Difference between revisions of "Pseudoatom"

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[[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]] adds a pseudoatom to a molecular object, and will create the molecular object if it does not yet exist.
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== USAGE ==
  
You can use a [[pseudoatom]] to make a label for a scene title.  See the following example
 
<source lang="python">
 
fetch 1rq5
 
pseudoatom forLabel
 
label forLabel, "This Protein is a Carbohydrate Active Enzyme"
 
set label_color, black
 
# png ray=1
 
</source>
 
which created the following image:
 
<gallery widths=300px heights=300px>
 
Image:Patom.png|You can use a pseudoatom for a movable scene label.
 
Image:Pseu1.png|Example of using a pseudoatom as placeholder (space holder?). File:Pseu1.png.
 
</gallery>
 
 
== USAGE ==
 
Using the mouse, you can add a label by right-clicking.
 
 
<source lang="python">
 
<source lang="python">
 
pseudoatom object [, selection [, name [, resn [, resi [, chain
 
pseudoatom object [, selection [, name [, resn [, resi [, chain
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[[select|selection]], [[name]], [[Property_Selectors|resn]], [[Property_Selectors|resi]], [[Property_Selectors|chain]], [[Property_Selectors|segi]], [[Property_Selectors|element]], [[Property_Selectors|vdw]], [[Property_Selectors|hetatm]], [[Property_Selectors|b-factor]], [[Property_Selectors|charge]], [[color]], [[label]], pos (location in space), [[state]], [[mode]], and quiet.
 
[[select|selection]], [[name]], [[Property_Selectors|resn]], [[Property_Selectors|resi]], [[Property_Selectors|chain]], [[Property_Selectors|segi]], [[Property_Selectors|element]], [[Property_Selectors|vdw]], [[Property_Selectors|hetatm]], [[Property_Selectors|b-factor]], [[Property_Selectors|charge]], [[color]], [[label]], pos (location in space), [[state]], [[mode]], and quiet.
  
== EXAMPLE ==
 
 
<source lang="python">
 
<source lang="python">
 
# create the pseudoatom
 
# create the pseudoatom
pseudoatom tmpPoint, pos=[10, 10, 10]
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pseudoatom tmpPoint
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ObjMol: created tmpPoint/PSDO/P/PSD`1/PS1
 
# show it as a sphere.
 
# show it as a sphere.
 
show spheres, tmpPoint
 
show spheres, tmpPoint
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# create another, with more options.
 
# create another, with more options.
 
pseudoatom tmpPoint2, resi=40, chain=ZZ, b=40, color=tv_blue, pos=[-10, 0, 10]
 
pseudoatom tmpPoint2, resi=40, chain=ZZ, b=40, color=tv_blue, pos=[-10, 0, 10]
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ObjMol: created tmpPoint2/PSDO/ZZ/PSD`40/PS1
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</source>
 +
 +
== EXAMPLES FOR USE ==
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 +
[[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.
  
# working example
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<source lang="python">
 +
# A pseudoatom as a placeholder for selections according to distance:
 
load $TUT/1hpv.pdb
 
load $TUT/1hpv.pdb
 
pseudoatom tmp, pos=[10.0, 17.0, -3.0]
 
pseudoatom tmp, pos=[10.0, 17.0, -3.0]
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delete tmp
 
delete tmp
  
# another example, place a pseudoatom at the center of an
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# A pseudoatom as placeholder for distance measurement:
# aromatic ring.  Then calc the distance from another atom
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# position it at the center of an aromatic ring.  Then  
# to the pseudoatom; see the image on this page, Pseu1.png
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# calc the distance from another atom to the pseudoatom.
 
load $TUT/1hpv.pdb
 
load $TUT/1hpv.pdb
 
pseudoatom pi_cent,b/53/cg+cz
 
pseudoatom pi_cent,b/53/cg+cz
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</source>
 
</source>
  
== NOTES ==
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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).
[[pseudoatom]] can be used for a wide variety of random tasks where on must place an atom or a label in 3D space.  
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 +
<source lang="python">
 +
fetch 1rq5
 +
pseudoatom forLabel
 +
label forLabel, "This Protein is a Carbohydrate Active Enzyme"
 +
set label_color, black
 +
# png ray=1
 +
</source>
 +
 
 +
<gallery widths=300px heights=300px>
 +
Image:Patom.png|You can use a pseudoatom for a movable scene label.
 +
Image:Pseu1.png|Example of using a pseudoatom for distance measurement.
 +
</gallery>
 +
 
 +
 
 +
 
 +
 
 +
 
  
 
== References ==
 
== References ==

Revision as of 06:41, 5 November 2010

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.

USAGE

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.

# 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




References

PyMOL Mailing List