selChain: Visualize occluded chains

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

Visualize occluded chains

Description

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

Usage

selChain(letter, pdbFile, name, style)

Arguments

letter	Valid chain letter that refers to a chain found in the protein. Run 'showInfoPDB' to get all possible chains in chain_info
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 chain, and it displays the 3D model of the protein with the selected chain 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.

Yao, X., G. Scarabelli, L. Skjaerven, and B. Grant (2020). chain.pdb: Find Possible PDB Chain Breaks. bio3D. https://rdrr.io/cran/bio3d/man/chain.pdb.html.

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

Examples

# Using pdb2 file available with package
#selChain("A", pdb2, "1SI4", "m_style_stick")

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