Ball and Stick - Revision history

Bell: 1 revision

2015-07-09T21:08:13Z

1 revision

New page

==Ball and Stick==
The '''ball and stick''' representation is very often used to display macromolecules. PyMOL allows the user the ability to turn on this representation for certain selections, or roll their own hand-made versions of the command (see below).

<gallery>
Image:Ball_stick.png|Example of Bal and Stick Repr.
</gallery>

==Usage==
===Builtin===
====GUI====

Using the mouse, for the desired object or selection click '''A > Preset > ball and stick'''.

====Command Line/API====
<source lang="python">
# turn on the representation for everything in PyMOL
preset.ball_and_stick(selection='all', mode=1)
</source>
or... (keeping in mind that the [[single-word selectors]] page includes more possible selections to substitute <code>r. STI</code> with)
<source lang = "python">
# turn on representation for one ligand (in this example STI or imatinib) in PyMOL
preset.ball_and_stick(selection='r. STI', mode=1)
</source>

Parameter ''mode'' can be 1 or 2. With ''mode=1'' you'll have...
<source lang="python">
set_bond stick_color, white, selection, selection
set_bond stick_radius, 0.14, selection, selection
set sphere_scale, 0.25, selection
show sticks, selection
show spheres, selection
</source>
If ''mode=2'' than you'll get...
<source lang="python">
set_bond stick_color, white, selection, selection
set_bond stick_radius, -0.14, selection, selection
set stick_ball, 1
set stick_ball_ratio, -1.0
set stick_ball_color, atomic
show sticks, selection
</source>

===Hand Made===
Balls with sticks really look nice. You can even create your own style of this, with control over '''[[sphere_scale]]''' and '''[[stick_radius]]'''.

<source lang="python">
hide lines
show sticks
show spheres
set stick_radius, 0.1, (all)
set sphere_scale, 0.25, (all)
</source>

Also OK:
<source lang="python">
show sticks
set valence, on
set stick_ball, on
set stick_ball_ratio, 3
set stick_radius, 0.12
</source>

You can adjust the two numbers above to your taste.

----
Ed. As of 0.98bXX there is a GUI-enable Ball & Stick representation available to users.
[[User:Tree|Tree]]

[[Category:Representations|Ball and Stick]]
[[Category:Sticks]]

Pyadmin: 6 revisions

2014-03-28T01:06:24Z

6 revisions

New page

==Ball and Stick==
The '''ball and stick''' representation is very often used to display macromolecules. PyMOL allows the user the ability to turn on this representation for certain selections, or roll their own hand-made versions of the command (see below).

<gallery>
Image:Ball_stick.png|Example of Bal and Stick Repr.
</gallery>

==Usage==
===Builtin===
====GUI====

Using the mouse, for the desired object or selection click '''A > Preset > ball and stick'''.

====Command Line/API====
<source lang="python">
# turn on the representation for everything in PyMOL
preset.ball_and_stick(selection='all', mode=1)
</source>

Parameter ''mode'' can be 1 or 2. With ''mode=1'' you'll have...
<source lang="python">
set_bond stick_color, white, selection, selection
set_bond stick_radius, 0.14, selection, selection
set sphere_scale, 0.25, selection
show sticks, selection
show spheres, selection
</source>
If ''mode=2'' than you'll get...
<source lang="python">
set_bond stick_color, white, selection, selection
set_bond stick_radius, -0.14, selection, selection
set stick_ball, 1
set stick_ball_ratio, -1.0
set stick_ball_color, atomic
show sticks, selection
</source>

===Hand Made===
Balls with sticks really look nice. You can even create your own style of this, with control over '''[[sphere_scale]]''' and '''[[stick_radius]]'''.

<source lang="python">
hide lines
show sticks
show spheres
set stick_radius, 0.1, (all)
set sphere_scale, 0.25, (all)
</source>

Also OK:
<source lang="python">
show sticks
set valence, on
set stick_ball, on
set stick_ball_ratio, 3
set stick_radius, 0.12
</source>

You can adjust the two numbers above to your taste.

----
Ed. As of 0.98bXX there is a GUI-enable Ball & Stick representation available to users.
[[User:Tree|Tree]]

[[Category:Representations|Ball and Stick]]
[[Category:Sticks]]

Dodomorandi: Added info about graphical transformations made by the command + changed two deprecated examples.

2010-06-01T13:17:30Z

Added info about graphical transformations made by the command + changed two deprecated examples.

New page

==Ball and Stick==
The '''ball and stick''' representation is very often used to display macromolecules. PyMOL allows the user the ability to turn on this representation for certain selections, or roll their own hand-made versions of the command (see below).

<gallery>
Image:Ball_stick.png|Example of Bal and Stick Repr.
</gallery>

==Usage==
===Builtin===
====GUI====
From the PyMOL representation menu choose, "Ball and Stick".

====Command Line/API====
<source lang="python">
# turn on the representation for everything in PyMOL
preset.ball_and_stick(selection='all', mode=1)
</source>

Parameter ''mode'' can be 1 or 2. With ''mode=1'' you'll have...
<source lang="python">
set_bond stick_color, white, selection, selection
set_bond stick_radius, 0.14, selection, selection
set sphere_scale, 0.25, selection
show sticks, selection
show spheres, selection
</source>
If ''mode=2'' than you'll get...
<source lang="python">
set_bond stick_color, white, selection, selection
set_bond stick_radius, -0.14, selection, selection
set stick_ball, 1
set stick_ball_ratio, -1.0
set stick_ball_color, atomic
show sticks, selection
</source>

===Hand Made===
Balls with sticks really look nice. You can even create your own style of this, with control over '''[[sphere_scale]]''' and '''[[stick_radius]]'''.

<source lang="python">
hide lines
show sticks
show spheres
set stick_radius, 0.1, (all)
set sphere_scale, 0.25, (all)
</source>

Also OK:
<source lang="python">
show sticks
set valence, on
set stick_ball, on
set stick_ball_ratio, 3
set stick_radius, 0.12
</source>

You can adjust the two numbers above to your taste.

----
Ed. As of 0.98bXX there is a GUI-enable Ball & Stick representation available to users.
[[User:Tree|Tree]]

[[Category:Representations|Ball and Stick]]
[[Category:Sticks]]