pdb2SketchMacro - Revision history

Kinoshita: Created page with "'''pdb2SketchMacro''' is Eos's Command. == List of option == === Main option === ..."
2014-08-07T05:46:06Z
Created page with "'''pdb2SketchMacro''' is Eos's Command. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essential/Optional</th>..."
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'''pdb2SketchMacro''' is [[Eos]]'s [[Command]].

== 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>Optional</td>
<td>Input: [[PDB]]</td>
<td>stdin</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: [[ASCII]]</td>
<td>stdout</td>
</tr>
<tr>
<td>-MolName</td>
<td>Optional</td>
<td>Molecule Name (recommend 2 words or less)</td>
<td>TS</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>15</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>1</td>
<td>Helix sketched with spirals </td>
</tr>
<tr>
<td>2</td>
<td>Sheet sketched with arrows </td>
</tr>
<tr>
<td>4</td>
<td>Turn sketched with rattler</td>
</tr>
<tr>
<td>8</td>
<td>No structure sketched with rattler </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>

=== Example of options only essential ===
<pre>
sam_atom_in Input.pdb TS
sketch_object TSH_A1
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone TS A16 A25 red
sketch_add TS A16 A25
end_object
sketch_object TSH_A2
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone TS A65 A74 red
sketch_add TS A65 A74
end_object
sketch_object TSH_A3
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone TS A87 A103 red
sketch_add TS A87 A103
end_object
sketch_object TSH_A4
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone TS A127 A137 red
sketch_add TS A127 A137
end_object
sketch_object TSH_A5
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone TS A152 A164 red
sketch_add TS A152 A164
end_object
sketch_object TSS__S
sketch_setup Arrow solid 2.5 0.5 3.75 2 7 3 2
sketch_type Arrow
paint_zone TS A37 A46 blue
sketch_add TS A37 A46
paint_zone TS A49 A58 blue
sketch_add TS A49 A58
paint_zone TS A2 A9 blue
sketch_add TS A2 A9
paint_zone TS A77 A83 blue
sketch_add TS A77 A83
paint_zone TS A111 A116 blue
sketch_add TS A111 A116
paint_zone TS A141 A143 blue
sketch_add TS A141 A143
end_oject
sketch_object TSN__1
sketch_setup Rattler solid 0.5 7 2
sketch_type Rattler
paint_zone TS A1 A2 white
sketch_add TS A1 A2
end_object
sketch_object TSN__2
sketch_setup Rattler solid 0.5 7 2
sketch_type Rattler
paint_zone TS A9 A16 white
sketch_add TS A9 A16
end_object

...

sketch_object TSN_11
sketch_setup Rattler solid 0.5 7 2
sketch_type Rattler
paint_zone TS A143 A152 white
sketch_add TS A143 A152
end_object
sketch_object TSN_12
sketch_setup Rattler solid 0.5 7 2
sketch_type Rattler
paint_zone TS A164 0 white
sketch_add TS A164 0
end_object
</pre>
<br>

=== Option -m===
====Case: m=1====
<pre>
sam_atom_in Input.pdb TS
sketch_object TSH_A1
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone TS A16 A25 red
sketch_add TS A16 A25
end_object
sketch_object TSH_A2
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone TS A65 A74 red
sketch_add TS A65 A74
end_object
sketch_object TSH_A3
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone TS A87 A103 red
sketch_add TS A87 A103
end_object
sketch_object TSH_A4
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone TS A127 A137 red
sketch_add TS A127 A137
end_object
sketch_object TSH_A5
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone TS A152 A164 red
sketch_add TS A152 A164
end_object
</pre>
<br>

====Case: m=8====
<pre>
sam_atom_in Input.pdb TS
sketch_object TSN__1
sketch_setup Rattler solid 0.5 7 2
sketch_type Rattler
paint_zone TS A1 A2 white
sketch_add TS A1 A2
end_object
sketch_object TSN__2
sketch_setup Rattler solid 0.5 7 2
sketch_type Rattler
paint_zone TS A9 A16 white
sketch_add TS A9 A16
end_object

...

sketch_object TSN_11
sketch_setup Rattler solid 0.5 7 2
sketch_type Rattler
paint_zone TS A143 A152 white
sketch_add TS A143 A152
end_object
sketch_object TSN_12
sketch_setup Rattler solid 0.5 7 2
sketch_type Rattler
paint_zone TS A164 0 white
sketch_add TS A164 0
end_object
</pre>
<br>

=== Option -MolName===
====Case: MolName=XX, m=1====
<pre>
Input.pdb XX
sketch_object XXH_A1
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone XX A16 A25 red
sketch_add XX A16 A25
end_object
sketch_object XXH_A2
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone XX A65 A74 red
sketch_add XX A65 A74
end_object
sketch_object XXH_A3
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone XX A87 A103 red
sketch_add XX A87 A103
end_object
sketch_object XXH_A4
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone XX A127 A137 red
sketch_add XX A127 A137
end_object
sketch_object XXH_A5
sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type Spiral
paint_zone XX A152 A164 red
sketch_add XX A152 A164
end_object
</pre>
<br>

Option Essential/Optional