From 8f544c46102ff4a8d4c85139f091dbcc07700893 Mon Sep 17 00:00:00 2001 From: Ian Fucci Date: Tue, 16 Aug 2022 13:22:48 -0400 Subject: [PATCH] Update README with peak transfer tutorial --- README.md | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index c9384f9..d2047d4 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ Peak assignments are pulled using the BMRB API (https://github.com/uwbmrb/BMRB-A If you find this code useful please cite our paper: -Fucci, I.J. and Byrd, R.A. (2021), nightshift: A Python program for plotting simulated NMR spectra from assigned chemical shifts from the Biological Magnetic Resonance Data Bank. Protein Science. https://doi.org/10.1002/pro.4181 +Fucci, I. J. and Byrd, R. A. nightshift: A Python program for plotting simulated NMR spectra from assigned chemical shifts from the Biological Magnetic Resonance Data Bank. Protein Sci. 2022, 31 (1), 63–74. https://doi.org/10.1002/pro.4181. ## Installation I recommend installing in a [virtualenv](https://docs.python.org/3/tutorial/venv.html) to avoid any conflicts with your python installation. @@ -168,3 +168,30 @@ Also accepts the `--showlegend` and `--nolabels` flags. `nightshift get 4493 --custom CD CE -r K --csv 4493_lys.csv` `nightshift open 4493_arg.csv 4493_lys.csv --showlegend` + +## Transfering assignments to nmrDraw +I have only tested that this works for amide and methyl because of limitations with NMRpipe. It is possible other correllations will work fine. See the `cs2pk.tcl` documentation. There is a hacky work around where methyl spectra are considered HA/CA spectra. +To generate the TALOS file required as input use the `--talos` flag: + `nightshift get 4493 --amide --talos 4493.tab` + + or + + `nightshift get 4493 --methyl -r ILV --talos 4493.tab` + +To transfer run the following for amide: + + `cs2pk.tcl -in 4493.tab -out sim.tab -type hn` + + and for methyl: + + `cs2pk.tcl -in -out -type haca` + +Compare against your spectrum visually (assuming the name of the file is test.ft2 and the peak list is test.tab): + + `specView.tcl -in test.ft2 -multiColor -peak -tab test.tab -pkLab ASS -ass sim.tab -outTab out.tab -xAssVar X_PPM -yAssVar Y_PPM` + + or automatically without an interface: + + `ipap.tcl -specName1 test.ft2 -inName1 test.tab -outName1 out.tab -assName sim.tab -xVar X_PPM -xAss X_PPM -yVar Y_PPM -yAss Y_PPM -single -ndim 2 -exit` + +See the documentation for `specView.tcl` and `ipap.tcl` for a full list of parameters. \ No newline at end of file