View source for mrcImageToNAMDConstantForces

'''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>