mrcImageDisplayDensityAsTempFactor - Revision history

Kinoshita: Created page with "'''mrcImageDisplayDensityAsTempFactor''' is Eos's Command that inserts the value of the image into PDB. == List of option == === Main option ===
2014-07-24T01:21:38Z
Created page with "'''mrcImageDisplayDensityAsTempFactor''' is Eos's Command that inserts the value of the image into PDB. == List of option == === Main option === <table border=..."
New page
'''mrcImageDisplayDensityAsTempFactor''' is [[Eos]]'s [[Command]] that inserts the value of the image into [[PDB]].

== 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>-p</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>-v</td>
<td>Optional</td>
<td>vaule to multiply density</td>
<td>1</td>
</tr>
<tr>
<td>-H</td>
<td>Optional</td>
<td>High Threshold</td>
<td>0.0</td>
</tr>
<tr>
<td>-L</td>
<td>Optional</td>
<td>Low Threshold</td>
<td>1.0</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 ==
=== Input file's image ===
<div>[[:Media:Input-121P.pdb.zip|-i data]]'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 data]]'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>Output</div>
<pre>
-7.176000 32.630001 -6.655000 1509.648804
-5.913000 31.927999 -6.676000 2213.066895
-5.903000 30.860001 -5.600000 2228.875000
-6.703000 30.881001 -4.654000 2064.481934
-4.712000 32.868999 -6.415000 1943.648804

...

14.813000 20.233000 17.454000 2143.264404
14.402000 19.552000 16.322001 1518.068115
13.147000 24.056000 19.362000 2450.569092
14.417000 24.796000 19.337999 1528.793213
15.540000 23.827999 19.671000 1766.275757
15.406000 23.021999 20.607000 1729.942139
14.390000 25.938999 20.368000 1603.061890
16.653999 23.891001 18.940001 2090.166992
17.724001 22.889000 19.091999 2350.993896
18.490999 22.983999 20.427000 1937.036377

...

-4.312000 38.870998 -6.155000 1683.501465
4.226000 11.323000 17.624001 1482.681030
22.341000 27.132000 10.735000 1622.591431
14.256000 10.610000 17.524000 1481.899658
26.542000 18.231001 27.104000 1683.129883
</pre>
<br>

<div>-o 's data</div>
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.001509.65 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.002213.07 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.002228.88 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.002064.48 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.001943.65 0 C

...

ATOM 641 CE2 PHE A 82 14.813 20.233 17.454 1.002143.26 0 C
ATOM 642 CZ PHE A 82 14.402 19.552 16.322 1.001518.07 0 C
ATOM 643 N ALA A 83 13.147 24.056 19.362 1.002450.57 0 N
ATOM 644 CA ALA A 83 14.417 24.796 19.338 1.001528.79 0 C
ATOM 645 C ALA A 83 15.540 23.828 19.671 1.001766.28 0 C
ATOM 646 O ALA A 83 15.406 23.022 20.607 1.001729.94 0 O
ATOM 647 CB ALA A 83 14.390 25.939 20.368 1.001603.06 0 C
ATOM 648 N ILE A 84 16.654 23.891 18.940 1.002090.17 0 N
ATOM 649 CA ILE A 84 17.724 22.889 19.092 1.002350.99 0 C
ATOM 650 C ILE A 84 18.491 22.984 20.427 1.001937.04 0 C

...

HETATM 1547 O HOH A 359 -4.312 38.871 -6.155 1.001683.50 0 O
HETATM 1548 O HOH A 360 4.226 11.323 17.624 1.001482.68 0 O
HETATM 1549 O HOH A 361 22.341 27.132 10.735 1.001622.59 0 O
HETATM 1550 O HOH A 362 14.256 10.610 17.524 1.001481.90 0 O
HETATM 1551 O HOH A 363 26.542 18.231 27.104 1.001683.13 0 O

...
</pre>
<br>

=== Option -v===
====Case: v=2====
<div>-o 's data</div>
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.003019.30 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.004426.13 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.004457.75 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.004128.96 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.003887.30 0 C

...

