pdbListRMSDCalc - Revision history

Kinoshita: Created page with "'''pdbListRMSDCalc''' is Eos's Command that outputs RMSD(Root Mean Square Deviation) from PDB File List. == List of option == === Main option ===
2014-08-08T01:06:41Z
Created page with "'''pdbListRMSDCalc''' is Eos's Command that outputs RMSD(Root Mean Square Deviation) from PDB File List. == List of option == === Main option === <table border..."
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'''pdbListRMSDCalc''' is [[Eos]]'s [[Command]] that outputs RMSD(Root Mean Square Deviation) from [[PDB]] File List.

== List of option ==
=== Main option ===
<table border="1">
<tr>
<th>Option</th>
<th>Essential/Optional</th>
<th>Description</th>
<th>Default</th>
</tr>
<tr>
<td>-i</td>
<td>Essential</td>
<td>Input: [[ASCII]](File List)</td>
<td>NULL</td>
</tr>
<tr>
<td>-r</td>
<td>Optional</td>
<td>Reference: [[PDB]](For m=1 only)</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-c</td>
<td>Optional</td>
<td>ConfigurationFile</td>
<td>NULL</td>
</tr>
<tr>
<td>-m</td>
<td>Optional</td>
<td>Mode</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</table>
<br>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>RMSD: against average</td>
</tr>
<tr>
<td>1</td>
<td>RMSD: against reference </td>
</tr>
</table>
<br>

===Input file list format===
<pre>
PDBfile1
PDBfile2
.
.
.

</pre>
<br>

== Execution example ==
===Input file's data===
<pre>
Input-121P-T1.pdb
Input-121P-T2.pdb
Input-121P-T3.pdb

</pre>
<br>

<div>[[:Media:Input-121P-T1.pdb.zip|Input-121P-T1.pdb]]'s image</div>
<table>
<tr>
<td>[[File:Input-121P-PDB1.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">6.053012e+00 9.408175e+00 2.622422e+01<br>
3.286665e+01<br>
24.77 22.88 23.78<br></p>
</td>
</tr>
</table>
<br>

<div>[[:Media:Input-121P-T2.pdb.zip|Input-121P-T2.pdb]]'s image</div>
<table>
<tr>
<td>[[File:Input-121P-PDB2.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">6.053012e+00 2.519590e+01 1.189075e+01<br>
3.286664e+01 <br>
24.77 23.85 28.04 <br></p>
</td>
</tr>
</table>
<br>

<div>[[:Media:Input-121P-T3.pdb.zip|Input-121P-T3.pdb]]'s image</div>
<table>
<tr>
<td>[[File:Input-121P-T3.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">5.097651e-01 1.932045e+01 1.188975e+01<br>
3.286711e+01 <br>
23.93 24.14 28.04<br> </p>
</td>
</tr>
</table>
<br>

=== Case: Options only essential ===
<div></div>
<table>
<tr>
<td>[[File:Outdata-pdbListRMSDCalc.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left"><br>
<br>
<br> </p>
</td>
</tr>
</table>
<br>

=== Option -m===
====Case: m=1====
<div>[[:Media:Input-121P.pdb.zip|Reference file]]'s image</div>
<table>
<tr>
<td>[[File:Input-121P-PDB.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">6.053012e+00 2.519590e+01 1.189075e+01<br>
3.286664e+01 <br>
24.77 23.85 28.04<br></p>
</td>
</tr>
</table>
<br>

<div></div>
<table>
<tr>
<td>[[File:Outdata-m1-pdbListRMSDCalc.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left"><br>
<br>
<br> </p>
</td>
</tr>
</table>
<br>