pdbHelix - Revision history

Kinoshita: Created page with "'''pdbHelix''' is Eos's Command that creates helix symmetrical PDB of mrcImage file from a PDB file. == List of option == === Main option ===
2014-08-08T00:27:11Z
Created page with "'''pdbHelix''' is Eos's Command that creates helix symmetrical PDB of mrcImage file from a PDB file. == List of option == === Main option === <table bo..."
New page
'''pdbHelix''' is [[Eos]]'s [[Command]] that creates helix symmetrical [[PDB]] of [[mrcImage]] file from a [[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>Optional</td>
<td>Output: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-3</td>
<td>Optional</td>
<td>Output: [[mrcImage]](3D)</td>
<td>NULL</td>
</tr>

<tr>
<td>-2</td>
<td>Optional</td>
<td>Output: [[mrcImage]](2D y-zProjection)</td>
<td>NULL</td>
</tr>
<tr>
<td>-d</td>
<td>Optional</td>
<td>delta[A]</td>
<td>5</td>
</tr>
<tr>
<td>-p</td>
<td>Essential</td>
<td>deltaPhi</td>
<td>165</td>
</tr>
<tr>
<td>-dp</td>
<td>Optional</td>
<td>deltaDeltaPhi</td>
<td>5</td>
</tr>
<tr>
<td>-z</td>
<td>Essential</td>
<td>deltaz</td>
<td>5</td>
</tr>
<tr>
<td>-n</td>
<td>Essential</td>
<td>NumberOfMolecules</td>
<td>1</td>
</tr>
<tr>
<td>-nx</td>
<td>Optional</td>
<td>Pixel x</td>
<td>1</td>
</tr>
<tr>
<td>-ny</td>
<td>Optional</td>
<td>Pixel y</td>
<td>1</td>
</tr>
<tr>
<td>-nz</td>
<td>Optional</td>
<td>Pixel z</td>
<td>1</td>
</tr>
<tr>
<td>-Sx</td>
<td>Optional</td>
<td>Start x: [A]</td>
<td>0.0</td>
</tr>
<tr>
<td>-Sy</td>
<td>Optional</td>
<td>Start y: [A]</td>
<td>0.0</td>
</tr>
<tr>
<td>-Sz</td>
<td>Optional</td>
<td>Start z: [A]</td>
<td>0.0</td>
</tr>
<tr>
<td>-w</td>
<td>Optional</td>
<td>Weight</td>
<td>1.0</td>
</tr>
<tr>
<td>-dx</td>
<td>Optional</td>
<td>dx</td>
<td>2.5</td>
</tr>
<tr>
<td>-dy</td>
<td>Optional</td>
<td>dy</td>
<td>2.5</td>
</tr>
<tr>
<td>-dz</td>
<td>Optional</td>
<td>dz</td>
<td>2.5</td>
</tr>
<tr>
<td>-startn</td>
<td>Optional</td>
<td>start molecule's index</td>
<td>0</td>
</tr>
<tr>
<td>-startC</td>
<td>Optional</td>
<td>Start chain ID</td>
<td>A</td>
</tr>
<tr>
<td>-deltaSeq</td>
<td>Optional</td>
<td></td>
<td>1000</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>

<div>[[PDB]] data (a 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

...

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>

=== Case: Options only essential ===
====Case: p=165, z=5, n=10====
<div>[[PDB]]'s image</div>
<table>
<tr>
<td>[[File:Outdata-pdbHelix.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">-3.945663e-01 2.493555e+00 3.439075e+01<br>
5.952335e+01<br>
49.44 48.84 50.54<br></p>
</td>
</tr>
</table>

<div>[[PDB]] data (a part)</div>
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00 14.06 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 17.27 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 16.41 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 16.12 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 17.94 0 C

...

HETATM 1547 O HOH A 359 -4.312 38.871 -6.155 1.00 34.57 0 O
HETATM 1548 O HOH A 360 4.226 11.323 17.624 1.00 41.71 0 O
HETATM 1549 O HOH A 361 22.341 27.132 10.735 1.00 24.44 0 O
HETATM 1550 O HOH A 362 14.256 10.610 17.524 1.00 40.11 0 O
HETATM 1551 O HOH A 363 26.542 18.231 27.104 1.00 35.00 0 O

...

