mrcImageUnexpectedMassFromPDB - Revision history

Kinoshita: Created page with "'''mrcImageUnexpectedMassFromPDB''' is Eos's Command. == List of option == === Main option ===

Option Essential/O..."
2014-08-04T05:51:47Z

Created page with "'''mrcImageUnexpectedMassFromPDB''' is Eos's Command. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essential/O..."

New page
'''mrcImageUnexpectedMassFromPDB''' is [[Eos]]'s [[Command]].

== 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>-p</td>
<td>Essential</td>
<td>Input: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-T</td>
<td>Essential</td>
<td>ThresHold</td>
<td>0.0</td>
</tr>
<tr>
<td>-D</td>
<td>Essential</td>
<td>AssignedData</td>
<td>0.0</td>
</tr>
<tr>
<td>-M</td>
<td>Optional</td>
<td>AtomMode</td>
<td>1</td>
</tr>
<tr>
<td>-r</td>
<td>Optional</td>
<td>Radius (for M=2, 3)</td>
<td>3.4</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>
<br>

===-m details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Origin is BottomLeft.</td>
</tr>
<tr>
<td>1</td>
<td>Origin is Center.(Helix)</td>
</tr>
<tr>
<td>2</td>
<td>Origin is Center.(3D Single)</td>
</tr>
<tr>
<td>3</td>
<td>Origin is shown by StartN.</td>
</tr>
<tr>
<td>16</td>
<td>MaxIsProtein : Default: MinIsProtein</td>
</tr>
</table>
<br>

===-M details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Nearest Voxel -> Data</td>
</tr>
<tr>
<td>1</td>
<td>Nearest and 6-linked voxel -> Data</td>
</tr>
<tr>
<td>2</td>
<td>Specified spheres(Outside) -> Data</td>
</tr>
<tr>
<td>3</td>
<td>Inside of Specified spheres -> Data</td>
</tr>
<tr>
<td> </td>
<td>Outside of Specified spheres -> Data</td>
</tr>
</table>
<br>

== Execution example ==
=== Input file's image ===
<div>[[Media:Input-1B7T.mrc | -i file]]'s image</div>
<table>
<tr>
<td><p align="Center">[[File:Input-1B7T.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Input1-1B7T.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>
21001.7 (30, 26, 27)<br>
213.171<br>
1416<br>
2.67599<br></p>
</td>
</tr>
</table>
<br>

<div>[[:Media:Input-1VOM.pdb.zip |-p file]]'s image</div>
<table>
<tr>
<td>[[File:Input-1VOM-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">6.727136e+01 3.631518e+01 -2.983928e+01<br>
5.314867e+01 <br>
40.92 41.49 48.47<br> </p>
</td>
</tr>
</table>
<br>

=== Example of options only essential ===
====Case: T=3000 ,D=3000====
<table>
<tr>
<td><p align="Center">[[File:Outdata-mrcImageUnexpectedMassFromPDB.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-mrcImageUnexpectedMassFromPDB.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>
21001.7 (30, 26, 27)<br>
320.702<br>
1506.71<br>
2.84741<br></p>
</td>
</tr>
</table>
<br>

<div>In the following, Setting at T=3000, D=3000</div>

=== Option -M===
====Case: M=0====
<table>
<tr>
<td><p align="Center">[[File:Outdata-M0-mrcImageUnexpectedMassFromPDB.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-M0-mrcImageUnexpectedMassFromPDB.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>
21001.7 (30, 26, 27)<br>
260.067<br>
1457.24<br>
2.75393<br></p>
</td>
</tr>
</table>
<br>

====Case: M=2====
=====Case: No other settings=====
<table>
<tr>
<td><p align="Center">[[File:Outdata-M2-mrcImageUnexpectedMassFromPDB.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-M2-mrcImageUnexpectedMassFromPDB.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>
21001.7 (30, 26, 27)<br>
322.335<br>
1508.01<br>
2.84988<br></p>
</td>
</tr>
</table>
<br>

=====Case: r=10=====
<table>
<tr>
<td><p align="Center">[[File:Outdata-M2r-mrcImageUnexpectedMassFromPDB.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-M2r-mrcImageUnexpectedMassFromPDB.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>
21001.7 (30, 26, 27)<br>
461.211<br>
1602.49<br>
3.02843<br></p>
</td>
</tr>
</table>
<br>

====Case: M=3====
=====Case: No other settings=====
<table>
<tr>
<td><p align="Center">[[File:Outdata-M3-mrcImageUnexpectedMassFromPDB.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-M3-mrcImageUnexpectedMassFromPDB.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>
21001.7 (30, 26, 27)<br>
213.171<br>
1416<br>
2.67599<br></p>
</td>
</tr>
</table>
<br>

=====Case: r=20=====
<table>
<tr>
<td><p align="Center">[[File:Outdata-M3r-mrcImageUnexpectedMassFromPDB.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-M3r-mrcImageUnexpectedMassFromPDB.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>
21001.7 (30, 26, 27)<br>
275.206<br>
1469.99<br>
2.77802<br></p>
</td>
</tr>
</table>
<br>

=== Option -m===
====Case: m=1====
<table>
<tr>
<td><p align="Center">[[File:Outdata-m1-mrcImageUnexpectedMassFromPDB.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-m1-mrcImageUnexpectedMassFromPDB.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>
21001.7 (30, 26, 27)<br>
313.849<br>
1504.75<br>
2.84371<br></p>
</td>
</tr>
</table>
<br>

====Case: m=2====
<table>
<tr>
<td><p align="Center">[[File:Outdata-m2-mrcImageUnexpectedMassFromPDB.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-m2-mrcImageUnexpectedMassFromPDB.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>
21001.7 (30, 26, 27)<br>
321.106<br>
1507.05<br>
2.84806<br></p>
</td>
</tr>
</table>
<br>

====Case: m=3====
<table>
<tr>
<td><p align="Center">[[File:Outdata-m3-mrcImageUnexpectedMassFromPDB.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-m3-mrcImageUnexpectedMassFromPDB.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>
21001.7 (30, 26, 27)<br>
320.731<br>
1506.76<br>
2.8475<br></p>
</td>
</tr>
</table>
<br>

====Case: m=16====
<table>
<tr>
<td><p align="Center">[[File:Outdata-m16-mrcImageUnexpectedMassFromPDB.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-m16-mrcImageUnexpectedMassFromPDB.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>
21001.7 (30, 26, 27)<br>
213.141<br>
1415.95<br>
2.67589<br></p>
</td>
</tr>
</table>
<br>