Create a directory for running your experiments (e.g. ). Copy the parameters.txt, nmrpipe.par, ORTHO_list.txt, ADAPT_list.txt files from the ~/adapt_src/essentials directory to the directory you just created (also copy a text file with the sequence for your protein). Update the parameters.txt file according to "http://pine.nmrfam.wisc.edu/ADAPT-NMR/parameter_file.htm". #################################################################### running ADAPT_ORTHO to collect and process orthogonal planes #################################################################### In terminal, move your current directory into the . $ cd . Run TopSpin, and run quick 2D experiments to establish spectral window and offset in the indirect dimension for: N15 (run N15-HSQC with modified pulse program 'hsqcfpf3gpphwg_hifi.khu', use SW[ppm], O3P[ppm] for N15-HSQC) CO (run HNCO with modified pulse program 'hncogpwg3dsc_hifi.khu', use SW[ppm], O2P[ppm] for HNCO HNCACO) CA (run HNCA with modified pulse program 'hncagpwg3dsc_hifi.khu', use SW[ppm], O2P[ppm] for HNCA HNCOCA) CB (run CBCACONH with modified pulse program 'cbcaconhgpwg3dsc_hifi.khu', use SW[ppm], O2P[ppm] for CBCACONH, HNCB) NOTE: do NOT make the spectral window in the indirect dimension too tight or the peaks may fold in the tilted planes Edit ORTHO_list.txt file: Enter the SW, O2/O3 values calibrated above (replace values given in the example input file). Edit nmrpipe.par file: From quick HNCO above, set parameters for extracting the amide region in the direct dimension for nmrpipe processing (remember that the values are in points and the final total size for the direct dimension is 2048). Enter these into the nmrpipe.par file. Apart from the N15-HSQC, for all other experiments the phasing parameters for the direct proton dimension should be identical, so you can just enter the rp value (lp should be zero) you get from the quick 2D HNCO your ran above into the nmrpipe.par file Go to topspin after cd into the directory, type ADAPT_ORTHO_run. All orthogonal planes listed in ORTHO_list.txt will be automatically collected and processed (you can look at spectra in topspin as they are being collected, but don't change experiment or quit topspin or you'll interrupt the run). If you need to adjust parameters and reprocess some of the spectra, edit the "ft_ortho.com" file that is saved with each experiment and run the "run_nmrpipe" macro to reprocess each spectrum NOTE. The processing parameters from the 0 degree orthogonal plane will be used to process the tilted planes. Once all orthogonal planes are collected and processed properly, you are ready to run ADAPT_NMR ################################### running ADAPT_NMR ################################### Edit ADAPT_list.txt file (very similar to ORTHO_list.txt) Type ADAPT_NMR_run in topspin command line and let the spectrometer and computer do their work !! At the end, the results should be located inside the output_files directory.