Sphere scale

2010-06-01T13:42:42Z

Dodomorandi: Added the complete command form and more exaustive examples

==Overview==

This setting affects the apparent radius of spheres in the sphere representation. Default scale is set to 1.0.

==Syntax==
<source lang="python">
# set the sphere scale to size for selection.
cmd.set ("sphere_scale", size=1, selection='', state=0, updates=1, log=0, quiet=1)
# generally it's simpler to use the console form
set sphere_scale, size, selection
# you can print the current value for sphere_scale
get sphere_scale
</source>
''size'' can be any floating point number, ''selection'' is the name of a selection.

==Examples==
Using 0.25 gives a nice balls&sticks representation with both lines and spheres turned on.
<source lang="python">
set_bond stick_color, white, (all), (all)
set_bond stick_radius, 0.14, (all), (all)
set sphere_scale, 0.25, (all)
show sticks
show spheres
</source>

'''set sphere_scale''' by itself will revert to default. Here you'll get a simple VDW rapresentation.
<source lang="python">
set_bond stick_color, blue, (all), (all)
set_bond stick_radius, 0.3, (all), (all)
set sphere_transparency, 0.3
set sphere_scale
</source>

==Related settings==
*[[sphere_color]]
*[[sphere_mode]]
*[[sphere_point_max_size]]
*[[sphere_point_size]]
*[[sphere_quality]]
*[[sphere_solvent]]
*[[sphere_transparency]]

[[Category:Settings]]
[[Category:Spheres]]

Ball and Stick

2010-06-01T13:17:30Z

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

==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]]

PyMOL Wiki - User contributions [en]

Sphere scale

Ball and Stick