pdbTempFactorSet - Revision history

Kinoshita: Created page with "'''pdbTempFactorSet''' is Eos's Command that that sets Temperature Factor to PDB file. == List of option == === Main option === ..."
2014-08-18T01:03:34Z
Created page with "'''pdbTempFactorSet''' is Eos's Command that that sets Temperature Factor to PDB file. == List of option == === Main option === <table border="1"> <tr>..."
New page
'''pdbTempFactorSet''' is [[Eos]]'s [[Command]] that that sets Temperature Factor to [[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>-r</td>
<td>Optional</td>
<td>Reference: [[ASCII]]</td>
<td>stdin</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[PDB]]</td>
<td>NULL</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>

===-r format===
<pre>
SequenceNo. SettingValueOfTemperatureFactor
.
.

</pre>
<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>by editor</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
ATOM 11 C THR A 2 -4.312 29.597 -3.441 1.00 16.63 C
ATOM 12 O THR A 2 -3.423 30.479 -3.406 1.00 17.08 O
ATOM 13 CB THR A 2 -3.707 27.952 -5.310 1.00 16.63 C
ATOM 14 OG1 THR A 2 -4.298 27.397 -6.486 1.00 20.57 O
ATOM 15 CG2 THR A 2 -3.318 26.861 -4.361 1.00 15.26 C
ATOM 16 N GLU A 3 -4.956 29.200 -2.361 1.00 16.48 N
ATOM 17 CA GLU A 3 -4.531 29.674 -1.062 1.00 19.32 C
ATOM 18 C GLU A 3 -4.016 28.444 -0.302 1.00 18.43 C
ATOM 19 O GLU A 3 -4.525 27.315 -0.502 1.00 18.03 O
ATOM 20 CB GLU A 3 -5.690 30.302 -0.312 1.00 21.18 C
ATOM 21 CG GLU A 3 -6.329 31.456 -1.109 1.00 26.05 C
ATOM 22 CD GLU A 3 -7.235 32.429 -0.346 1.00 28.96 C
ATOM 23 OE1 GLU A 3 -7.498 32.239 0.846 1.00 30.26 O
ATOM 24 OE2 GLU A 3 -7.662 33.416 -0.948 1.00 31.23 O
ATOM 25 N TYR A 4 -2.943 28.607 0.490 1.00 16.16 N
ATOM 26 CA TYR A 4 -2.465 27.513 1.336 1.00 15.13 C

...
</pre>
<br>

=== Option -r===
<div>execute by using following data.</div>
<pre>
1 11
3 33

</pre>
<br>

<div>-o's file by editor</div>
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00 11.00 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 11.00 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 11.00 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 11.00 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 11.00 0 C
ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 11.00 0 C
ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 11.00 0 S
ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00 11.00 0 C
ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 15.08 0 N
ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 16.71 0 C
ATOM 11 C THR A 2 -4.312 29.597 -3.441 1.00 16.63 0 C
ATOM 12 O THR A 2 -3.423 30.479 -3.406 1.00 17.08 0 O
ATOM 13 CB THR A 2 -3.707 27.952 -5.310 1.00 16.63 0 C
ATOM 14 OG1 THR A 2 -4.298 27.397 -6.486 1.00 20.57 0 O
ATOM 15 CG2 THR A 2 -3.318 26.861 -4.361 1.00 15.26 0 C
ATOM 16 N GLU A 3 -4.956 29.200 -2.361 1.00 33.00 0 N
ATOM 17 CA GLU A 3 -4.531 29.674 -1.062 1.00 33.00 0 C
ATOM 18 C GLU A 3 -4.016 28.444 -0.302 1.00 33.00 0 C
ATOM 19 O GLU A 3 -4.525 27.315 -0.502 1.00 33.00 0 O
ATOM 20 CB GLU A 3 -5.690 30.302 -0.312 1.00 33.00 0 C
ATOM 21 CG GLU A 3 -6.329 31.456 -1.109 1.00 33.00 0 C
ATOM 22 CD GLU A 3 -7.235 32.429 -0.346 1.00 33.00 0 C
ATOM 23 OE1 GLU A 3 -7.498 32.239 0.846 1.00 33.00 0 O
ATOM 24 OE2 GLU A 3 -7.662 33.416 -0.948 1.00 33.00 0 O
ATOM 25 N TYR A 4 -2.943 28.607 0.490 1.00 16.16 0 N
ATOM 26 CA TYR A 4 -2.465 27.513 1.336 1.00 15.13 0 C

...
</pre>
<br>