ATOM 1 N MET B 1 -1.514 -33.375 -1.655 1.00 14.06 0 N
ATOM 2 CA MET B 1 -2.552 -32.370 -1.676 1.00 17.27 0 C
ATOM 3 C MET B 1 -2.285 -31.336 -0.600 1.00 16.41 0 C
ATOM 4 O MET B 1 -1.518 -31.564 0.346 1.00 16.12 0 O
ATOM 5 CB MET B 1 -3.956 -32.969 -1.415 1.00 17.94 0 C

...

HETATM 1547 O HOH B 359 -5.895 -38.663 -1.155 1.00 34.57 0 O
HETATM 1548 O HOH B 360 -7.013 -9.843 22.624 1.00 41.71 0 O
HETATM 1549 O HOH B 361 -28.602 -20.425 15.735 1.00 24.44 0 O
HETATM 1550 O HOH B 362 -16.516 -6.559 22.524 1.00 40.11 0 O
HETATM 1551 O HOH B 363 -30.356 -10.740 32.104 1.00 35.00 0 O

...

HETATM 1547 O HOH J 359 -30.535 24.437 38.845 1.00 34.57 0 O
HETATM 1548 O HOH J 360 -5.018 10.995 62.624 1.00 41.71 0 O
HETATM 1549 O HOH J 361 -3.388 34.983 55.735 1.00 24.44 0 O
HETATM 1550 O HOH J 362 2.578 17.583 62.524 1.00 40.11 0 O
HETATM 1551 O HOH J 363 5.877 31.659 72.104 1.00 35.00 0 O

...
</pre>
<br>

<div>[[mrcImage]](3D)'s image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata3-pdbHelix.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata4-pdbHelix.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>
7 (26, 47, 0)<br>
0.144624<br>
0.572148<br>
0.00195444<br></p>
</td>
</tr>
</table>

<div>[[mrcImage]](2D y-zProjection)'s image</div>
<table>
<tr>
<td>[[File:Outdata2-pdbHelix.png]]</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>
63 (35, 6, 0)<br>
9.93639<br>
14.2042<br>
0.403048<br></p>
</td>
</tr>
</table>
<br>

<div>In the following, Setting at p=165, z=5, n=10</div>
=== Option -w===
====Case: w=100====
<div>[[PDB]]'s image</div>
<table>
<tr>
<td>[[File:Outdata-w-pdbHelix.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">-3.945663e-01 2.493555e+00 3.439075e+01<br>
5.952335e+01<br>
49.44 48.84 50.54<br></p>
</td>
</tr>
</table>

<div>[[mrcImage]](3D)'s image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata3-w-pdbHelix.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata4-w-pdbHelix.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>
700 (26, 47, 0)<br>
14.4624<br>
57.2148<br>
0.195444<br></p>
</td>
</tr>
</table>
<br>

=== Option -dp===
====Case: dp=30====
<div>[[PDB]]'s image</div>
<table>
<tr>
<td>[[File:Outdata-dp-pdbHelix.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">-1.673933e+00 3.870905e+00 3.439075e+01<br>
6.023098e+01 <br>
50.70 51.34 50.54<br></p>
</td>
</tr>
</table>

<div>[[mrcImage]](3D)'s image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata3-dp-pdbHelix.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata4-dp-pdbHelix.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>
8 (31, 25, 4)<br>
0.144624<br>
0.584935<br>
0.00199812<br></p>
</td>
</tr>
</table>
<br>

=== Option -nx, -ny, -nz===
====Case: nx=100, ny=100, nz=100====
=====Case: No other settings=====
<div>[[PDB]]'s image</div>
<table>
<tr>
<td>[[File:Outdata-nxnynz-pdbHelix.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">-3.945663e-01 2.493555e+00 3.439075e+01<br>
5.952335e+01 <br>
49.44 48.84 50.54<br></p>
</td>
</tr>
</table>

<div>[[mrcImage]](3D)'s image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata3-nxnynz-pdbHelix.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata4-nxnynz-pdbHelix.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>
63 (35, 6, 0)<br>
1.4243<br>
6.15131<br>
0.0615131<br></p>
</td>
</tr>
</table>
<br>

