nightshift 0.0.1

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nightshift

A python library and command line program for plotting simulated 2D and 3D NMR spectra from assigned chemical shifts from the BMRB

Peak assignments are pulled using the BMRB API (https://github.com/uwbmrb/BMRB-API) and plotted with matplotlib. Spectra produced by this script do not always reflect reality, as many entries do not have 100% assignments. Be sure to know what assignments are contained in the entry beforehand.

Installation

I'll assume the reader may not necessarily familiar with python and installing dependencies. These scripts require python 3.7 or later, matplotlib and requests. I recommend installing in a virtual environment (so that you don't mess up anything else on your system). These instructions are adapted from https://docs.python.org/3/tutorial/venv.html

Navigate to the directory containing these scripts and run: python3 -m venv plot_bmrb

This will create a new directory called plot_bmrb. On Windows activate the virtual environment by running:

plot_bmrb/Scripts/activate.bat

or on Linux/macOS:

source plot_bmrb/bin/activate

Note: this virtual environment should be re-activated whenever you want to run these scripts.

Your shell should reflect that you have activated the virtual environment. You can check by running which python which should return that python points within this directory.

To install the dependencies run: pip install -r requirements.txt

Usage

You will need to know your protein of interest's BMRB entry number. We'll use 4493 Solution structure of the designed hydrophobic core mutant of ubiquitin, 1D7 for our examples.

Basic spectra

Two major use cases are getting an idea what a amide or methyl spectrum of your protein would look like

To simulate 1H-15N HSQC spetra can be plotted using the --amide flag

python bmrb_shifts.py get 4493 --amide

Simulate 1H-13C HMQC spetra can be plotted using the --methyl flag, additionally providing the optional proS or proR will filter LV atoms by prochirality

python bmrb_shifts.py get 4493 --methyl proS

All plots can be filtered based on residue type by passing the --residues or -r flag and providing one-letter amino acid codes. For instance an ILV methyl labeled spectrum can be plotted using

python bmrb_shifts.py get 4493 --methyl -r ILV

Custom correlations

For arbitrary correlations use the --custom flag followed by two atom names. Consider yourself warned that labeling schemes and/or experiments to produce these correlations may not (currently) exist. Atoms for custom correlations are specified using standard PDB atom names: H for amide proton, N for amide nitrogen, C for carbonyl carbon, CA for alpha carbon, HA for alpha proton and so on. FOr particular residues two or more atoms may exist at a position (i.e. CG for Val could be CG1 or CG2). To specify both CG1 and CG2 for Val pass CG

python bmrb_shifts.py get 4493 --custom CG CA -r V

or specify the full atom name to only get those atoms

python bmrb_shifts.py get 4493 --custom CG1 CA -r V

Two special atom names also exist for custom correlations: Hmethyl and Cmethyl. Which correspond to these atoms in MILVAT residues and are the same atoms selected by using the --methyl flag.

Residue	Hmethyl	Cmethyl
Met	HE1	CE
Ile	HD11	CD1
Leu	HD11, HD21	CD1,CD2
Val	HG11, HG21	CG1,CG2
Ala	HB1	CB
Thr	CG2	HG21

This allows for correlations of methyl groups to any other atom to be plotted. For instance Cmethyl to CA

python bmrb_shifts.py get 4493 --custom Cmethyl CA -r ILV

Adding '-1' to the end of a custom atom name allows correlation to the i-1 residue. For instance correlation of the CO of the i-1 residue to the amide N of the i residue

python bmrb_shifts.py get 4493 --custom C-1 N

Other options

By default plots are generated in matplotlib and are interactive. To save directly to an image file use the --output or -o flag and provide a file name and extension (.eps, .pdf, .pgf, .png, .ps, .raw, .rgba, .svg, and .svgz are all acceptable).

Formatting options include:

• --showlegend to add a legend
• --nolabels to remove the residue/atom name and numbers from the plot, also shows the legend
• --offset to add a constant to the indices used by BMRB (to reflect the numbering you are used to)

A csv file containing the label and chemical shifts of both atoms can be saved using the --csv flag and providing a file name

python bmrb_shifts.py get 4493 --methyl -r ILV --csv output.csv

this can be opened in other software to generate plots with different formatting. Also the auxiliary script plot_outputs.py can be used to overlay multiple spectra (i.e. different domains of the same protein or a protein complex).

This example is nonsense, but illustrates how it could be done. First, generate two output files

python bmrb_shifts.py get 4493 --amide --csv output1.csv

python bmrb_shifts.py 3433 --amide --csv output2.csv

Then plot their overlay (Note: plot_output.py is used here)

python plot_output.py output1.csv output2.csv

This script also accepts the --showlegend and --nolabels flags.

Interesting examples

• ILV methyl spectrum:

  python bmrb_shifts.py get 4493 --methyl -r ILV

• ILV methyl spectrum with proR LV:

  python bmrb_shifts.py get 4493 --methyl proR -r ILV

• Amide spectrum of only lysines and arginines:

  python bmrb_shifts.py get 4493 --amide -r KR

• 2D HMBC-HMQC (intra-residue methyl-methyl correlations):

  python bmrb_shifts.py get 4493 --custom Cmethyl Cmethyl -r LV

• 2D NCO:

  python bmrb_shifts.py get 4493 --custom C-1 N

• Arg/Lys side chain carbon correlations (a la Pritchard and Hansen, 2019)

  python bmrb_shifts.py get 4493 --custom CG CD -r R --csv 4493_arg.csv

  python bmrb_shifts.py get 4493 --custom CD CE -r K --csv 4493_lys.csv

  python bmrb_shifts.py plot 4493_arg.csv 4493_lys.csv --showlegend