https://wiki.pymol.org/index.php?title=Dots&feed=atom&action=historyDots - Revision history2024-03-29T10:47:53ZRevision history for this page on the wikiMediaWiki 1.35.1https://wiki.pymol.org/index.php?title=Dots&diff=8225&oldid=prevPyadmin: 5 revisions2014-03-28T02:18:14Z<p>5 revisions</p>
<p><b>New page</b></p><div>[[Image:Dots_ex.png|thumb|Dots Representation Example]]<br />
= Overview =<br />
A simple PyMol representation. Use<br />
<code><br />
show dots, SELECTION<br />
</code><br />
where SELECTION is a valid selection or previously defined selection name.<br />
<br />
<br />
==Dots Settings==<br />
The differences in dot_radius and dot_width arise from the differences between the rasterization of OpenGL and ray tracing. PyMOL line and dot widths have the name meaning as their underlying OpenGL<br />
primitives (pixel widths), and they dominate over line and dot radii settings such that you get WYSIWYG raytracing output which is faithful to the OpenGL view in terms of cross-sectional area. If you set the radii values explicitly (Angstroms), then the ray tracer will be affected, but not the OpenGL viewer.<br />
<br />
=== dot_radius (dot weight)===<br />
Controls the dot radius when ray tracing (that is, it is apparent only after the scene is ray traced).<br />
This option can take any value, values from 0 to whatever (4 is huge!)<br />
If dot_radius is set to zero, then it is subordinated to dot_width; if dot_radius is a non-zero value, then it will take priority.<br />
<br />
To check/change dots_radius:<br />
<source lang="python"><br />
set dot_radius, VALUE<br />
# equivalent to<br />
set dot_radius=VALUE<br />
<br />
# to get the current setting, use<br />
get dot_radius<br />
</source><br />
* The default value is: 0<br />
<br />
===dot_width (dot weight)===<br />
This setting defines the size of the dots, in (screen) pixels.<br />
It is subordinate to dot_radius, that is dot_radius takes precedence over dot_width unless dot_radius=0.<br />
<source lang="python"><br />
set dot_width, VALUE<br />
# equivalent to<br />
set dot_width=VALUE<br />
<br />
# to get the current setting, use<br />
get dot_width<br />
</source><br />
* The default value is: 2<br />
<br />
===dot_density (dot density)===<br />
Determines the density of dots in the dot representation; the existing dot densities arise from successive cycles of isocosohedral interpolation.. It takes only integer values from 0 to 4.<br />
<br />
<source lang="python"><br />
set dot_density, VALUE<br />
# equivalent to<br />
set dot_density=VALUE<br />
<br />
# to get the current setting, use<br />
get dot_density<br />
</source><br />
* The default value is: 2<br />
<br />
==Possible Other Settings==<br />
* dot_solvent, default is off. This setting controls whether the dots are representing the vdW surface; when the setting is on, it's the solvent accessible surface area.<br />
* dot_color, default is default<br />
* cgo_dot_width, default is 2.00000<br />
* cgo_dot_radius, default is -1.00000<br />
* dot_normals, default is on<br />
* dot_lighting, default is on<br />
<br />
==Unused Settings==<br />
* dot_mode, default is 0<br />
<br />
<br />
== See Also ==<br />
[[Cmd isodot]]<br />
<br />
[[Category:Representations|Dots]]</div>Pyadminhttps://wiki.pymol.org/index.php?title=Dots&diff=8222&oldid=prevOjganesh: /* dot_radius (dot weight) */2008-07-29T19:30:56Z<p><span dir="auto"><span class="autocomment">dot_radius (dot weight)</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:30, 29 July 2008</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Controls the dot radius when ray tracing (that is, it is apparent only after the scene is ray traced).</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Controls the dot radius when ray tracing (that is, it is apparent only after the scene is ray traced).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This option can take any value, values from 0 to whatever (4 is huge!)</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This option can take any value, values from 0 to whatever (4 is huge!)</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>If dot_radius is set to zero, then it is subordinated to dot_width; if <del class="diffchange diffchange-inline">changed to </del>a non-zero value, then <del class="diffchange diffchange-inline">dot_radius </del>will take priority.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>If dot_radius is set to zero, then it is subordinated to dot_width; if <ins class="diffchange diffchange-inline">dot_radius is </ins>a non-zero value, then <ins class="diffchange diffchange-inline">it </ins>will take priority.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>To check/change dots_radius:</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>To check/change dots_radius:</div></td></tr>
</table>Ojganeshhttps://wiki.pymol.org/index.php?title=Dots&diff=8221&oldid=prevOjganesh at 19:26, 29 July 20082008-07-29T19:26:25Z<p></p>
<p><b>New page</b></p><div>[[Image:Dots_ex.png|thumb|Dots Representation Example]]<br />
= Overview =<br />
A simple PyMol representation. Use<br />
<code><br />
show dots, SELECTION<br />
</code><br />
where SELECTION is a valid selection or previously defined selection name.<br />
<br />
<br />
==Dots Settings==<br />
=== dot_radius (dot weight)===<br />
Controls the dot radius when ray tracing (that is, it is apparent only after the scene is ray traced).<br />
This option can take any value, values from 0 to whatever (4 is huge!)<br />
If dot_radius is set to zero, then it is subordinated to dot_width; if changed to a non-zero value, then dot_radius will take priority.<br />
<br />
To check/change dots_radius:<br />
<source lang="python"><br />
set dot_radius, VALUE<br />
# equivalent to<br />
set dot_radius=VALUE<br />
<br />
# to get the current setting, use<br />
get dot_radius<br />
</source><br />
* The default value is: 0<br />
<br />
===dot_width (dot weight)===<br />
This setting defines the size of the dots, in (screen) pixels.<br />
It is subordinate to dot_radius, that is dot_radius takes precedence over dot_width unless dot_radius=0.<br />
<source lang="python"><br />
set dot_width, VALUE<br />
# equivalent to<br />
set dot_width=VALUE<br />
<br />
# to get the current setting, use<br />
get dot_width<br />
</source><br />
* The default value is: 2<br />
<br />
===dot_density (dot density)===<br />
Determines the density of dots in the dot representation.<br />
It takes only integer values from 0 to 4.<br />
<source lang="python"><br />
set dot_density, VALUE<br />
# equivalent to<br />
set dot_density=VALUE<br />
<br />
# to get the current setting, use<br />
get dot_density<br />
</source><br />
* The default value is: 2<br />
<br />
==Possible Other Settings==<br />
* dot_solvent, default is off<br />
* dot_color, default is default<br />
* cgo_dot_width, default is 2.00000<br />
* cgo_dot_radius, default is -1.00000<br />
* dot_normals, default is on<br />
* dot_lighting, default is on<br />
<br />
<br />
==Unused Settings==<br />
* dot_mode, default is 0<br />
<br />
<br />
== See Also ==<br />
[[Cmd isodot]]<br />
<br />
[[Category:Representations|Dots]]</div>Ojganesh