mrcImagepdbFileReduce - Revision history

Kinoshita: Created page with "'''mrcImagepdbFileReduce''' is Eos's Command that subtracts expected density from PDB. == List of option == === Main option === ..."
2014-08-25T03:04:14Z
Created page with "'''mrcImagepdbFileReduce''' is Eos's Command that subtracts expected density from PDB. == List of option == === Main option === <table border="1"> <tr>..."
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'''mrcImagepdbFileReduce''' is [[Eos]]'s [[Command]] that subtracts expected density from [[PDB]].

== 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</td>
</tr>
<tr>
<td>-r</td>
<td>Optional</td>
<td>Radius of Atom</td>
<td>1</td>
</tr>
<tr>
<td>-v</td>
<td>Optional</td>
<td>[PDB]] file's PixelVaule</td>
<td>0</td>
</tr>
<tr>
<td>-IT</td>
<td>Optional</td>
<td>Threshold for interface recognition</td>
<td>0</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></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>

=== Case: Options only essential ===
====Case: t=10000====
<table>
<tr>
<td><p align="Center">[[File:Outdata-mrcImagepdbFileReduce.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-mrcImagepdbFileReduce.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>
102.239<br>
1187.54<br>
2.24424<br></p>
</td>
</tr>
</table>
<br>

<div>In the following, Setting att=10000</div>

=== Option -r===
====Case: r=70====
=====Case: No other settings=====
<div>Output</div>
<pre>
3A
4A
5A
6A
7A
8A
9A
10A
11A
12A

...

1691A
1693A
1695A
1696A
1697A
1698A
1699A
1700A
1703A
1704A
</pre>
<br>

<div>-o 's image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata-r-mrcImagepdbFileReduce.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-r-mrcImagepdbFileReduce.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>
20982.9 (33, 29, 34)<br>
72.6667<br>
1003.8<br>
1.897<br></p>
</td>
</tr>
</table>
<br>

=====Case: ITh=20000=====
<div>Output</div>
<pre>
6A
7A
8A
9A
10A
14A
20A
22A
23A
24A
1231A
1242A
1344A
1360A
1361A
1540A
1553A
1616A
1663A
</pre>
<br>

<div>-o 's image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata-ITh-mrcImagepdbFileReduce.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-ITh-mrcImagepdbFileReduce.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>
20982.9 (33, 29, 34)<br>
72.6667<br>
1003.8<br>
1.897<br></p>
</td>
</tr>
</table>
<br>

=== Option -v===
====Case: v=10000====
<table>
<tr>
<td><p align="Center">[[File:Outdata-v-mrcImagepdbFileReduce.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-v-mrcImagepdbFileReduce.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">10000 (0, 0, 0)<br>
21001.7 (30, 26, 27)<br>
10026.6<br>
362.839<br>
0.685702<br></p>
</td>
</tr>
</table>
<br>