Hello,
I am trying to import a sparky project in ccpn but I get this error, but I don’t know how I shoul proceed.
Thank you in advance.
Andromachi
Hello,
I am trying to import a sparky project in ccpn but I get this error, but I don’t know how I shoul proceed.
Hi Andromachi,
we probably won’t get a chance to look at this properly until after tomorrow’s workshop (things are usually pretty hectic around here in advance of a workshop or conference).
Clearly the issue is that the program is trying to create a new NmrAtom that already exists. So one question is whether perhaps you already have an NmrChain called molecule in your project and which is causing these issues. If so, you could rename the existing NmrChain before doing the import.
Alternatively, there are two parts of the Sparky project which are both referencing the same NmrAtom and the program hasn’t realised that it has already created this.
So if the issue is not that you already have an NC:molecule NmrChain in your project, then I would suggest you send us the Sparky project and we’ll take a look.
Vicky
Dear Vicky,
I tried to create NEF format of the SPARKY list so I can import them on ccpn but it seemed more difficult than I thought.
I have tried once to import sparky project to ccpn with similar lists and it worked but this time I don’t seem to understand what the problem is.
If you could have a look maybe you spot something I cannot.
Thank you a lot for your help.
Best,
Andromachi
(Attachment IDR_sparky_ccpn.zip is missing)
Hi Andromachi,
very happy to take a look. I think you’ll have to send us the project to support@ccpn.ac.uk, rather than uploading it here, though.
Vicky
Yes I did.
Let me know if you received it! Thanks again
Andromachi
(Attachment IDR_sparky_ccpn.zip is missing)
Yes, got it now. Thanks.
Vicky
Hi,
I’ve had a look at your project and there are a number of different issues going on here, related to the way in which the Sparky importer works. The big issue with importing from Sparky has always been that Sparky doesn’t impose a particular format on assignments etc., so it is very difficult to recognise these automatically.
So let’s start with a few things the Sparky Importer does/assumes:
So hopefully, armed with this information, you might manage to sort out your Sparky import. I’ll send you the amended .proj file that I created and that does load.
But please be aware that there is still a bug in the import of peak lists which means if the order of the dimensions is different to what Analysis is expecting, you it won’t import them properly. I’ll see if I can look into that later this week to work out how we can solve this. Changing the order in the .save files is quite tedious, I think, because it isn’t really in a list format.
The other thing you can try for Sparky import, is that the latest version (NMRFAM-SPARKY, I think) actually includes a NEF writer - but apparently only for the Chemical Shift and Chain, not the Peaks. It did at one point have a bug: a mismatch between the order of the column headers and the data, so do check those are all correct, if you go down that route.
Vicky