http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?action=history&feed=atom&title=mrcImageSolventFlattening
mrcImageSolventFlattening - Revision history
2026-05-05T15:09:42Z
Revision history for this page on the wiki
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http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImageSolventFlattening&diff=2416&oldid=prev
Kinoshita: /* Main option */
2014-07-31T05:20:58Z
<p><span dir="auto"><span class="autocomment">Main option</span></span></p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 05:20, 31 July 2014</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>-m</td>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>-m</td>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>Optional</td>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>Optional</td>  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> <td><del class="diffchange diffchange-inline">Modeを設定</del>(-density is stronger)</td>  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> <td><ins class="diffchange diffchange-inline">Mode</ins>(-density is stronger)</td>  </div></td></tr>
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Kinoshita
http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImageSolventFlattening&diff=2415&oldid=prev
Kinoshita: Created page with "'''mrcImageSolventFlattening''' is Eos's Command that performs smoothing about solvent. == List of option == === Main option === <table border="1"> <tr> <t..."
2014-07-31T05:20:40Z
<p>Created page with "'''mrcImageSolventFlattening''' is <a href="/Eos/index.php/Eos" title="Eos">Eos</a>'s <a href="/Eos/index.php/Command" title="Command">Command</a> that performs smoothing about solvent. == List of option == === Main option === <table border="1"> <tr> <t..."</p>
<p><b>New page</b></p><div>'''mrcImageSolventFlattening''' is [[Eos]]'s [[Command]] that performs smoothing about solvent.<br />
<br />
<br />
== List of option ==<br />
=== Main option ===<br />
<table border="1"><br />
<tr> <br />
<th>Option</th> <br />
<th>Essential/Optional</th> <br />
<th>Description</th> <br />
<th>Default</th> <br />
</tr> <br />
<tr> <br />
<td>-i</td> <br />
<td>Essential</td> <br />
<td>Input: [[mrcImage]]</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-o</td> <br />
<td>Essential</td> <br />
<td>Output: [[mrcImage]]</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-rmax</td> <br />
<td>Optional</td> <br />
<td>rmax [A]</td> <br />
<td>190</td> <br />
</tr> <br />
<tr> <br />
<td>-sd</td> <br />
<td>Optional</td> <br />
<td>Assign voxels below MeanOfSolvent+Range*SDofSolvent as Solvent</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-density</td> <br />
<td>Optional</td> <br />
<td>embed mean lower than density value</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-Floating</td> <br />
<td>Optional</td> <br />
<td>data minus mean of Solvent</td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>-oparam</td> <br />
<td>Optional</td> <br />
<td>Output: Parameter</td> <br />
<td>stdout</td> <br />
</tr> <br />
<tr> <br />
<td>-c</td> <br />
<td>Optional</td> <br />
<td>ConfigurationFile</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-m</td> <br />
<td>Optional</td> <br />
<td>Modeを設定(-density is stronger)</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-h</td> <br />
<td>Optional</td> <br />
<td>Help</td> <br />
<td> </td> <br />
</tr> <br />
</table> <br />
<br />
<div>-SD range : assign the voxels whose density is less than maen + range*SD as solvent range</div><br />
<br />
=== -m details ===<br />
<table border="1"><br />
<tr> <br />
<th>Value</th> <br />
<th>Description</th> <br />
</tr> <br />
<tr> <br />
<td>0</td> <br />
<td>mean of all density</td> <br />
</tr> <br />
<tr> <br />
<td>1</td> <br />
<td>mean of sphere surface density at rmax</td> <br />
</tr> <br />
<tr> <br />
<td>2</td> <br />
<td>mean of cylinder surface density at rmax</td> <br />
</tr> <br />
<tr> <br />
<td>6</td> <br />
<td>mean of 2D Edge X=0 or N.x-1</td> <br />
</tr> <br />
</table> <br />
<br />
<br />
== Execution example ==<br />
=== Input file's image ===<br />
<table> <br />
<tr> <br />
<td>[[File:Input-mrcImageSolventFlattening.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">0 (41, 10, 0)<br> <br />
255 (42, 36, 0)<br> <br />
111.211<br> <br />
32.7239<br> <br />
0.409049<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<br />
<div>[[Media:Input-121P-O-N.mrc | Input file]]'s image for m=1</div><br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Input1-mrcImageSolventFlattening.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Input2-mrcImageSolventFlattening.png]]<br><br />
yz-plane<br></p> <br />
</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-2255.49 (1, 42, 21)<br> <br />
4032.8 (49, 53, 30)<br> <br />
12.0338<br> <br />
475.034<br> <br />
0.48225<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<br />
<div>[[Media:Input-ThickFilaments0-N.mrc | Input file]]'s image for m=2</div><br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Input3-mrcImageSolventFlattening.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Input4-mrcImageSolventFlattening.png]]<br><br />
yz-plane<br></p> <br />
</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-0.307724 (52, 10, 79)<br> <br />
