Draw bonds pymol

[Former user]

Bio3D team:

This is very much a user question, rather than a development question. I hope I am posting this in the correct forum. I would like to draw bonds between successive atoms using the pymol module in Bio3D - is this possible?

# 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)

As an output I would like to generate a PyMOL script, which draws a bond between the two above groups (sele.1 and sele.2). Can I do this with the pymol() function?

Many thanks.

[Lars Skjærven]

Nope. pymol() in bio3d does not operate on a single pdb object (only objects of class pdbs).

In pymol you can do distance d1, name CA and resi 43, name CA and resi 54to draw a dashed line between the two atoms..