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== DESCRIPTION ==
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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.
 
  
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>
 
Image:Patom.png|Example of using a pseudoatom as a scene label.
 
</gallery>
 
   
 
 
== USAGE ==
 
== 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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         [, pos [, state [, mode [, quiet ]]]]]]]]]]]]]]]]]
 
         [, pos [, state [, mode [, quiet ]]]]]]]]]]]]]]]]]
 
</source>
 
</source>
You can set the following:
 
[[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 ==
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== ARGUMENTS ==
 +
 
 +
* object = string: name of object to create or modify
 +
 
 +
* selection = string: optional atom selection. If given, calculate position (pos) as center of this selection (like [[Center Of Mass|center of mass]] without atom masses).
 +
 
 +
* name, resn, resi, chain, segi, elem, vdw, hetatm, b, q = string: [[Property_Selectors|atom properties]] of pseutoatom
 +
 
 +
* color = string: [[color]] of pseudoatom
 +
 
 +
* label = string: place a [[label|text label]] and hide all other representations
 +
 
 +
* pos = 3-element tuple of floats: location in space (only if no selection given)
 +
 
 +
* state = integer: [[state]] to modify, 0 for current state, -1 for all states {default: 0}
 +
 
 +
* mode = string: determines the vdw property if vdw is not given. Either as RMS distance (mode=rms, like [[radius of gyration]] without atom masses) or as maximum distance (mode=extent) from pseudoatom to selection {default: rms}
 +
 
 
<source lang="python">
 
<source lang="python">
 
# create the pseudoatom
 
# create the pseudoatom
pseudoatom tmpPoint, pos=[10, 10, 10]
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pseudoatom tmpPoint
 +
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]
 +
ObjMol: created tmpPoint2/PSDO/ZZ/PSD`40/PS1
 +
</source>
  
# working example
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== 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.
 +
 
 +
<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]
 
show sticks, tmp expand 6
 
show sticks, tmp expand 6
 
delete tmp
 
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
 
</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.  
+
 
 +
<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 ==

Latest revision as of 03:08, 28 March 2014

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 ]]]]]]]]]]]]]]]]]

ARGUMENTS

  • object = string: name of object to create or modify
  • selection = string: optional atom selection. If given, calculate position (pos) as center of this selection (like center of mass without atom masses).
  • name, resn, resi, chain, segi, elem, vdw, hetatm, b, q = string: atom properties of pseutoatom
  • color = string: color of pseudoatom
  • label = string: place a text label and hide all other representations
  • pos = 3-element tuple of floats: location in space (only if no selection given)
  • state = integer: state to modify, 0 for current state, -1 for all states {default: 0}
  • mode = string: determines the vdw property if vdw is not given. Either as RMS distance (mode=rms, like radius of gyration without atom masses) or as maximum distance (mode=extent) from pseudoatom to selection {default: rms}
# 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