Kinoshita: Created page with "'''mrcImageToNAMDConstantForces''' is Eos's Command that performs modeling to PDB by using Differential image of 3D image. == List of option == === Main option ===..."

2014-08-04T02:35:22Z

Created page with "'''mrcImageToNAMDConstantForces''' is Eos's Command that performs modeling to PDB by using Differential image of 3D image. == List of option == === Main option ===..."

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'''mrcImageToNAMDConstantForces''' is [[Eos]]'s [[Command]] that performs modeling to PDB by using Differential image of 3D image.

== 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: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-ip</td>
<td>Essential</td>
<td>Input: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: [[PDB]] with Constant Force</td>
<td>stdout</td>
</tr>
<tr>
<td>-w</td>
<td>Optional</td>
<td>Input: Weight for Constant Force</td>
<td>1.0</td>
</tr>
<tr>
<td>-s</td>
<td>Optional</td>
<td>Input: Scaling Factor for Constant Force</td>
<td>1.0</td>
</tr>
<tr>
<td>-C</td>
<td>Optional</td>
<td>Input: Contour[if density>Contour, force=0]</td>
<td>0.0</td>
</tr>
<tr>
<td>-R</td>
<td>Optional</td>
<td>Input: RotateMode</td>
<td>0</td>
</tr>
<tr>
<td>-RW</td>
<td>Optional</td>
<td>Input: RotateWeight</td>
<td>0.1</td>
</tr>
<tr>
<td>-S</td>
<td>Optional</td>
<td>Input: Seed</td>
<td>0.0</td>
</tr>
<tr>
<td>-nowat</td>
<td>Optional</td>
<td>No force for WAT (water residue) </td>
<td></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>
<div>More Density is lower potential.</div>
<br>

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

== Execution example ==
=== Input file's image ===
<div>[[Media:Input-121P.mrc|-i file]]'s image</div>
<table>
<tr>
<td><p align="Center">[[File:Input-mrcImageTrans.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Input1-mrcImageTrans.png]]<br>
yz-plane<br></p>
</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (0, 0, 0)<br>
3500.79 (49, 53, 30)<br>
11.0585<br>
118.123<br>
0.118123<br></p>
</td>
</tr>
</table>
<br>

<div>[[:Media:Input-121P.pdb.zip|-ip 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>

=== Example of options only essential ===
<table>
<tr>
<td>[[File:Outdata-mrcImageToNAMDConstantForces.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">3.329278e+01 4.215719e+01 4.546610e+01<br>
1.405992e+03<br>
1199.81 1200.39 1195.50<br> </p>
</td>
</tr>
</table>
<br>

mrcImageToNAMDConstantForces - Revision history

Kinoshita: Created page with "'''mrcImageToNAMDConstantForces''' is Eos's Command that performs modeling to PDB by using Differential image of 3D image. == List of option == === Main option ===..."