Getting all dihedral angles in Pymol - pymol

Question

I want to get all the dihedral angles of a protein in Pymol (phi, psi, chi1, chi2, chi3, chi4) but I only manage to find a function that can shows me the phi and psi.
For instance:
PyMOL>phi_psi 1a11
SER-2: ( 67.5, 172.8 )
GLU-3: ( -59.6, -19.4 )
LYS-4: ( -66.4, -61.7 )
MET-5: ( -64.1, -17.9 )
SER-6: ( -78.3, -33.7 )
THR-7: ( -84.0, -18.1 )
ALA-8: ( -85.7, -40.8 )
ILE-9: ( -75.1, -30.8 )
SER-10: ( -77.6, -47.0 )
VAL-11: ( -61.3, -27.4 )
LEU-12: ( -60.7, -47.5 )
LEU-13: ( -71.1, -38.6 )
ALA-14: ( -46.2, -50.7 )
GLN-15: ( -69.1, -47.4 )
ALA-16: ( -41.9, -52.6 )
VAL-17: ( -82.6, -23.7 )
PHE-18: ( -53.4, -63.4 )
LEU-19: ( -61.2, -30.4 )
LEU-20: ( -61.1, -32.3 )
LEU-21: ( -80.6, -60.1 )
THR-22: ( -45.9, -34.4 )
SER-23: ( -74.5, -47.8 )
GLN-24: ( -83.5, 11.0 )
It's missing the chiral angles. Does anyone know how to get all the dihedral angles?
Many thanks!

Answer 1

You can get arbitrary dihedral angles with get_dihedral. Create four selections, each with a single atom and then use it like this:
get_dihedral s1, s2, s3, s4
It's exposed to the Python API as cmd.get_dihedral(). I suggest writing a Python script that uses this function along with cmd.iterate() to loop over residues. Create a dict so that on each residue you can look up a list of atom quadruples that define the chi-angles.

Answer 2

You can easily do it in R. This is the link containing information on how to calculate the main chain and side chain Torsion/Dihedral Angles:
http://thegrantlab.org/bio3d/html/torsion.pdb.html
But first you have to install the Bio3D package for R: http://thegrantlab.org/bio3d/download
After installing the package, load it by typing library(bio3d) at the R console prompt.
>library(bio3d)
This R script answers your question:
#returns the file path of the current working directory.
getwd()
#sets the working directory to where you want.
setwd("home/R/Rscripts")
#fetches the pdb file from the protein data bank and saves to dataframe 'pb'
pb <- read.pdb("insert PDB ID")
#trim to protein only
pb.prot <- trim.pdb(pb, "protein")
#calculates the torsion angles of the protein and save to dataframe 'tor'
tor <- torsion.pdb(pb.prot)
#to get the number of rows and columns of 'tor'
dim(tor$tbl)
#identify each row by their chain, residue ID and residue Number obtained from your PDB entry
res_label <- paste(pb.prot$atom$chain[pb.prot$calpha], pb.prot$atom$resid[pb.prot$calpha], pb.prot$atom$resno[pb.prot$calpha], sep="-")
rownames(tor$tbl) <- res_label
#creates a table of the torsion angle
torsion <- tor$tbl
#For example, to look at the angles for VAL, residue 223 from chain A
tor$tbl["A-VAL-223",]
#writes out the table to a file
write.table(torsion, file = "torsion_angles.txt", quote = F, sep = "\t")
Your output file which is saved in your working directory will contain a table of the chain-resID-resNo and their corresponding phi, psi, chi1, chi2, chi3, chi4, and chi5 values. Goodluck!

Answer 3

#install bio3d library and call
library(bio3d)
#returns the file path of the current working directory.
getwd()
#sets the working directory to where you want.
setwd("home/R/Rscripts")
#fetches the pdb file from the protein data bank and saves to dataframe 'pb'
pb <- read.pdb("insert PDB ID")
#trim to protein only
pb.prot <- trim.pdb(pb, "protein")
#calculates the torsion angles of the protein and save to dataframe 'tor'
tor <- torsion.pdb(pb.prot)
#to get the number of rows and columns of 'tor'
dim(tor$tbl)
#identify each row by their chain, residue ID and residue Number obtained from your PDB entry
res_label <- paste(pb.prot$atom$chain[pb.prot$calpha], pb.prot$atom$resid[pb.prot$calpha], pb.prot$atom$resno[pb.prot$calpha], sep="-")
rownames(tor$tbl) <- res_label
#creates a table of the torsion angle
torsion <- tor$tbl
#For example, to look at the angles for VAL, residue 223 from chain A
tor$tbl["A-GLY-65",]
#convert "double" into a datatype
dataframe_df=as.data.frame.matrix(torsion)
#write dataframe to a .csv file
write.csv(dataframe_df, file="name.csv", row.names=TRUE,col.names=TRUE)