View source for mrcImage2pdb

'''mrcImage2pdb''' is [[Eos]]'s [[Command]] that converts [[mrcImage]] file to [[PDB]] file. Output [[PDB]] file consists of all alpha carbon.


== 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>-o</td> 
				<td>Essential</td> 
				<td>Output: [[PDB]]</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-hi</td> 
				<td>Optional</td> 
				<td>Value of high threshold. Default is the MAX.</td> 
				<td>0</td> 
			</tr> 
			<tr> 
				<td>-lo</td> 
				<td>Optional</td> 
				<td>Value of low threshold. Default is the MIN.(Only m=0, 1)</td> 
				<td>0</td> 
			</tr> 
			<tr> 
				<td>-L</td> 
				<td>Optional</td> 
				<td>Atoms are on lattice points. (Only m=2 - 4)</td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>-Skip</td> 
				<td>Optional</td> 
				<td>Skip atoms.</td> 
				<td>1</td> 
			</tr> 
			<tr> 
				<td>-R</td> 
				<td>Optional</td> 
				<td>Random</td> 
				<td>0</td> 
			</tr> 
			<tr> 
				<td>-d</td> 
				<td>Optional</td> 
				<td>Delta to select atoms to avoid too much concentration.<br>
					(Range: 0 - 0.5) (Only m=2 - 4)</td> 
				<td>0.1</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>5</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>One atom for one boxel.</td> 
			</tr> 
			<tr> 
				<td>1</td> 
				<td>Eight atoms for one boxel.</td> 
			</tr> 
			<tr> 
				<td>2</td> 
				<td>On the surface of high threshold. Atoms few.</td> 
			</tr> 
			<tr> 
				<td>3</td> 
				<td>On the surface of high threshold. Atoms medium.</td> 
			</tr> 
			<tr> 
				<td>4</td> 
				<td>On the surface of high threshold. Atoms many</td> 
			</tr> 
			<tr> 
				<td>5</td> 
				<td>(Default) : On the surface of high threshold. Mesh mode.</td> 
			</tr> 
		</table> 
<br>

== Execution example ==
===[[Media:Input-ThickFilaments1.mrc | Input file]] image===
	<table> 
		<tr> 
			<td><p align="Center">[[File:Input-mrcImageHelicalAveraging.png]]<br>
				xy-plane<br></p> 
			</td>  
			<td><p align="Center">[[File:Input1-mrcImageHelicalAveraging.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> 
				4.07334 (34, 9, 75)<br> 
				0.00164516<br> 
				0.0572113<br> 
				8.29149e-05<br></p> 
			</td> 
		</tr> 
	</table> 
<br>

=== Option -hi===
====Case: hi=1e-3==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-hi-mrcImage2pdb.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">2.708889e+02    2.744812e+02    3.518376e+02<br> 
				3.279044e+02 <br> 
				205.11     206.48     252.16<br></p>
			</td> 
	</table>
<br>

=== Option -Skip===
====Case: Skip=10, hi=1e-3==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-Skip-mrcImage2pdb.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">2.617321e+02    2.673613e+02    3.468850e+02<br> 
				3.360901e+02 <br> 
				214.27     208.64     253.12<br></p>
			</td> 
	</table>
<br>

=== Option -R===
====Case: R=10, hi=1e-3==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-R-mrcImage2pdb.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">2.707916e+02    2.743434e+02    3.520507e+02<br> 
				3.468584e+02 <br> 
				225.08     226.31     271.93<br></p>
			</td> 
	</table>
<br>

=== Option -m===
====Case: m=0==== 
=====Case: No other settings=====
	<table> 
		<tr> 
			<td>[[File:Outdata-m0-mrcImage2pdb.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">2.703961e+02    2.755795e+02    3.510611e+02<br> 
				3.218664e+02 <br> 
				201.60     203.58     248.94<br></p>
			</td> 
	</table>
<br>

====Case: lo=2====
	<table> 
		<tr> 
			<td>[[File:Outdata-m0lo-mrcImage2pdb.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">2.782154e+02    2.705846e+02    3.485538e+02<br> 
				3.201251e+02<br> 
				206.22     201.42     251.45<br></p>
			</td> 
	</table>
<br>

====Case: m=1==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-m1-mrcImage2pdb.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">2.703961e+02    2.755795e+02    3.510611e+02<br> 
				3.251428e+02<br> 
				203.60     205.58     250.94<br></p>
			</td> 
	</table>
<br>

====Case: m=2, hi=1e-3==== 
=====Case: No other settings=====
	<table> 
		<tr> 
			<td>[[File:Outdata-m2-mrcImage2pdb.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">2.705893e+02    2.743574e+02    3.518459e+02<br> 
				3.277470e+02<br> 
				209.41     210.36     256.15<br></p>
			</td> 
	</table>
<br>

=====Option -L=====
	<table> 
		<tr> 
			<td><p align="Center">[[File:Outdata-m2L-mrcImage2pdb.png]]<br>
				Blue: With -L Brown: Without -L<br></p> 
			</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">2.706073e+02    2.744103e+02    3.517186e+02<br> 
				3.247068e+02<br> 
				205.39     206.41     252.28<br></p>
			</td> 
	</table>
<br>

=====Case: d=1e-3=====
	<table> 
		<tr> 
			<td>[[File:Outdata-m2d-mrcImage2pdb.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">2.704110e+02    2.745547e+02    3.517133e+02<br> 
				3.278861e+02<br> 
				209.59     210.55     256.28<br></p>
			</td> 
	</table>
<br>

====Case: m=3, hi=1e-3==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-m3-mrcImage2pdb.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">2.706223e+02    2.741782e+02    3.517764e+02<br> 
				3.322329e+02 <br> 
				209.37     210.18     256.22<br></p>
			</td> 
	</table>
<br>

====Case: m=4, hi=1e-3==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-m4-mrcImage2pdb.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">2.707323e+02    2.740721e+02    3.517465e+02<br> 
				3.347665e+02 <br> 
				209.26     210.07     256.25<br></p>
			</td> 
	</table>
<br>