pseudoatom creates a molecular object with a pseudoatom or adds a pseudoatom to a molecular object if the specified object already exists. Default position is in the middle of the viewing window.
pseudoatom object [, selection [, name [, resn [, resi [, chain [, segi [, elem [, vdw [, hetatm [, b [, q [, color [, label [, pos [, state [, mode [, quiet ]]]]]]]]]]]]]]]]]
# create the pseudoatom pseudoatom tmpPoint ObjMol: created tmpPoint/PSDO/P/PSD`1/PS1 # 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] ObjMol: created tmpPoint2/PSDO/ZZ/PSD`40/PS1
EXAMPLES FOR USE
pseudoatom can be used for a wide variety of tasks where on must place an atom or a label in 3D space, e.g. as a placeholder for distance measurement or distance specifications.
# A pseudoatom as a placeholder for selections according to distance: load $TUT/1hpv.pdb pseudoatom tmp, pos=[10.0, 17.0, -3.0] show sticks, tmp expand 6 delete tmp # A pseudoatom as placeholder for distance measurement: # position it at the center of an aromatic ring. Then # calc the distance from another atom to the pseudoatom. load $TUT/1hpv.pdb pseudoatom pi_cent,b/53/cg+cz dist pi_cent////ps1, b/met`46/ce
You can use a pseudoatom to make a label for a scene title. Move the protein to the bottom of the window before the pseudoatom is created. Or move the label after creating it (Shift + Middle mouse button in editing mode).
fetch 1rq5 pseudoatom forLabel label forLabel, "This Protein is a Carbohydrate Active Enzyme" set label_color, black # png ray=1
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