Draw bonds PyMOL using R package Bio3d

Question

Using the R package bio3d I would like to draw bonds between two atoms on a protein and parse the structure to PyMOL using the pymol().

library(bio3d)

# Import PDB file
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )

# Atom 1
sele.1 <- atom.select(pdb, "calpha", resno=43, verbose=TRUE)

# Atom 2
sele.2 <- atom.select(pdb, "calpha", resno=54, verbose=TRUE)

In this example I would like to draw a bond/tangent/line between atoms sele.1 and sele.2 - a fairly trivial problem, is this possible?

score 1 · Accepted Answer · answered Dec 05 '17 at 11:18

It is possible to parse a PyMOL script from R:

# Return a string of commands to draw 
pymol.bond.sele.command = function(atom1, atom2, nbond, chainID){

    # return PyMOL command to draw a bond between atoms 1 and 2
    return(paste(paste('distance ', paste('mydist', nbond, ', ', sep=''),
        'chain ', pymolchain, ' and ', atom1, '/CA, ', 'chain ', pymolchain, ' and ', atom2, '/CA', sep='')))
}

> pymol.bond.sele.command(43, 54, 1, A)

[1] distance mydist1, chain A and 43/CA, chain A and 54/CA

Copy output of pymol.bond.sele.command() into the PyMOL terminal.

To remove the distance label:

pymol.bond.lab.rm.command = function(nbond, chainID){

    # return PyMOL command to remove the distance label drawn for distance element x
    return(paste('hide labels, mydist', nbond, sep=''))
}

> pymol.bond.lab.rm.command(1, A)
[1] hide labels, mydist1

Copy output of pymol.bond.lab.rm.command() into the PyMOL terminal.

Draw bonds PyMOL using R package Bio3d

1 Answers1