pdbSurface - Revision history

Kinoshita: Created page with "'''pdbSurface''' is Eos's Command that gets Information of atom surface from PDB file. == List of option == === Main option === ..."
2014-08-18T00:57:11Z
Created page with "'''pdbSurface''' is Eos's Command that gets Information of atom surface from PDB file. == List of option == === Main option === <table border="1"> <tr>..."
New page
'''pdbSurface''' is [[Eos]]'s [[Command]] that gets Information of atom surface from [[PDB]] 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>-o</td>
<td>Essential</td>
<td>Output: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-order</td>
<td>Optional</td>
<td>order: [A]</td>
<td>1.7</td>
</tr>
<tr>
<td>-refine</td>
<td>Optional</td>
<td>Refine: Meshsize = Order/Refine</td>
<td>2</td>
</tr>
<tr>
<td>-size</td>
<td>Optional</td>
<td>Refine: Shell thickness = Order/Refine*Size</td>
<td>3</td>
</tr>
<tr>
<td>-weight</td>
<td>Optional</td>
<td>weight</td>
<td>100.0</td>
</tr>
<tr>
<td>-mergin</td>
<td>Optional</td>
<td>SearchArea</td>
<td>3.0</td>
</tr>
<tr>
<td>-thres</td>
<td>Optional</td>
<td>threshold</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>
<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>
<div>Inputdata(part)</div>
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00 14.06 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 17.27 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 16.41 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 16.12 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 17.94 C
ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 19.41 C
ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 21.82 S
ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00 23.68 C
ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 15.08 N
ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 16.71 C

...
</pre>
<br>

=== Case: Options only essential ===
<div>Outputdata(part)</div>
<pre>
...

↓Items of Temperature Factor is changed.

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 72.48 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 3.60 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 52.08 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00100.00 0 C
ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00100.00 0 C
ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 21.50 0 S
ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C
ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.93 0 N
ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 3.23 0 C

...
</pre>
<br>

=== Option -order===
====Case: order=1.9====
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 24.74 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 1.05 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 8.75 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 34.92 0 C
ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 0.12 0 C
ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 5.53 0 S
ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C
ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.12 0 N
ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.00 0 C

...
</pre>
<br>

=== Option -refine===
====Case: refine=1====
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 17.24 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 16.69 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00100.00 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 32.91 0 C
ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 9.69 0 C
ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 68.76 0 S
ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00 68.76 0 C
ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 16.69 0 N
ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 26.46 0 C

...
</pre>
<br>

=== Option -size===
====Case: size=5====
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00100.00 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 32.30 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 90.33 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00100.00 0 C
ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00100.00 0 C
ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 42.23 0 S
ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C
ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 8.91 0 N
ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 12.07 0 C

...
</pre>
<br>

=== Option -mergin=2.8===
====Case: mergin=2.8====
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00100.00 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 3.60 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 52.08 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00100.00 0 C
ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00100.00 0 C
ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 96.55 0 S
ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C
ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 12.72 0 N
ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.93 0 C

...
</pre>
<br>

=== Option -thres===
====Case: thres=0.1====
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 37.57 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 1.46 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 32.12 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 62.40 0 C
ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 36.08 0 C
ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 12.52 0 S
ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C
ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.53 0 N
ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.93 0 C

...
</pre>
<br>

=== Option -weight===
====Case: weight=1000, thres=0.1====
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 37.57 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 1.46 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 32.12 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 62.40 0 C
ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 36.08 0 C
ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 12.52 0 S
ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C
ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.53 0 N
ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.93 0 C

...
</pre>
<br>