Pseudoatom - Revision history

Bell: 12 revisions

2014-03-28T03:08:51Z

12 revisions

Speleo3: ARGUMENTS

2011-05-24T13:40:22Z

ARGUMENTS

Karo: Reorganisation of the page.

2010-11-05T10:41:06Z

Reorganisation of the page.

New page

[[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 ==

<source lang="python">
pseudoatom object [, selection [, name [, resn [, resi [, chain
[, segi [, elem [, vdw [, hetatm [, b [, q [, color [, label
[, pos [, state [, mode [, quiet ]]]]]]]]]]]]]]]]]
</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.

<source lang="python">
# 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
</source>

== 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
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
</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>

== References ==
PyMOL Mailing List

[[Category:Commands|Pseudoatom]]
[[Category:States|Pseudoatom]]
[[Category:Labeling|Pseudoatom]]

Vinnyrose at 13:38, 20 June 2009

2009-06-20T13:38:31Z

New page

== DESCRIPTION ==
[[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 ==
Using the mouse, you can add a label by right-clicking.
<source lang="python">
pseudoatom object [, selection [, name [, resn [, resi [, chain
[, segi [, elem [, vdw [, hetatm [, b [, q [, color [, label
[, pos [, state [, mode [, quiet ]]]]]]]]]]]]]]]]]
</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 ==
<source lang="python">
# 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
</source>

== 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

[[Category:Commands|Pseudoatom]]
[[Category:States|Pseudoatom]]
[[Category:Labeling|Pseudoatom]]

Aaronc at 05:01, 3 November 2008

2008-11-03T05:01:54Z

New page

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

== USAGE ==
<source lang="python">
pseudoatom object [, selection [, name [, resn [, resi [, chain
[, segi [, elem [, vdw [, hetatm [, b [, q [, color [, label
[, pos [, state [, mode [, quiet ]]]]]]]]]]]]]]]]]
</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 ==
<source lang="python">
# 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
</source>

== 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

[[Category:Commands|Pseudoatom]]

← Older revision	Revision as of 03:08, 28 March 2014
(No difference)

@@ Line 8: / Line 8: @@
          [, pos [, state [, mode [, quiet ]]]]]]]]]]]]]]]]]
 </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.
+== ARGUMENTS ==
 <source lang="python">