http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?action=history&feed=atom&title=pdbMove
pdbMove - Revision history
2026-05-04T15:30:16Z
Revision history for this page on the wiki
MediaWiki 1.23.6
http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=pdbMove&diff=3291&oldid=prev
Kinoshita at 01:37, 18 August 2014
2014-08-18T01:37:58Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 01:37, 18 August 2014</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; 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>'''pdbMove''' is [[Eos]]'s [[Command]] that performs parallel <del class="diffchange diffchange-inline">movement </del>for atom model of [[PDB]] file.</div></td><td class='diff-marker'>+</td><td style="color:black; 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>'''pdbMove''' is [[Eos]]'s [[Command]] that performs parallel <ins class="diffchange diffchange-inline">transformation </ins>for atom model of [[PDB]] file.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== List of option ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== List of option ==</div></td></tr>
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Kinoshita
http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=pdbMove&diff=3155&oldid=prev
Kinoshita at 01:26, 8 August 2014
2014-08-08T01:26:42Z
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<table class='diff diff-contentalign-left'>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 01:26, 8 August 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; 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>'''pdbMove''' is<del class="diffchange diffchange-inline">[[PDB]]fileの原子モデルを平行移動するための </del>[[Eos]]'s [[Command]].</div></td><td class='diff-marker'>+</td><td style="color:black; 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>'''pdbMove''' is [[Eos]]'s [[Command]] <ins class="diffchange diffchange-inline">that performs parallel movement for atom model of [[PDB]] file</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== List of option ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== List of option ==</div></td></tr>
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Kinoshita
http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=pdbMove&diff=3147&oldid=prev
Kinoshita: Created page with " '''pdbMove''' isPDBfileの原子モデルを平行移動するための Eos's Command. == List of option == === Main option === <table border="1"> <div ali..."
2014-08-08T01:19:09Z
<p>Created page with " '''pdbMove''' is<a href="/Eos/index.php/PDB" title="PDB">PDBfile</a>の原子モデルを平行移動するための <a href="/Eos/index.php/Eos" title="Eos">Eos</a>'s <a href="/Eos/index.php/Command" title="Command">Command</a>. == List of option == === Main option === <table border="1"> <div ali..."</p>
<p><b>New page</b></p><div><br />
'''pdbMove''' is[[PDB]]fileの原子モデルを平行移動するための [[Eos]]'s [[Command]].<br />
<br />
== List of option ==<br />
=== Main option ===<br />
<table border="1"> <br />
<div align="left"> <br />
<tr> <br />
<th>Option</th> <br />
<th>Essential/Optional</th> <br />
<th>Description</th> <br />
<th>Default</th> <br />
</tr> <br />
<tr> <br />
<td>-i</td> <br />
<td>Essential</td> <br />
<td>Input:[[PDB]]</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-o</td> <br />
<td>Essential</td> <br />
<td>Output:[[PDB]]</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-x</td> <br />
<td>Optional</td> <br />
<td>Move X: [A]</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-y</td> <br />
<td>Optional</td> <br />
<td>Move Y: [A]</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-z</td> <br />
<td>Optional</td> <br />
<td>Move Z: [A]</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-originTo</td> <br />
<td>Optional</td> <br />
<td>move (0,0,0) to (X,Y,Z)</td> <br />
<td>(0.0, 0.0, 0.0)</td> <br />
</tr> <br />
<tr> <br />
<td>-toOrigin</td> <br />
<td>Optional</td> <br />
<td>move (X,Y,Z) to (0,0,0)</td> <br />
<td>(0.0, 0.0, 0.0)</td> <br />
</tr> <br />
<tr> <br />
<td>-GCtoOrigin</td> <br />
<td>Optional</td> <br />
<td>GC(Gravity Centre) to origin</td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>-c</td> <br />
<td>Optional</td> <br />
<td>ConfigurationFile</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-m</td> <br />
<td>Optional</td> <br />
<td>Mode</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-h</td> <br />
<td>Optional</td> <br />
<td>Help</td> <br />
<td> </td> <br />
</tr> <br />
</div><br />
</table><br />
<br><br />
<br />
=== -m details ===<br />
<table border="1"> <br />
<div align="left"> <br />
<tr> <br />
<th>Value</th> <br />
<th>Description</th> <br />
</tr> <br />
<tr> <br />
<td>0</td> <br />
<td></td> <br />
</tr> <br />
</div> <br />
</table><br />
<br><br />
<br />
== Execution example ==<br />
=== Option -h ===<br />
<pre><br />
$ pdbMove -h<br />
Usage: /Applications/Eos.app/Eos/bin/X86MAC64/pdbMove<br />
Options:<br />
[-i[nput] In (NULL )] :Essential :InputDataFile<br />
[-o[utput] Out (NULL )] :Essential :OutputDataFile<br />
[-x X (0.0 )] :Optional :Move X[A]<br />
[-y Y (0.0 )] :Optional :Move Y[A]<br />
[-z Z (0.0 )] :Optional :Move Z[A]<br />
[-c[onfig] configFile (NULL )] :Optional :ConfigurationFile<br />
[-m[ode] mode (0 )] :Optional :Mode<br />
----- Additional Usage -----<br />
</pre><br />
<br><br />
<br />
===[[:Media:Input-121P.pdb.zip|Input file]] details===<br />
<div>[[File:Input-121P-PDB.png]]<br><br />
<br><br />
[[File:121p.pdb-pdbMove.png]]</div><br />
<br><br />
<br><br />
<br />
===Case: Options only essential===<br />
<div>[[File:Outdata-pdbMove.png]]<br><br />
<br><br />
<div>[[File:121p-pdbMove.png]]<br><br />
There is no change, because default of x, y, z is 0.0.</div><br />
<br><br />
<br><br />
<br />
===Setting Moving width (Option -x,-y,-z)===<br />
====Case: All moving width = 1====<br />
<div>White is Input file.</div><br />
<div>[[File:Outdata-xyz1-pdbMove.png]]<br><br />
<br><br />
[[File:121p.1xyz-pdbMove.png]]<br><br />
<br><br />
<br><br />
<br />
====Case: x=-6.053012e+00,y=-2.519590e+01,z=-1.189075e+01====<br />
<div>White is Input file.</div><br />
<div>[[File:Outdata-xyz-pdbMove.png]]<br><br />
<br><br />
[[File:121p.-xyz-pdbMove.png]]<br><br />
<br><br />
<br></div>
Kinoshita