1.52145 (47, 41, 47)<br> <br />
0.00295664<br> <br />
0.0916201<br> <br />
0.000132783<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<br />
=== Example of options only essential ===<br />
<div>-o 's image </div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-mrcImageSolventFlattening.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">111 (0, 0, 0)<br> <br />
255 (42, 36, 0)<br> <br />
123.826<br> <br />
21.2012<br> <br />
0.265015<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>-oparam 's data</div><br />
<pre><br />
Mean: 111.211<br />
SD: 32.7239<br />
</pre><br />
<br />
<br />
=== Option -sd===<br />
====Case: sd=1==== <br />
<div>-o 's image </div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-sd-mrcImageSolventFlattening.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">143 (0, 0, 0)<br> <br />
255 (42, 36, 0)<br> <br />
146.528<br> <br />
11.5143<br> <br />
0.143928<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>-oparam 's data</div><br />
<pre><br />
Mean: 111.211<br />
SD: 32.7239<br />
</pre><br />
<br />
<br />
=== Option -density===<br />
====Case: density=64==== <br />
<div>-o 's image </div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-density-mrcImageSolventFlattening.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">64 (8, 0, 0)<br> <br />
255 (42, 36, 0)<br> <br />
111.86<br> <br />
31.5489<br> <br />
0.394361<br></p> <br />
</td> <br />
</tr> <br />
</table><br />
<br />
<div>-oparam 's data</div><br />
<pre><br />
Mean: 64<br />
SD: 0<br />
</pre><br />
<br />
<br />
=== Option -Floating===<br />
<div>-o 's image </div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-Floating-mrcImageSolventFlattening.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">0 (0, 0, 0)<br> <br />
143 (42, 36, 0)<br> <br />
12.3614<br> <br />
20.8806<br> <br />
0.261008<br></p> <br />
</td> <br />
</tr> <br />
</table><br />
<br />
<div>-oparam 's data</div><br />
<pre><br />
Mean: 111.211<br />
SD: 32.7239<br />
</pre><br />
<br />
<br />
=== Option -m===<br />
====Case: m=1==== <br />
=====Case: No other settings=====<br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Outdata-m1-mrcImageSolventFlattening.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Outdata1-m1-mrcImageSolventFlattening.png]]<br><br />
yz-plane<br></p> <br />
</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">5.93088 (2, 0, 0)<br> <br />
4032.8 (49, 53, 30)<br> <br />
195.824<br> <br />
288.816<br> <br />
0.293204<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>-oparam 's data</div><br />
<pre><br />
rmax from caliculate:49.000000<br />
meanOfSphereSurface 5.93088 at rmax 49[A]<br />
Mean: 5.93088<br />
SD: 391.086<br />
</pre><br />
<br />
=====Case: rmax=10===== <br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Outdata-m1rmax-mrcImageSolventFlattening.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Outdata1-m1rmax-mrcImageSolventFlattening.png]]<br><br />
yz-plane<br></p> <br />
</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">334.514 (0, 0, 0)<br> <br />
4032.8 (49, 53, 30)<br> <br />
404.478<br> <br />
184.129<br> <br />
0.186926<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>-oparam 's data</div><br />
<pre><br />
rmax from option:10.000000<br />
meanOfSphereSurface 334.514 at rmax 10[A]<br />
Mean: 334.514<br />
SD: 673.352<br />
</pre><br />
<br />
<br />
====Case: m=2==== <br />
=====Case: No other settings=====<br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Outdata-m2-mrcImageSolventFlattening.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Outdata1-m2-mrcImageSolventFlattening.png]]<br><br />
yz-plane<br></p> <br />
</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">0.00126069 (0, 0, 0)<br> <br />
1.52145 (47, 41, 47)<br> <br />
0.0323659<br> <br />
0.0689534<br> <br />
9.99325e-05<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>-oparam 's data</div><br />
<pre><br />
rmax from caliculate:340.000000<br />
meanOfCylinderSurface 0.00126069 at rmax 340[A]<br />
Mean: 0.00126069<br />
SD: 0.065755<br />
</pre><br />
<br />
=====Case: rmax=100===== <br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Outdata-m2rmax-mrcImageSolventFlattening.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Outdata1-m2rmax-mrcImageSolventFlattening.png]]<br><br />
yz-plane<br></p> <br />
</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">0.000652629 (0, 0, 0)<br> <br />
1.52145 (47, 41, 47)<br> <br />
0.0320589<br> <br />
0.0690925<br> <br />
0.000100134<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>-oparam 's data</div><br />
<pre><br />
rmax from option:100.000000<br />
meanOfCylinderSurface 0.000652629 at rmax 100[A]<br />
Mean: 0.000652629<br />
SD: 0.0645217<br />
</pre><br />
<br />
<br />
====Case: m=6==== <br />
<div>-o 's image </div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-m6-mrcImageSolventFlattening.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">102 (0, 0, 0)<br> <br />
255 (42, 36, 0)<br> <br />
119.567<br> <br />
24.0291<br> <br />
0.300364<br></p> <br />
</td> <br />
</tr> <br />
</table><br />
<br />
<div>-oparam 's data</div><br />
<pre><br />
Mean: 102.875<br />
SD: 24.7022<br />
</pre></div>
Kinoshita