I am new in the CCPN community. I downloaded the latest version as well as the 2.4 version with the format converter in order to import a project from CARA (or at least find a way to import existing peaklists, atomlist and spectra) into CCPN.
I could not succeed and would need some help if anyone as a clue how to do that.
Thanks a lot in advance.
is there are particular step at which you got stuck?
If you are wanting to use Analysis in combination with CARA you may be better off using V2 for the time being, depending on how you are using the programmes.
At the moment I think you can only import CARA data in V2 (using the Format Converter). You can then open a V2 project in V3. So if you want to start your V3 project based on some CARA data, you could do this fairly easily.
If you want to add the CARA data to an existing V3 project you would have to add an additional conversion. You could open the V2 project in V3, save it as a NEF file and then import the NEF file to your V3 project - I think. But @ElizaP would be your expert on this.
For V3, import is going to be restricted to NEF and NmrStar files. Many popular NMR programmes are currently becoming NEF compatible and we are busy testing this (e.g. XPLOR, ARIA, CYANA, YASARA). Whether CARA is going to become NEF-enabled I don`t know. @ElizaP may know more.
Thanks for the answer.
I could not find a way to do it properly, and just decided to start from scratch on CCPNv3 directly.
I`m having similar issues with format conversion trying to use CCPN v3 with CYANA. Have there been any developments in this area? As far as I can see, CYANA still requires invididual .peaks and .prot files as inputs.
as far as I am aware, it is to some extent possible to read and write NEF files with CYANA (`read file.nef` and `write file.nef` in the CYANA), but requires a few manual workarounds/edits to make sure it all works correctly. Eliza is the one who would know which bits currently still trip CYANA up etc., but I think she may be off until after Christmas, now.
I do know that the CYANA developers are now actively working on improving their NEF compatibility, so I`m hoping that some time in the new year this will become easier - perhaps in time for their next release? Whenever that will be...
Thanks for your help. I have now got cyana to try and read the .nef file and am trying to figure out the manual workarounds. It seems to not like my 1H-1H peak lists (from TOCSY and NOESY spectra), even though the dimensions, axes and experiment types seem to be correctly identified (copied below). Do you know of a quick fix for this? Otherwise I`ll contact Eliza and/or the cyana developers in the new year.
As you say, hopefully the new release will have ironed out some of these.
cyana> read nef CX0011_CCPproj1.nef
*** WARNING: Unsupported NEF format version `1.0`.
*** ERROR: Cannot read line 235 in frame `nef_nmr_spectrum_CX0011_TOCSY_pH6_298K`:
1 ppm 1H 700.4732992 12.01688691 10.79905619 circular true .
NMR exchange format file `CX0011_CCPproj1.nef` read.
Thanks and best wishes,