pdbNearAtomListShow - Revision history

Kinoshita: Created page with "'''pdbNearAtomListShow''' is Eos's Command that shows near atom information. == List of option == === Main option ===

Option
2014-08-08T01:43:23Z

Created page with "'''pdbNearAtomListShow''' is Eos's Command that shows near atom information. == List of option == === Main option === <table border="1"> <tr> <th>Option</t..."

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'''pdbNearAtomListShow''' is [[Eos]]'s [[Command]] that shows near atom information.

== 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: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: [[ASCII]](Coordinates List)</td>
<td>stdout</td>
</tr>
<tr>
<td>-P</td>
<td>Optional</td>
<td>POI: (Px, Py, Pz)</td>
<td>(0.0, 0.0, 0.0)</td>
</tr>
<tr>
<td>-V</td>
<td>Optional</td>
<td>VOI: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-C</td>
<td>Optional</td>
<td>ContourLevel for VolumeOfInterest(For -V only)</td>
<td>0.0</td>
</tr>
<tr>
<td>-d</td>
<td>Optional</td>
<td>Distance: [A]</td>
<td>0.0</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>
<div>Select either -P or -V. (-P takes priority.)</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 ==
===[[:Media:Input-121P.pdb.zip|Input file]] image===
<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>

=== Case: Options only essential ===
<pre>
No ATOM
</pre>
<div>On this input file and default setting, it can't find atoms.</div>
<br>

=== Option -P, -d===
====Case: P=(25, 25, 25), d=4====
<table>
<tr>
<td>[[File:Outdata-P-pdbNearAtomListShow.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">2.462900e+01 2.550600e+01 2.299300e+01<br>
5.227511e+00<br>
2.81 2.28 5.20<br></p>
</td>
</tr>
</table>
<br>

=== Option -V===
====[[Media:Input-121P1.mrc |-V file]]'s image====
<table>
<tr>
<td><p align="Center">[[File:Input-121P1.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Input1-121P1.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 (24, 28, 5)<br>
88.3104<br>
323.414<br>
0.914753<br></p>
</td>
</tr>
</table>
<br>

====Case: d=0.3====
<table>
<tr>
<td>[[File:Outdata-V-pdbNearAtomListShow.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">4.250222e+00 2.688167e+01 1.551100e+01<br>
2.727775e+01 <br>
21.57 22.63 26.38<br></p>
</td>
</tr>
</table>
<br>

====Case: C=3500, d=0.3====
<table>
<tr>
<td>[[File:Outdata-VC-pdbNearAtomListShow.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">5.977000e+00 2.695800e+01 -1.009600e+01<br>
0.000000e+00 <br>
0.00 0.00 0.00<br></p>
</td>
</tr>
</table>
<br>