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==Displaying dashed lines between two atoms== | =Overview= | ||
'''Lines''' is name of the basic representation for atoms and bonds in PyMOL. '''Lines''' is a very simple representation, where each atom bond is displayed as a single colored line, and each atom is displayed as the intersection of any two or more non-terminal bonds. | |||
=Usage= | |||
<source lang="python"> | |||
# show everything as lines | |||
show lines | |||
# only show residues 50-80 as lines | |||
show lines, i.50-80 | |||
</source> | |||
==Examples== | |||
===Example: Displaying dashed lines between two atoms=== | |||
The following commands will create a dashed line between two atoms. | The following commands will create a dashed line between two atoms. | ||
<source lang="python"> | <source lang="python"> | ||
# first, create two named selections | |||
select a, ///A/501/02 | select a, ///A/501/02 | ||
select b, ///B/229/N | select b, ///B/229/N | ||
# calculate & show the distance from selection a to selection b. | |||
distance d, a, b | distance d, a, b | ||
# hide just the distance labels; the | |||
# dashed bars should still be shown | |||
hide labels, d | hide labels, d | ||
</source> | </source> | ||
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[[Image:Lines_ex.png|thumb|Lines Representation Example]] | [[Image:Lines_ex.png|thumb|Lines Representation Example]] | ||
[[Category:Representations | ==See Also== | ||
Please read about other representations in the '''Representation Category''' (link at bottom of page). | |||
[[Category:Representations]] | |||
Revision as of 11:51, 23 February 2007
Overview
Lines is name of the basic representation for atoms and bonds in PyMOL. Lines is a very simple representation, where each atom bond is displayed as a single colored line, and each atom is displayed as the intersection of any two or more non-terminal bonds.
Usage
# show everything as lines
show lines
# only show residues 50-80 as lines
show lines, i.50-80
Examples
Example: Displaying dashed lines between two atoms
The following commands will create a dashed line between two atoms.
# first, create two named selections
select a, ///A/501/02
select b, ///B/229/N
# calculate & show the distance from selection a to selection b.
distance d, a, b
# hide just the distance labels; the
# dashed bars should still be shown
hide labels, d
Technically, the object d is a labelled distance, only the label is hidden. When ray-tracing the image, the dashes come out a bit fat. You can slim them with
set dash_gap, 0.5
set dash_radius, 0.1
before the 'ray' command.
See Also
Please read about other representations in the Representation Category (link at bottom of page).