hphobScale: Visualize hydrophobicity

In JerrieFeng/pdbSelectOcclude: Select occluding structures in a 3D molecular visualization environment

Visualize hydrophobicity

Description

Function that takes a PDB file and visualizes it as a 3D model. The user to select on a scale to view hydrophobicity. Uses Kyte & Doolittle scale.

Usage

hphobScale(polarity)

Arguments

polarity	Enter 'nonpolar' to select all nonpolar AA, 'polar' to select all polar/uncharged AA, 'positive' to select all positively charged AA, 'negative' to select all negatively charged AA. Make sure to add quotation marks.
pdbFile	A PDB file, could be downloaded from PDB online
name	the 4-letter PDB codes/identifiers of the PDB file to be visualized.

Value

Displays the 3D model of the protein with the selected hydrophobicity.

References

Yao, X., G. Scarabelli, L. Skjaerven, and B. Grant (2020). Protein Structure Networks with Bio3D. bio3D. http://thegrantlab.org/bio3d/articles/online/cna_vignette/cna_vignette.spin.html#references-1.

McFadden, W.M. (2020). Charge and Hydropathy Vignette. https://rdrr.io/bioc/idpr/f/vignettes/chargeHydropathy-vignette.Rmd.

Examples

# Using pdb file available with package
# ?idpr
#selHphob("polar", pdb, "1bm8")

JerrieFeng/pdbSelectOcclude documentation built on May 12, 2022, 8:07 a.m.