pdbTwoProteinFit - Revision history

Kinoshita: Created page with "'''pdbTwoProteinFit''' is Eos's Command for fitting position between two proteins. == List of option == === Main option ===

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2014-08-18T01:50:09Z

Created page with "'''pdbTwoProteinFit''' is Eos's Command for fitting position between two proteins. == List of option == === Main option === <table border="1"> <tr> <th>Opt..."

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'''pdbTwoProteinFit''' is [[Eos]]'s [[Command]] for fitting position between two proteins.

== 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: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-ires</td>
<td>Optional</td>
<td>Input: [[ASCII]](ResidueInformation)</td>
<td>NULL</td>
</tr>
<tr>
<td>-isel</td>
<td>Optional</td>
<td>Output: Selected residue of in after fitting</td>
<td>NULL</td>
</tr>
<tr>
<td>-r</td>
<td>Essential</td>
<td>Reference: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-rres</td>
<td>Optional</td>
<td>Reference: [[ASCII]](ResidueInformation)</td>
<td>NULL</td>
</tr>
<tr>
<td>-rsel</td>
<td>Optional</td>
<td>Output: Selected residue of in after fitting</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-oMatrix</td>
<td>Optional</td>
<td>Output: Matrix: [[ASCII]]</td>
<td>stdout</td>
</tr>
<tr>
<td>-oParam</td>
<td>Optional</td>
<td>Output: Param: [[ASCII]]</td>
<td>stdout</td>
</tr>
<tr>
<td>-oDis</td>
<td>Optional</td>
<td>Output: PDB Distance as Temp: [[PDB]]</td>
<td>stdout</td>
</tr>
<tr>
<td>-oDis2</td>
<td>Optional</td>
<td>Output: Distance List for Ca: [[ASCII]]</td>
<td>stdout</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>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>

===Input fileとReference file format===
<pre>
ResidueNumberToBeFitted
...
If |, all residules are sellected till the residue in the next line
</pre>

== Execution example ==
===[[:Media:Input-121P-T2.pdb.zip|Input file]] image===
<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>

===[[:Media:Input-121P.pdb.zip|Reference file]] image===
<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>

=== Option -ires, -rres===
<div>-ires, -rrse: use the following data</div>
<div>-ires 's data</div>
<pre>
1
2
3
4
5
6

</pre>

<div>-rres 's data</div>
<pre>
1
2
3
4
5
6

</pre>
<br>

<div>-o 's data(White: Input file)</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata-pdbTwoProteinFit.png]]<br>
same angle to Reference file<br></p>
</td>
<td><p align="Center">[[File:Outdata1-pdbTwoProteinFit.png]]<br>
another angle<br></p>
</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>

<div>-oMatrix 's data</div>
<pre>
0.058145 -0.998308 0.000001
-0.998308 -0.058145 -0.000001
0.000001 -0.000001 -1.000000
25.311117 26.828215 -0.000868
</pre>
<br>

<div>-oParam 's data</div>
<pre>
RMSBefore: 26.607964
RMSSelectedBefore: 9.794701
RMSSelectedAfter: 1.277625
RMSAfter: 17.793636
</pre>
<br>

<div>-oDis 's data</div>
<table>
<tr>
<td>[[File:Outdata2-pdbTwoProteinFit.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>-oDis2 's data</div>
<pre>
00001 1.447996
00002 1.329491
00003 0.065775
00004 0.242391
00005 1.683475
00006 1.741168
00007 1.578526
00008 6.625490
00009 3.641384

...

00157 12.396196
00158 8.092867
00159 3.598508
00160 3.239969
00161 1.259487
00162 4.196125
00163 7.037861
00164 6.740162
00165 11.073485
00166 16.325453
</pre>
<br>