View source for mrcImageDisplayDensityAsTempFactor

'''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>