=====Case: Sx=-50, Sy=-50, Sz=-10=====
<div>[[PDB]]'s image</div>
<table>
<tr>
<td>[[File:Outdata-SxSySz-pdbHelix.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">-3.945663e-01 2.493555e+00 3.439075e+01<br>
5.952335e+01<br>
49.44 48.84 50.54<br></p>
</td>
</tr>
</table>

<div>[[mrcImage]](3D)'s image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata3-SxSySz-pdbHelix.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata4-SxSySz-pdbHelix.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>
7 (30, 31, 12)<br>
0.015491<br>
0.189655<br>
0.000189655<br></p>
</td>
</tr>
</table>
<br>

=====Case: dx=1, dy=1, dz=1, Sx=-50, Sy=-50, Sz=-10=====
<div>[[PDB]]'s image</div>
<table>
<tr>
<td>[[File:Outdata-dxdydz-pdbHelix.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">-3.945663e-01 2.493555e+00 3.439075e+01<br>
5.952335e+01<br>
49.44 48.84 50.54<br></p>
</td>
</tr>
</table>

<div>[[mrcImage]](3D)'s image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata3-dxdydz-pdbHelix.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata4-dxdydz-pdbHelix.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>
3 (70, 49, 38)<br>
0.015491<br>
0.125423<br>
0.000125423<br></p>
</td>
</tr>
</table>
<br>

=== Option -startn===
====Case: startn=5====
<div>[[PDB]]'s image</div>
<table>
<tr>
<td>[[File:Outdata-startn-pdbHelix.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">-2.306476e+00 -1.026480e+00 5.939075e+01<br>
5.952301e+01<br>
51.35 49.89 50.54<br></p>
</td>
</tr>
</table>

<div>[[mrcImage]](3D)'s image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata3-startn-pdbHelix.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata4-startn-pdbHelix.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>
7 (25, 24, 0)<br>
0.140522<br>
0.565188<br>
0.00190309<br></p>
</td>
</tr>
</table>
<br>

=== Option -deltaSeq===
====Case: deltaSeq=1====
<div>[[PDB]] data (a part)</div>
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00 14.06 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 17.27 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 16.41 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 16.12 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 17.94 0 C

...

HETATM 1547 O HOH A 359 -4.312 38.871 -6.155 1.00 34.57 0 O
HETATM 1548 O HOH A 360 4.226 11.323 17.624 1.00 41.71 0 O
HETATM 1549 O HOH A 361 22.341 27.132 10.735 1.00 24.44 0 O
HETATM 1550 O HOH A 362 14.256 10.610 17.524 1.00 40.11 0 O
HETATM 1551 O HOH A 363 26.542 18.231 27.104 1.00 35.00 0 O

...

ATOM 1 N MET B 2 -1.514 -33.375 -1.655 1.00 14.06 0 N
ATOM 2 CA MET B 2 -2.552 -32.370 -1.676 1.00 17.27 0 C
ATOM 3 C MET B 2 -2.285 -31.336 -0.600 1.00 16.41 0 C
ATOM 4 O MET B 2 -1.518 -31.564 0.346 1.00 16.12 0 O
ATOM 5 CB MET B 2 -3.956 -32.969 -1.415 1.00 17.94 0 C

...

HETATM 1547 O HOH B 360 -5.895 -38.663 -1.155 1.00 34.57 0 O
HETATM 1548 O HOH B 361 -7.013 -9.843 22.624 1.00 41.71 0 O
HETATM 1549 O HOH B 362 -28.602 -20.425 15.735 1.00 24.44 0 O
HETATM 1550 O HOH B 363 -16.516 -6.559 22.524 1.00 40.11 0 O
HETATM 1551 O HOH B 364 -30.356 -10.740 32.104 1.00 35.00 0 O

...

HETATM 1547 O HOH J 368 -30.535 24.437 38.845 1.00 34.57 0 O
HETATM 1548 O HOH J 369 -5.018 10.995 62.624 1.00 41.71 0 O
HETATM 1549 O HOH J 370 -3.388 34.983 55.735 1.00 24.44 0 O
HETATM 1550 O HOH J 371 2.578 17.583 62.524 1.00 40.11 0 O
HETATM 1551 O HOH J 372 5.877 31.659 72.104 1.00 35.00 0 O

...
</pre>
<br>