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. | ||
| − | + | == USAGE == | |
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<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. | ||
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<source lang="python"> | <source lang="python"> | ||
# create the pseudoatom | # create the pseudoatom | ||
| − | pseudoatom tmpPoint | + | 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> | ||
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| + | == 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. | ||
| − | # | + | <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 | ||
| − | # | + | # 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 | load $TUT/1hpv.pdb | ||
pseudoatom pi_cent,b/53/cg+cz | pseudoatom pi_cent,b/53/cg+cz | ||
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</source> | </source> | ||
| − | == | + | 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). |
| − | + | ||
| + | <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> | ||
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== 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
You can use a pseudoatom for a movable scene label.
Example of using a pseudoatom for distance measurement.
References
PyMOL Mailing List