Pseudoatom

pseudoatom adds a pseudoatom to a molecular object, and will create the molecular object if it does not yet exist.

You can use a pseudoatom to make a label for a scene title. See the following example

fetch 1rq5
pseudoatom forLabel
label forLabel, "This Protein is a Carbohydrate Active Enzyme"
set label_color, black
# png ray=1

which created the following image:

• 

  You can use a pseudoatom for a movable scene label.

• 

  Example of using a pseudoatom as placeholder (space holder?). File:Pseu1.png.

USAGE

Using the mouse, you can add a label by right-clicking.

pseudoatom object [, selection [, name [, resn [, resi [, chain
        [, segi [, elem [, vdw [, hetatm [, b [, q [, color [, label
        [, pos [, state [, mode [, quiet ]]]]]]]]]]]]]]]]]

You can set the following: selection, name, resn, resi, chain, segi, element, vdw, hetatm, b-factor, charge, color, label, pos (location in space), state, mode, and quiet.

EXAMPLE

# create the pseudoatom
pseudoatom tmpPoint, pos=[10, 10, 10]
# show it as a sphere.
show spheres, tmpPoint

# create another, with more options.
pseudoatom tmpPoint2, resi=40, chain=ZZ, b=40, color=tv_blue, pos=[-10, 0, 10]

# working example
load $TUT/1hpv.pdb
pseudoatom tmp, pos=[10.0, 17.0, -3.0]
show sticks, tmp expand 6
delete tmp

# another example, place a pseudoatom at the center of an
# aromatic ring.  Then calc the distance from another atom
# to the pseudoatom; see the image on this page, Pseu1.png
load $TUT/1hpv.pdb
pseudoatom pi_cent,b/53/cg+cz
dist pi_cent////ps1, b/met`46/ce

NOTES

pseudoatom can be used for a wide variety of random tasks where on must place an atom or a label in 3D space.

References

PyMOL Mailing List