Kinoshita: Created page with "'''mrcImage2pdb''' is Eos's Command that converts mrcImage file to PDB file. Output PDB file consists of all alpha carbon. == List of option == === Main ..."

2014-07-16T02:39:20Z

Created page with "'''mrcImage2pdb''' is Eos's Command that converts mrcImage file to PDB file. Output PDB file consists of all alpha carbon. == List of option == === Main ..."

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'''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. 
(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>
 

=== -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>
 

== Execution example ==
===[[Media:Input-ThickFilaments1.mrc | Input file]] image===
<table>
<tr>
<td>[[File:Input-mrcImageHelicalAveraging.png]] 
xy-plane 
</td>
<td>[[File:Input1-mrcImageHelicalAveraging.png]] 
yz-plane 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
4.07334 (34, 9, 75) 
0.00164516 
0.0572113 
8.29149e-05 
</td>
</tr>
</table>
 

=== Option -hi===
====Case: hi=1e-3====
<table>
<tr>
<td>[[File:Outdata-hi-mrcImage2pdb.png]]</td>
<td>Gravity Centre(CA) 
Atom far from Centre(CA) 
Atom far from Centre(CA, Axis) 
</td>
<td>2.708889e+02 2.744812e+02 3.518376e+02 
3.279044e+02 
205.11 206.48 252.16 
</td>
</table>
 

=== Option -Skip===
====Case: Skip=10, hi=1e-3====
<table>
<tr>
<td>[[File:Outdata-Skip-mrcImage2pdb.png]]</td>
<td>Gravity Centre(CA) 
Atom far from Centre(CA) 
Atom far from Centre(CA, Axis) 
</td>
<td>2.617321e+02 2.673613e+02 3.468850e+02 
3.360901e+02 
214.27 208.64 253.12 
</td>
</table>
 

=== Option -R===
====Case: R=10, hi=1e-3====
<table>
<tr>
<td>[[File:Outdata-R-mrcImage2pdb.png]]</td>
<td>Gravity Centre(CA) 
Atom far from Centre(CA) 
Atom far from Centre(CA, Axis) 
</td>
<td>2.707916e+02 2.743434e+02 3.520507e+02 
3.468584e+02 
225.08 226.31 271.93 
</td>
</table>
 

=== Option -m===
====Case: m=0====
=====Case: No other settings=====
<table>
<tr>
<td>[[File:Outdata-m0-mrcImage2pdb.png]]</td>
<td>Gravity Centre(CA) 
Atom far from Centre(CA) 
Atom far from Centre(CA, Axis) 
</td>
<td>2.703961e+02 2.755795e+02 3.510611e+02 
3.218664e+02 
201.60 203.58 248.94 
</td>
</table>
 

====Case: lo=2====
<table>
<tr>
<td>[[File:Outdata-m0lo-mrcImage2pdb.png]]</td>
<td>Gravity Centre(CA) 
Atom far from Centre(CA) 
Atom far from Centre(CA, Axis) 
</td>
<td>2.782154e+02 2.705846e+02 3.485538e+02 
3.201251e+02 
206.22 201.42 251.45 
</td>
</table>
 

====Case: m=1====
<table>
<tr>
<td>[[File:Outdata-m1-mrcImage2pdb.png]]</td>
<td>Gravity Centre(CA) 
Atom far from Centre(CA) 
Atom far from Centre(CA, Axis) 
</td>
<td>2.703961e+02 2.755795e+02 3.510611e+02 
3.251428e+02 
203.60 205.58 250.94 
</td>
</table>
 

====Case: m=2, hi=1e-3====
=====Case: No other settings=====
<table>
<tr>
<td>[[File:Outdata-m2-mrcImage2pdb.png]]</td>
<td>Gravity Centre(CA) 
Atom far from Centre(CA) 
Atom far from Centre(CA, Axis) 
</td>
<td>2.705893e+02 2.743574e+02 3.518459e+02 
3.277470e+02 
209.41 210.36 256.15 
</td>
</table>
 

=====Option -L=====
<table>
<tr>
<td>[[File:Outdata-m2L-mrcImage2pdb.png]] 
Blue: With -L Brown: Without -L 
</td>
<td>Gravity Centre(CA) 
Atom far from Centre(CA) 
Atom far from Centre(CA, Axis) 
</td>
<td>2.706073e+02 2.744103e+02 3.517186e+02 
3.247068e+02 
205.39 206.41 252.28 
</td>
</table>
 

=====Case: d=1e-3=====
<table>
<tr>
<td>[[File:Outdata-m2d-mrcImage2pdb.png]]</td>
<td>Gravity Centre(CA) 
Atom far from Centre(CA) 
Atom far from Centre(CA, Axis) 
</td>
<td>2.704110e+02 2.745547e+02 3.517133e+02 
3.278861e+02 
209.59 210.55 256.28 
</td>
</table>
 

====Case: m=3, hi=1e-3====
<table>
<tr>
<td>[[File:Outdata-m3-mrcImage2pdb.png]]</td>
<td>Gravity Centre(CA) 
Atom far from Centre(CA) 
Atom far from Centre(CA, Axis) 
</td>
<td>2.706223e+02 2.741782e+02 3.517764e+02 
3.322329e+02 
209.37 210.18 256.22 
</td>
</table>
 

====Case: m=4, hi=1e-3====
<table>
<tr>
<td>[[File:Outdata-m4-mrcImage2pdb.png]]</td>
<td>Gravity Centre(CA) 
Atom far from Centre(CA) 
Atom far from Centre(CA, Axis) 
</td>
<td>2.707323e+02 2.740721e+02 3.517465e+02 
3.347665e+02 
209.26 210.07 256.25 
</td>
</table>

mrcImage2pdb - Revision history

Kinoshita: Created page with "'''mrcImage2pdb''' is Eos's Command that converts mrcImage file to PDB file. Output PDB file consists of all alpha carbon. == List of option == === Main ..."