View source for pdbSurface

'''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>