View source for mrcImageSolventFlattening

'''mrcImageSolventFlattening''' is [[Eos]]'s [[Command]] that performs smoothing about solvent.


== 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>-o</td> 
				<td>Essential</td> 
				<td>Output: [[mrcImage]]</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-rmax</td> 
				<td>Optional</td> 
				<td>rmax [A]</td> 
				<td>190</td> 
			</tr> 
			<tr> 
				<td>-sd</td> 
				<td>Optional</td> 
				<td>Assign voxels below MeanOfSolvent+Range*SDofSolvent as Solvent</td> 
				<td>0</td> 
			</tr> 
			<tr> 
				<td>-density</td> 
				<td>Optional</td> 
				<td>embed mean lower than density value</td> 
				<td>0</td> 
			</tr> 
			<tr> 
				<td>-Floating</td> 
				<td>Optional</td> 
				<td>data minus mean of Solvent</td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>-oparam</td> 
				<td>Optional</td> 
				<td>Output: Parameter</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(-density is stronger)</td> 
				<td>0</td> 
			</tr> 
			<tr> 
				<td>-h</td> 
				<td>Optional</td> 
				<td>Help</td> 
				<td>　</td> 
			</tr> 
		</table> 

<div>-SD range : assign the voxels whose density is less than maen + range*SD as solvent range</div>

=== -m details ===
		<table border="1">
			<tr> 
				<th>Value</th> 
				<th>Description</th> 
			</tr> 
			<tr> 
				<td>0</td> 
				<td>mean of all density</td> 
			</tr> 
			<tr> 
				<td>1</td> 
				<td>mean of sphere surface density at rmax</td> 
			</tr> 
			<tr> 
				<td>2</td> 
				<td>mean of cylinder surface density at rmax</td> 
			</tr> 
			<tr> 
				<td>6</td> 
				<td>mean of 2D Edge X=0 or N.x-1</td> 
			</tr> 
		</table> 


== Execution example ==
=== Input file's image ===
	<table> 
		<tr> 
			<td>[[File:Input-mrcImageSolventFlattening.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">0 (41, 10, 0)<br> 
				255 (42, 36, 0)<br> 
				111.211<br> 
				32.7239<br> 
				0.409049<br></p> 
			</td> 
		</tr> 
	</table> 


<div>[[Media:Input-121P-O-N.mrc | Input file]]'s image for m=1</div>
	<table> 
		<tr> 
			<td><p align="Center">[[File:Input1-mrcImageSolventFlattening.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Input2-mrcImageSolventFlattening.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">-2255.49 (1, 42, 21)<br> 
				4032.8 (49, 53, 30)<br> 
				12.0338<br> 
				475.034<br> 
				0.48225<br></p> 
			</td> 
		</tr> 
	</table> 


<div>[[Media:Input-ThickFilaments0-N.mrc | Input file]]'s image for m=2</div>
	<table> 
		<tr> 
			<td><p align="Center">[[File:Input3-mrcImageSolventFlattening.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Input4-mrcImageSolventFlattening.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">-0.307724 (52, 10, 79)<br> 
				1.52145 (47, 41, 47)<br> 
				0.00295664<br> 
				0.0916201<br> 
				0.000132783<br></p> 
			</td> 
		</tr> 
	</table> 


=== Example of options only essential ===
<div>-o 's image </div>
	<table> 
		<tr> 
			<td>[[File:Outdata-mrcImageSolventFlattening.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">111 (0, 0, 0)<br> 
				255 (42, 36, 0)<br> 
				123.826<br> 
				21.2012<br> 
				0.265015<br></p> 
			</td> 
		</tr> 
	</table> 

<div>-oparam 's data</div>
<pre>
Mean: 111.211
SD: 32.7239
</pre>


=== Option -sd===
====Case: sd=1==== 
<div>-o 's image </div>
	<table> 
		<tr> 
			<td>[[File:Outdata-sd-mrcImageSolventFlattening.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">143 (0, 0, 0)<br> 
				255 (42, 36, 0)<br> 
				146.528<br> 
				11.5143<br> 
				0.143928<br></p> 
			</td> 
		</tr> 
	</table> 

