pdb2mrc - Revision history

Kinoshita: /* Main option */

2014-08-07T02:51:01Z

‎Main option

Kinoshita: Created page with "'''pdb2mrc''' is Eos's Command that converts from PDB file to mrcImage file by calculation of density. == List of option == === Main option ===
2014-08-07T02:03:21Z
Created page with "'''pdb2mrc''' is Eos's Command that converts from PDB file to mrcImage file by calculation of density. == List of option == === Main option === <table border..."
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'''pdb2mrc''' is [[Eos]]'s [[Command]] that converts from [[PDB]] file to [[mrcImage]] file by calculation of density.

== List of option ==
=== Main option ===
<table border="1">
<div align="left">
<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: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-nx</td>
<td>Optional</td>
<td>Width x of Output image</td>
<td>1</td>
</tr>
<tr>
<td>-ny</td>
<td>Optional</td>
<td>Width y of Output image</td>
<td>1</td>
</tr>
<tr>
<td>-nz</td>
<td>Optional</td>
<td>Width z of Output image</td>
<td>1</td>
</tr>
<tr>
<td>-Sx</td>
<td>Optional</td>
<td>Reading start position x</td>
<td>0.0</td>
</tr>
<tr>
<td>-Sy</td>
<td>Optional</td>
<td>Reading start position y</td>
<td>0.0</td>
</tr>
<tr>
<td>-Sz</td>
<td>Optional</td>
<td>Reading start position z</td>
<td>0.0</td>
</tr>
<tr>
<td>-dx</td>
<td>Optional</td>
<td>Width of x per 1pixel</td>
<td>2.5</td>
</tr>
<tr>
<td>-dy</td>
<td>Optional</td>
<td>Width of y per 1pixel</td>
<td>2.5</td>
</tr>
<tr>
<td>-dz</td>
<td>Optional</td>
<td>Width of z per 1pixel</td>
<td>2.5</td>
</tr>
<tr>
<td>-w</td>
<td>Optional</td>
<td>Weight</td>
<td>1.0</td>
</tr>
<tr>
<td>-sig</td>
<td>Optional</td>
<td>Radius of Atom</td>
<td>0.0</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>
</div>
</table>
<br>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Gaussian</td>
</tr>
<tr>
<td>1</td>
<td>WentzelAtomModel</td>
</tr>
</table>
<br>

== Execution example ==
=== [[:Media:Input-121P.pdb.zip |Input file]]'s image ===
[[file:121p.png]]<br>
by [[pdbInfo]]<br>
[[file:121p-Info.png]]
<br>
<br>

===Input data===
<div>Use the options as the object falls within image.<br>
In the case of this Input file, set the options as the following.<br></div>
<table border="1">
<tr>
<td>-nx</td>
<td>100</td>
</tr>
<tr>
<td>-ny</td>
<td>100</td>
</tr>
<tr>
<td>-nz</td>
<td>1</td>
</tr>
<tr>
<td>-Sx</td>
<td>-18</td>
</tr>
<tr>
<td>-Sy</td>
<td>-1</td>
</tr>
<tr>
<td>-Sz</td>
<td>0.5</td>
</tr>
<tr>
<td>-dx</td>
<td>0.5</td>
</tr>
<tr>
<td>-dy</td>
<td>0.5</td>
</tr>
<tr>
<td>-dz</td>
<td>60</td>
</tr>
</table>
<br>

=== Option -m===
====Case: m=0====
<table>
<tr>
<td>[[file:121p.m3.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
Sum</p>
</td>
<td><p align="left">0<br>
4<br>
0.1364<br>
0.39089<br>
0.0039089<br>
1364</p>
</td>
</tr>
</table>
<br>

====Case: m=1====
<table>
<tr>
<td>[[file:121p.m2.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
Sum</p>
</td>
<td><p align="left">0<br>
9516.95<br>
1100.45<br>
1467.25<br>
14.6725<br>
1.10045e+07</p>
</td>
</tr>
</table>
<br>

=== Option -w ===
====Case: w=10====
<br>
image data before setting option<br>
[[file:121p.m5.info.png]]<br>
<br>
image data after setting option<br>
[[file:121p.m5.info2.png]]
<br>
<br>

=== Option -sig ===
====Case: sig=1====
<table>
<tr>
<td>[[file:121p.m4.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
Sum</p>
</td>
<td><p align="left">0<br>
0.251258<br>
0.0430626<br>
0.0499095<br>
0.000499095<br>
430.626</p>
</td>
</tr>
</table>
<br>