selAA: Visualize occluded AA

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

Visualize occluded AA

Description

Function that takes a PDB file and visualizes it as a 3D model. The user to select which AA to view. This function allows user to interact and view occluded AA.

Usage

selAA(index, pdbFile, name)

Arguments

index	Valid residue index that refers to a AA code found in sequence. The index can be found in showInfoPDB as the a number within the range of code_unique.
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

Returns output-text stating the chosen AA, and it displays the 3D model of the protein with the selected AA visible.

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.

Su, W. (2021). Introduction to r3dmol. r3dmol. https://cran.r-project.org/web/packages/r3dmol/vignettes/r3dmol.html.

Examples

# Using pdb file available with package
#selAA(1, pdb, "1bm8")

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