Chemical shift histogram

BMRB serves Nuclear Magnetic Resonance(NMR) community by providing high quality curated chemical shift data of various biologically important macro molecules like proteins and nucleic acids and small molecules like ligands , co-factors, small peptides and metabolites. Chemical shift distribution of an atom in an amino acid or nucleic acid helps us to understand its diverse chemical environment. Chemical shift histograms from a database like BMRB will help us to understand the biophysical nature bio-molecules and provides a priory probabilities for resonance assignments.

Initialization



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from pybmrb import csviz

The default output for any visualization generated using this library is an interactive html file. It also supports the famous Notebook style embaded visualizations. To enable Notebook mode set the NOTEBOOK varibale True.



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csviz.NOTEBOOK = True

Let's call the histogram method



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h = csviz.Histogram()

Histograms

Histograms are generated by fetching checmial shift data of a given amino acid or atom from BMRB database using BMRB-API.



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help(h.hist)

The function hist may take any one of the parameters residue/atom/atom_list or two parameters residue and atom along with filtering and normalization parameters. The outfilename is used to generate visualizations as a stand alone html file.

Chemical shift filter

BMRB contains chemical shifts of atom in different experimental conditions. In order to get a clean distribution, exoctic values(arising from say para-magnetic substances or different experimental conditions) should be removed. This is done by a filter based on standard deviation of that particularity distribution. For a given distribution, the values lie outside sd_limt x standard deviation will be removed. By default this filter is enabled and the sd_litmit is set to 10

Normalization

One can also plot probability density instead of count. This can be controlled by the parameter normalized. By default its false, which means it will plot the count/frequency.

Let's see some examples



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h.hist(residue='LYS',atom='C*')

To filter only unambiguously assigned checmical shifts use ambiguity = 1. The ambiguity codes are defined in the NMR-STAR dictionary.



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h.hist(residue='LYS',atom='C*',ambiguity=1)



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h.hist(atom_list=['LYS-CB','CYS-CB','ALA-CA'])



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h.hist(atom_list=['LYS-CB','CYS-CB','ALA-CA'],normalized=True)



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h.hist(atom='CB')

2D chemical shift correlation

It is also possible to plot the chemical shift correlation of any two atom in a given amino acid. This will help us to understand the distribution of a particular resonance peak in a 2D correlation experiment.

Let's see some examples



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h.hist2d(residue='CYS',atom1='CB',atom2='N')



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h.hist2d('ASN','HD21','HD22',sd_limit=3)



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h.hist2d('ASN','HD21','HD22',sd_limit=3,ambiguity1=1,ambiguity2=1)

Conditional histogram

One can also search in BMRB for chemical shift distribution of a particular atom in an amino acid with one or more known set of assigned chemical shift from the same residue. This is especially useful to restrict or define a search range for unassigned side chain atoms with back bone resonances are already assigned.

Here are some examples



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h.conditional_hist(residue='CYS',atom='CB',atomlist=['CA'],cslist=[64.5])



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h.conditional_hist(residue='GLN',atom = 'HE21', atomlist = ['HE22'], cslist=[6.85])



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