ATOM 641 CE2 PHE A 82 14.813 20.233 17.454 1.004286.53 0 C
ATOM 642 CZ PHE A 82 14.402 19.552 16.322 1.003036.14 0 C
ATOM 643 N ALA A 83 13.147 24.056 19.362 1.004901.14 0 N
ATOM 644 CA ALA A 83 14.417 24.796 19.338 1.003057.59 0 C
ATOM 645 C ALA A 83 15.540 23.828 19.671 1.003532.55 0 C
ATOM 646 O ALA A 83 15.406 23.022 20.607 1.003459.88 0 O
ATOM 647 CB ALA A 83 14.390 25.939 20.368 1.003206.12 0 C
ATOM 648 N ILE A 84 16.654 23.891 18.940 1.004180.33 0 N
ATOM 649 CA ILE A 84 17.724 22.889 19.092 1.004701.99 0 C
ATOM 650 C ILE A 84 18.491 22.984 20.427 1.003874.07 0 C

...

HETATM 1547 O HOH A 359 -4.312 38.871 -6.155 1.003367.00 0 O
HETATM 1548 O HOH A 360 4.226 11.323 17.624 1.002965.36 0 O
HETATM 1549 O HOH A 361 22.341 27.132 10.735 1.003245.18 0 O
HETATM 1550 O HOH A 362 14.256 10.610 17.524 1.002963.80 0 O
HETATM 1551 O HOH A 363 26.542 18.231 27.104 1.003366.26 0 O

...
</pre>
<br>

=== Option -H===
====Case: H=1999====
<div>-o 's data</div>
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.001509.65 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.001999.00 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.001999.00 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.001999.00 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.001943.65 0 C

...

ATOM 641 CE2 PHE A 82 14.813 20.233 17.454 1.001999.00 0 C
ATOM 642 CZ PHE A 82 14.402 19.552 16.322 1.001518.07 0 C
ATOM 643 N ALA A 83 13.147 24.056 19.362 1.001999.00 0 N
ATOM 644 CA ALA A 83 14.417 24.796 19.338 1.001528.79 0 C
ATOM 645 C ALA A 83 15.540 23.828 19.671 1.001766.28 0 C
ATOM 646 O ALA A 83 15.406 23.022 20.607 1.001729.94 0 O
ATOM 647 CB ALA A 83 14.390 25.939 20.368 1.001603.06 0 C
ATOM 648 N ILE A 84 16.654 23.891 18.940 1.001999.00 0 N
ATOM 649 CA ILE A 84 17.724 22.889 19.092 1.001999.00 0 C
ATOM 650 C ILE A 84 18.491 22.984 20.427 1.001937.04 0 C

...

HETATM 1547 O HOH A 359 -4.312 38.871 -6.155 1.001683.50 0 O
HETATM 1548 O HOH A 360 4.226 11.323 17.624 1.001482.68 0 O
HETATM 1549 O HOH A 361 22.341 27.132 10.735 1.001622.59 0 O
HETATM 1550 O HOH A 362 14.256 10.610 17.524 1.001481.90 0 O
HETATM 1551 O HOH A 363 26.542 18.231 27.104 1.001683.13 0 O

...
</pre>
<br>

=== Option -L===
====Case: L=1999====
<div>-o 's data</div>
<pre>
...

ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.001999.00 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.002213.07 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.002228.88 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.002064.48 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.001999.00 0 C

...

ATOM 641 CE2 PHE A 82 14.813 20.233 17.454 1.002143.26 0 C
ATOM 642 CZ PHE A 82 14.402 19.552 16.322 1.001999.00 0 C
ATOM 643 N ALA A 83 13.147 24.056 19.362 1.002450.57 0 N
ATOM 644 CA ALA A 83 14.417 24.796 19.338 1.001999.00 0 C
ATOM 645 C ALA A 83 15.540 23.828 19.671 1.001999.00 0 C
ATOM 646 O ALA A 83 15.406 23.022 20.607 1.001999.00 0 O
ATOM 647 CB ALA A 83 14.390 25.939 20.368 1.001999.00 0 C
ATOM 648 N ILE A 84 16.654 23.891 18.940 1.002090.17 0 N
ATOM 649 CA ILE A 84 17.724 22.889 19.092 1.002350.99 0 C
ATOM 650 C ILE A 84 18.491 22.984 20.427 1.001999.00 0 C

...

HETATM 1547 O HOH A 359 -4.312 38.871 -6.155 1.001999.00 0 O
HETATM 1548 O HOH A 360 4.226 11.323 17.624 1.001999.00 0 O
HETATM 1549 O HOH A 361 22.341 27.132 10.735 1.001999.00 0 O
HETATM 1550 O HOH A 362 14.256 10.610 17.524 1.001999.00 0 O
HETATM 1551 O HOH A 363 26.542 18.231 27.104 1.001999.00 0 O

...
</pre>
<br>