<div>-oparam 's data</div>
<pre>
Mean: 111.211
SD: 32.7239
</pre>


=== Option -density===
====Case: density=64==== 
<div>-o 's image </div>
	<table> 
		<tr> 
			<td>[[File:Outdata-density-mrcImageSolventFlattening.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">64 (8, 0, 0)<br> 
				255 (42, 36, 0)<br> 
				111.86<br> 
				31.5489<br> 
				0.394361<br></p> 
			</td> 
		</tr> 
	</table>

<div>-oparam 's data</div>
<pre>
Mean: 64
SD: 0
</pre>


=== Option -Floating===
<div>-o 's image </div>
	<table> 
		<tr> 
			<td>[[File:Outdata-Floating-mrcImageSolventFlattening.png]]</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> 
				143 (42, 36, 0)<br> 
				12.3614<br> 
				20.8806<br> 
				0.261008<br></p> 
			</td> 
		</tr> 
	</table>

<div>-oparam 's data</div>
<pre>
Mean: 111.211
SD: 32.7239
</pre>


=== Option -m===
====Case: m=1==== 
=====Case: No other settings=====
	<table> 
		<tr> 
			<td><p align="Center">[[File:Outdata-m1-mrcImageSolventFlattening.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Outdata1-m1-mrcImageSolventFlattening.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">5.93088 (2, 0, 0)<br> 
				4032.8 (49, 53, 30)<br> 
				195.824<br> 
				288.816<br> 
				0.293204<br></p> 
			</td> 
		</tr> 
	</table> 

<div>-oparam 's data</div>
<pre>
rmax from caliculate:49.000000
meanOfSphereSurface 5.93088 at rmax 49[A]
Mean: 5.93088
SD: 391.086
</pre>

=====Case: rmax=10===== 
	<table> 
		<tr> 
			<td><p align="Center">[[File:Outdata-m1rmax-mrcImageSolventFlattening.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Outdata1-m1rmax-mrcImageSolventFlattening.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">334.514 (0, 0, 0)<br> 
				4032.8 (49, 53, 30)<br> 
				404.478<br> 
				184.129<br> 
				0.186926<br></p> 
			</td> 
		</tr> 
	</table> 

<div>-oparam 's data</div>
<pre>
rmax from option:10.000000
meanOfSphereSurface 334.514 at rmax 10[A]
Mean: 334.514
SD: 673.352
</pre>


====Case: m=2==== 
=====Case: No other settings=====
	<table> 
		<tr> 
			<td><p align="Center">[[File:Outdata-m2-mrcImageSolventFlattening.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Outdata1-m2-mrcImageSolventFlattening.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">0.00126069 (0, 0, 0)<br> 
				1.52145 (47, 41, 47)<br> 
				0.0323659<br> 
				0.0689534<br> 
				9.99325e-05<br></p> 
			</td> 
		</tr> 
	</table> 

<div>-oparam 's data</div>
<pre>
rmax from caliculate:340.000000
meanOfCylinderSurface 0.00126069 at rmax 340[A]
Mean: 0.00126069
SD: 0.065755
</pre>

=====Case: rmax=100===== 
	<table> 
		<tr> 
			<td><p align="Center">[[File:Outdata-m2rmax-mrcImageSolventFlattening.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Outdata1-m2rmax-mrcImageSolventFlattening.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">0.000652629 (0, 0, 0)<br> 
				1.52145 (47, 41, 47)<br> 
				0.0320589<br> 
				0.0690925<br> 
				0.000100134<br></p> 
			</td> 
		</tr> 
	</table> 

<div>-oparam 's data</div>
<pre>
rmax from option:100.000000
meanOfCylinderSurface 0.000652629 at rmax 100[A]
Mean: 0.000652629
SD: 0.0645217
</pre>


====Case: m=6==== 
<div>-o 's image </div>
	<table> 
		<tr> 
			<td>[[File:Outdata-m6-mrcImageSolventFlattening.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">102 (0, 0, 0)<br> 
				255 (42, 36, 0)<br> 
				119.567<br> 
				24.0291<br> 
				0.300364<br></p> 
			</td> 
		</tr> 
	</table>

<div>-oparam 's data</div>
<pre>
Mean: 102.875
SD: 24.7022
</pre>