Hi there
I am using a mac. I re-installed the latest version of ccpnmr not the app but via terminal as instructed on the webpage. I followed the tutorial for reading in the BRMB star file, changing the chem_shift_list as instructed. When I read that star file into ccpnmr and select simulate spectra, I get a warning message saying it may not work well. But I get a NH spectrum folder and peak list for the NH spectra. If I drag the “NH spectra” into the assign window I only ever get the NH icon in the tool bar, that says I have NH spectra in the window. Nothing else appears, no axis or peaks etc. I only get a spectrum to work by generating an NMRpipe simulated fft, from the BRMB star file, which I read into ccpnmr and then I have to drop the peak list from NH, read in from the BMRB star file as in the tutorial, onto the nmrpipe sim.fft spectrum. The peaklist is then transferrred onto the nmrpipe spectra. Seems to work OK(since they should be the same). But I was wondering why i cannot get the simulated spectra from the initial read-in as per the tutorial. I tried changing the names of the various N H etc that didn`t help.
Hi Gina,
I`m afraid CcpNmr Analysis can`t (yet, but one day we may add this?) simulate spectra, in the sense of creating artificial contours. It can only create simulated peak lists (which is the nomenclature used in the program). And this is exactly what it seems to have done in your case. The program creates a dummy spectrum which is empty and which the peak list is then associated with (as every peak list has to belong to a spectrum). By dragging it onto another spectrum you are copying it to that spectrum. Because the dummy spectrum doesn`t have any data associated with it, it doesn`t show any axes etc. if you create a Spectrum Display with it. Sorry if you were confused by this, but I hope it makes sense.
Best wishes,
Vicky
Hi re the sim file situation. I updated to the newer CCPNMR version because I was getting the multiple chain errors for BMRB files ( I need the NH peak list to drop onto my sim file peaks so that I have a peak list associated with the simulated peaks I created) . When I read in BMRB file 30206, I can now read that in without the error messages. However when I read in the BMRB file 15057 I sill get an error. The error message `Existing NMR residue: 1.2 LYS does not match `GLN``. If I remove residue 1...4 I get a new error message that goes to the next residue. So the program thinks there is a one residue shift in the sequence. I have looked in the str file but I don`t see the issue? Is there a way around this? Thanks
Hi Gina,
I think there is a bug which means that BMRB files are always imported to the NC:1 NmrChain and so you will run into problems if you import multiple BMRB files where the residue numbers overlap. The solution to this for the moment is that after importing the first BMRB file, you rename it to something else before importing the next one. Hope that works for you.
Best wishes,
Vicky
(04-30-2021, 01:45 pm)VickyH Wrote: Hi Gina,
I think there is a bug which means that BMRB files are always imported to the NC:1 NmrChain and so you will run into problems if you import multiple BMRB files where the residue numbers overlap. The solution to this for the moment is that after importing the first BMRB file, you rename it to something else before importing the next one. Hope that works for you.
Best wishes,
Vicky
Hi Vicky yes I finally realized the import was reading my other imported sim file, after I selected import. I did rename the first imported sim file. Im not sure that it works if I rename it. I tried it but there was still an issue. So I ended up importing only one sim file, which got rid of the error and that was OK :) G