mrcImageMappingtoPdb - Revision history

Kinoshita: Created page with "'''mrcImageMappingtoPdb''' is Eos's Command that assigns PDB file to the value of mrcimage. == List of option == === Main option === ..."
2014-07-27T23:59:19Z
Created page with "'''mrcImageMappingtoPdb''' is Eos's Command that assigns PDB file to the value of mrcimage. == List of option == === Main option === <table border="1">..."
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'''mrcImageMappingtoPdb''' is [[Eos]]'s [[Command]] that assigns [[PDB]] file to the value of [[mrcimage]].

== 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:[[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-ipdb</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>-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 ==
=== Input file's image ===
<div>[[:Media:Input-121P.pdb.zip|-i file]]'s image</div>
<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>

<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 641 CE2 PHE A 82 14.813 20.233 17.454 1.00 9.42 C
ATOM 642 CZ PHE A 82 14.402 19.552 16.322 1.00 10.16 C
ATOM 643 N ALA A 83 13.147 24.056 19.362 1.00 8.77 N
ATOM 644 CA ALA A 83 14.417 24.796 19.338 1.00 10.28 C
ATOM 645 C ALA A 83 15.540 23.828 19.671 1.00 9.49 C
ATOM 646 O ALA A 83 15.406 23.022 20.607 1.00 8.40 O
ATOM 647 CB ALA A 83 14.390 25.939 20.368 1.00 9.40 C
ATOM 648 N ILE A 84 16.654 23.891 18.940 1.00 10.76 N
ATOM 649 CA ILE A 84 17.724 22.889 19.092 1.00 12.94 C
ATOM 650 C ILE A 84 18.491 22.984 20.427 1.00 14.25 C

...

HETATM 1547 O HOH A 359 -4.312 38.871 -6.155 1.00 34.57 O
HETATM 1548 O HOH A 360 4.226 11.323 17.624 1.00 41.71 O
HETATM 1549 O HOH A 361 22.341 27.132 10.735 1.00 24.44 O
HETATM 1550 O HOH A 362 14.256 10.610 17.524 1.00 40.11 O
HETATM 1551 O HOH A 363 26.542 18.231 27.104 1.00 35.00 O

...
</pre>
<br>

<div>[[Media:Input-121P1.mrc|-p file]]'s image</div>
<table>
<tr>
<td><p align="Center">[[File:Input-121P1.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Input1-121P1.png]]<br>
yz-plane<br></p>
</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (0, 0, 0)<br>
3500.79 (24, 28, 5)<br>
88.3104<br>
323.414<br>
0.914753<br></p>
</td>
</tr>
</table>
<br>

=== Example of options only essential ===
<div>-o 's data</div>
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00-3090.49 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00485.63 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 0.00 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 0.00 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 0.00 0 C

...

ATOM 641 CE2 PHE A 82 14.813 20.233 17.454 1.00132.76 0 C
ATOM 642 CZ PHE A 82 14.402 19.552 16.322 1.00505.69 0 C
ATOM 643 N ALA A 83 13.147 24.056 19.362 1.00160058.34 0 N
ATOM 644 CA ALA A 83 14.417 24.796 19.338 1.00166476.73 0 C
ATOM 645 C ALA A 83 15.540 23.828 19.671 1.00188632.66 0 C
ATOM 646 O ALA A 83 15.406 23.022 20.607 1.00241683.72 0 O
ATOM 647 CB ALA A 83 14.390 25.939 20.368 1.0053644.95 0 C
ATOM 648 N ILE A 84 16.654 23.891 18.940 1.0030992.45 0 N
ATOM 649 CA ILE A 84 17.724 22.889 19.092 1.0017561.63 0 C
ATOM 650 C ILE A 84 18.491 22.984 20.427 1.0011657.85 0 C

...

HETATM 1547 O HOH A 359 -4.312 38.871 -6.155 1.00 0.00 0 O
HETATM 1548 O HOH A 360 4.226 11.323 17.624 1.00 0.00 0 O
HETATM 1549 O HOH A 361 22.341 27.132 10.735 1.0035609.15 0 O
HETATM 1550 O HOH A 362 14.256 10.610 17.524 1.00307.89 0 O
HETATM 1551 O HOH A 363 26.542 18.231 27.104 1.0093878.00 0 O

...
</pre>
<br>