Currently, this package requires pluq to function. Make sure pluq is installed by following the instructions here. https://github.com/kfritzsc/pluq
To use: a) as a python package: download files, cd to this directory, then run:
pip install .
pip install -r requirements.txt Some requirement installations will fail. Additionally, python3.8 or above is required.
For examples of python package use, see development jupyter notebooks.
b) as a poky plugin: download files, make sure all requirements from requirements.txt are installed. One way to do this is to cd to this directory, then run: pip install -r requirements.txt
Then, 1) Start POKY 2) Select spectrum 3) use the 2-letter command "py", then click Load Module... and open cops_init.py
For use: 4) click on "Initialize" to initialize with spectrum names and experiment settings 5) click on a peak, then click on "Calculate" or "Predict". Output calculations and predictions will appear in the terminal window from which POKY was started.
GUI features: Saving and loading initial state calculating CB ("Calculate") Predicting best match lineshapes ("predict") - If a peak list is included with the initialization, it is used as the search space for best matches - If no peak list is included, NMRglue's automated peak picker is used instead, and the routine searches the entire spectrum. Change prediction options - SNR: ask NMRglue to only pick peaks above a certain SNR. - turn prediction plot on and off. - turn verbose output on and off. If verbose output is on, CB for each candidate match is calculated.
Spectrum requirements: NMRpipe- or UCSF-format. All must be aligned.
pluq references:
- K. J. Fritzsching, Mei Hong, K. Schmidt-Rohr. "Conformationally Selective Multidimensional Chemical Shift Ranges in Proteins from a PACSY Database Purged Using Intrinsic Quality Criteria " J. Biomol. NMR 2016, 64 (2), 115–130 doi:10.1007/s10858-016-0013-5
- Lee, W.; Yu, W.; Kim, S.; Chang, I.; Lee, W. PACSY, a Relational Database Management System for Protein Structure and Chemical Shift Analysis. J Biomol NMR 2012, 54 (2),169–179. doi:10.1109/BIBMW.2012.6470267