getPTM: Show the information on chosen PDB file

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

Show the information on chosen PDB file

Description

Function that takes a PDB file as input, and then extracts the AA (amino acid) information, and chain information of the chosen protein.

Usage

getPTM(accession)

Arguments

pdbFile	A PDB file, could be downloaded from PDB online
name	the 4-letter PDB codes/identifiers of the PDB file that was chosen as 'pdbFile' input

Value

Returns a list of containing 2 pieces information from the PDB file: AA and chain information.

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.

Examples

# Using pdb2 and pdb file available with package
#showInfoPDB(pdb, "1bm8")

#showInfoPDB(pdb2, "1si4")

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