is actually the following error message:
Traceback (most recent call last):
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/ui/gui/widgets/Action.py`, line 75, in <lambda>
self.triggered.connect(lambda checked, *args, **kwds: callback(*args, **kwds))
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/framework/Framework.py`, line 1483, in _loadNMRStarFile
dataBlock = self.nefReader.getNMRStarData(path)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/core/lib/CcpnNefIo.py`, line 2391, in getNMRStarData
nmrDataExtent = StarIo.parseNmrStarFile(path)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 118, in parseNmrStarFile
converter.preValidate()
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 259, in preValidate
self.preValidateDataBlock(dataBlock)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 295, in preValidateDataBlock
self.preValidateSaveFrame(saveFrame)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 342, in preValidateSaveFrame
self.raiseValidationError(`SaveFrame lacks .sf_framecode item`)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 531, in raiseValidationError
raise StarValidationError(self._errorMessage(msg))
ccpn.util.nef.StarIo.StarValidationError: Error in context: [`data_/users/paul/desktop/test_bmrb6457.str`, `save_global_mr_file_characteristics`]
SaveFrame lacks .sf_framecode item
Traceback (most recent call last):
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/ui/gui/widgets/CcpnModuleArea.py`, line 154, in dropEvent
objs = self.mainWindow._processDroppedItems(data)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/ui/gui/lib/GuiMainWindow.py`, line 987, in _processDroppedItems
objs = self._processUrls(urls)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/ui/gui/lib/GuiMainWindow.py`, line 1047, in _processUrls
self.application._loadNMRStarFile(url)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/framework/Framework.py`, line 1483, in _loadNMRStarFile
dataBlock = self.nefReader.getNMRStarData(path)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/core/lib/CcpnNefIo.py`, line 2391, in getNMRStarData
nmrDataExtent = StarIo.parseNmrStarFile(path)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 118, in parseNmrStarFile
converter.preValidate()
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 259, in preValidate
self.preValidateDataBlock(dataBlock)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 295, in preValidateDataBlock
self.preValidateSaveFrame(saveFrame)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 342, in preValidateSaveFrame
self.raiseValidationError(`SaveFrame lacks .sf_framecode item`)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 531, in raiseValidationError
raise StarValidationError(self._errorMessage(msg))
ccpn.util.nef.StarIo.StarValidationError: Error in context: [`data_/users/paul/desktop/test_bmrb6457.str`, `save_global_mr_file_characteristics`]
SaveFrame lacks .sf_framecode item
Traceback (most recent call last):
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/ui/gui/widgets/CcpnModuleArea.py`, line 154, in dropEvent
objs = self.mainWindow._processDroppedItems(data)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/ui/gui/lib/GuiMainWindow.py`, line 987, in _processDroppedItems
objs = self._processUrls(urls)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/ui/gui/lib/GuiMainWindow.py`, line 1047, in _processUrls
self.application._loadNMRStarFile(url)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/framework/Framework.py`, line 1483, in _loadNMRStarFile
dataBlock = self.nefReader.getNMRStarData(path)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/core/lib/CcpnNefIo.py`, line 2391, in getNMRStarData
nmrDataExtent = StarIo.parseNmrStarFile(path)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 118, in parseNmrStarFile
converter.preValidate()
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 259, in preValidate
self.preValidateDataBlock(dataBlock)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 295, in preValidateDataBlock
self.preValidateSaveFrame(saveFrame)
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 334, in preValidateSaveFrame
% [tt[0] for tt in saveFrame.items() if isinstance(tt[1], str)]
File `/Users/paul/programdownloads/ccpnmr3.0.0/src/python/ccpn/util/nef/StarIo.py`, line 531, in raiseValidationError
raise StarValidationError(self._errorMessage(msg))
ccpn.util.nef.StarIo.StarValidationError: Error in context: [`data_6457`, `save_entry_information`]
Saveframe tags do not start with a common dot-separated prefix: [`_saveframe_category`, `_entry_title`, `_bmrb_accession_number`, `_bmrb_flat_file_name`, `_entry_type`, `_submission_date`, `_accession_date`, `_entry_origination`, `_nmr_star_version`, `_experimental_method`, `_details`, `_original_release_date`]
When importing, in the `Import from NMRSTAR` window, none of the boxes can be ticked, it seems like CCPN3 does not recognize that there are assigned chemical shifts inside.
The same is true for e.g. BMRB file 30693.
Hi Paul,
I`ll have a look at these entries for you. In the mean time, have you seen the info here:
https://www.ccpn.ac.uk/forums/misc.php?a...elp&hid=60
There is a bit of an issue that the BMRB files on the BMRB server are all in different versions and each one has different specs. We can`t possibly cater to them all, but a small amount of manual curation of the file may make it readable by V3.
Vicky
Hi Paul,
I had a look at the two BMRB entries you mentioned. Both need the little fix described at
https://www.ccpn.ac.uk/forums/misc.php?a...elp&hid=60
It is a bit frustrating that you have to do this manual fix, but the BMRB have so many different versions and don`t seem to have kept up with updating files deposited previously that it is almost impossible for us to make sure every file will work.
It is worth noting that at the moment V3 does not yet have the same facility as V2 to create peak lists from shift lists (see https://www.ccpn.ac.uk/forums/misc.php?a...elp&hid=64). During the import you can create some peak lists, but anything more involved than an HSQC or HNCA/HNCO is liable not to work. We did write a macro to create CC peaks lists:
https://www.ccpn.ac.uk/forums/showthread.php?tid=73
If there is a particular type of peak list you wanted, I could probably write you another macro, or based on the CC one, you could have a go at writing your own.
Best wishes,
Vicky
Hi Vicky,
I am also running into problems importing NMR-STAR file from BMRB. It supposed to be ver. 3.2.14.0.
When I try to load it I get this:
WARNING: Loading “C:\Users\jrlew\Desktop\bmr50938_3.str” failed:
‘NoneType’ object has no attribute ‘isMethyl’ (ContextManagers.catchExceptions:220)
Any obvious quick suggestions on how to import chemical shifts from this entry?
Thank you,
Józef
Hi Józef,
Sorry - this was due to the presence of non-standard amino acids in the sequence. We’ve added a fix to the update server, so once you’ve installed the updates you should be able to read this in without problems in 3.1.0.
Vicky
Thank you, Vicky.