AlloViz.AlloViz.trajutils.get_GPCRdb_numbering#

AlloViz.AlloViz.trajutils.get_GPCRdb_numbering(protein)[source]#

Retrieve the GPCRdb-assigned generic numbering of a GPCR structure

A PDB file with GPCR generic numbering of residues in the B-factor column of the file is retrieved through the GPCRdb API and the GPCRdb-scheme generic numbers are transfered to the protein CA atoms’ tempfactors.

GPCRdb assigns Ballesteros-Weinstein generic numbers to the N atoms’ B-factors, and the GPCRdb-scheme ones to the CA atoms’. GPCRdb “bulges” are marked by repeating the generic number but making it negative (negative B-factor instead of a three-decimal B-factor) and must be transformed by -b + 0.001. Some residual 1.00 B-factors remain and must be taken care of.

Parameters:

proteinAtomGroup: Atoms of the protein for which to retrieve generic numbers and that will be transformed (its CA atoms’ tempfactors) in-place.

Notes

GPCRdb provides a PyMOL file to expedite the visualization of the two schemes of generic numbers as text tags over the structure, which is where the information about what is stored in which atom’s B-factor column is taken from:

print "GPCRdb script labeling generic numbers on the annotated pdb structure\nKey bindings for labels:\nF1 - show generic numbers\nF2 - show Ballesteros-Weinstein numbers\nF3 - clear labels"
label n. CA or n. N
cmd.set_key('F1', 'label n. CA & (b >-8.1 and  b <8.1), str("%1.2f" %b).replace(".","x") if b > 0 else str("%1.3f" %(-b + 0.001)).replace(".", "x")')
cmd.set_key('F2', 'label n. N & (b > 0 and  b <8.1), "%1.2f" %b')
cmd.set_key('F3', 'label n. CA or n. N')