pdbAtomSection - Revision history

Kinoshita: /* Main option */

2014-08-07T06:35:22Z

‎Main option

Kinoshita: /* Main option */

2014-08-07T06:10:39Z

‎Main option

Kinoshita: Created page with "'''pdbAtomSection''' is Eos's Command that cuts out section from Atoms Model, and outputs to ps file. == List of option == === Main option === ..."
2014-08-07T06:08:28Z
Created page with "'''pdbAtomSection''' is Eos's Command that cuts out section from Atoms Model, and outputs to ps file. == List of option == === Main option === <table border="1">..."
New page
'''pdbAtomSection''' is [[Eos]]'s [[Command]] that cuts out section from Atoms Model, and outputs to ps file.

== 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>-if</td>
<td>Optional</td>
<td>Input: FlagsFile</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: psfile</td>
<td>NULL</td>
</tr>
<tr>
<td>-dist</td>
<td>Optional</td>
<td>Distance of Sections</td>
<td>2.5</td>
</tr>
<tr>
<td>-zmin</td>
<td>Optional</td>
<td>zの最小値</td>
<td>0.0</td>
</tr>
<tr>
<td>-zmax</td>
<td>Optional</td>
<td>zの最大値</td>
<td>90.0</td>
</tr>
<tr>
<td>-fm</td>
<td>Optional</td>
<td>flag mode</td>
<td>13</td>
</tr>
<tr>
<td>-r</td>
<td>Optional</td>
<td>半径</td>
<td>1.0</td>
</tr>
<tr>
<td>-clw</td>
<td>Optional</td>
<td>円周のWidth</td>
<td>0.1</td>
</tr>
<tr>
<td>-plw</td>
<td>Optional</td>
<td>ペプチド結合のWidth</td>
<td>0.1</td>
</tr>
<tr>
<td>-fontsize</td>
<td>Optional</td>
<td>font size</td>
<td>2.0</td>
</tr>
<tr>
<td>-AS</td>
<td>Optional</td>
<td>absolute scale of PS file (-AS 1 := 1 mm/A)</td>
<td>1.0</td>
</tr>
<tr>
<td>-shiftx</td>
<td>Optional</td>
<td>pdb Shift x [A]</td>
<td>0.0</td>
</tr>
<tr>
<td>-shifty</td>
<td>Optional</td>
<td>pdb Shift y [A]</td>
<td>0.0</td>
</tr>
<tr>
<td>-shiftz</td>
<td>Optional</td>
<td>pdb Shift z [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>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>

===-fm details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>display nothing</td>
</tr>
<tr>
<td>1</td>
<td>one char amino acid name</td>
</tr>
<tr>
<td>2</td>
<td>three char amino acid name</td>
</tr>
<tr>
<td>4</td>
<td>chain identifier</td>
</tr>
<tr>
<td>8</td>
<td>sequence number</td>
</tr>
<tr>
<td>16</td>
<td>display any atom</td>
</tr>
</table>

===-if format===
<pre>
chainIdertifier&sequenceNumber(R123) FlagMode circleRedius circlelinewidth fontsize
</pre>

== 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>

=== Example of options only essential ===
<table>
<tr>
<th>[[File:Outdata-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page (Left bottom part)</th>
</tr>
</table>
<br>

=== Option -AS===
====Case: AS=5====
<table>
<tr>
<th>[[File:Outdata-AS-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>

<div>In the following, Setting at AS=5</div>

=== Option -shiftx===
====Case: shiftx=10====
<table>
<tr>
<th>[[File:Outdata-shiftx-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>

<div>In the following, Setting at shiftx=10</div>

=== Option -shifty===
====Case: shifty=10====
<table>
<tr>
<th>[[File:Outdata-shifty-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>

=== Option -shiftz===
====Case: shiftz=1====
<table>
<tr>
<th>[[File:Outdata-shiftz-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>

=== Option -dist===
====Case: dist=3====
<table>
<tr>
<th>[[File:Outdata-dist-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>5/90 Page</th>
</tr>
</table>
<br>

=== Option -zmin===
====Case: zmin=1====
<table>
<tr>
<th>[[File:Outdata-zmin-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>5/89 Page</th>
</tr>
</table>
<br>

=== Option -zmax===
====Case: zmax=15====
<table>
<tr>
<th>[[File:Outdata-zmax-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/15 Page</th>
</tr>
</table>
<br>

=== Option -r===
====Case: r=0.5====
<table>
<tr>
<th>[[File:Outdata-r-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>

=== Option -plw===
====Case: plw=0.3====
<table>
<tr>
<th>[[File:Outdata-plw-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>

=== Option -fontsize===
====Case: fontsize=1====
<table>
<tr>
<th>[[File:Outdata-fontsize-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>

=== Option -fm===
====Case: fm=0====
<table>
<tr>
<th>[[File:Outdata-fm0-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>

====Case: fm=1====
<table>
<tr>
<th>[[File:Outdata-fm1-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>

====Case: fm=2====
<table>
<tr>
<th>[[File:Outdata-fm2-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>

====Case: fm=4====
<table>
<tr>
<th>[[File:Outdata-fm4-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>

====Case: fm=8====
<table>
<tr>
<th>[[File:Outdata-fm8-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>

====Case: fm=16====
<table>
<tr>
<th>[[File:Outdata-fm16-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>

=== Option -if===
<div>-if 's data</div>
<pre>
A28 0 2.0 0.3 2
A147 1 0.5 0.3 4
A114 2 1.0 0.3 1
A128 4 1.0 0.3 4
A8 8 1.0 0.3 4
A56 16 0.5 0.3 4
A39 31 0.7 0.3 3

</pre>
<br>

<div>Output</div>
<table>
<tr>
<th>[[File:Outdata-if-pdbAtomSection.png]]</th>
</tr>
<tr>
<th>6/90 Page</th>
</tr>
</table>
<br>