pdbRhoFit - Revision history

Kinoshita: Created page with "'''pdbRhoFit''' is Eos's Command. == List of option == === Main option ===
2014-08-08T02:52:15Z

Created page with "'''pdbRhoFit''' is Eos's Command. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essential/Optional</th> <t..."

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'''pdbRhoFit''' is [[Eos]]'s [[Command]].

== 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>-ipdb</td>
<td>Essential</td>
<td>Input: [[PDB]] (atom model)</td>
<td>NULL</td>
</tr>
<tr>
<td>-imrc</td>
<td>Essential</td>
<td>Input: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-omrc</td>
<td>Essential</td>
<td>Output: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-otxt</td>
<td>Optional</td>
<td>Output: [[ASCII]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-opar</td>
<td>Optional</td>
<td>Output: [[ASCII]](Parameter)</td>
<td>stdout</td>
</tr>
<tr>
<td>-opdb</td>
<td>Optional</td>
<td>Output: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-xmin</td>
<td>Optional</td>
<td>xmin</td>
<td>0</td>
</tr>
<tr>
<td>-xmax</td>
<td>Optional</td>
<td>xmax</td>
<td>0</td>
</tr>
<tr>
<td>-xd</td>
<td>Optional</td>
<td>delta x</td>
<td>1</td>
</tr>
<tr>
<td>-ymin</td>
<td>Optional</td>
<td>ymin</td>
<td>0</td>
</tr>
<tr>
<td>-ymax</td>
<td>Optional</td>
<td>ymax</td>
<td>0</td>
</tr>
<tr>
<td>-yd</td>
<td>Optional</td>
<td>delta y</td>
<td>1</td>
</tr>
<tr>
<td>-zmin</td>
<td>Optional</td>
<td>zmin</td>
<td>0</td>
</tr>
<tr>
<td>-zmax</td>
<td>Optional</td>
<td>zmax</td>
<td>82</td>
</tr>
<tr>
<td>-zd</td>
<td>Optional</td>
<td>delta z</td>
<td>1</td>
</tr>
<tr>
<td>-EA</td>
<td>Optional</td>
<td>[[Euler Angle]]'s Rotation Mode</td>
<td>ZOYS</td>
</tr>
<tr>
<td>-phimin</td>
<td>Optional</td>
<td>phimin: [degree]</td>
<td>0</td>
</tr>
<tr>
<td>-phimax</td>
<td>Optional</td>
<td>phimax: [degree]</td>
<td>194</td>
</tr>
<tr>
<td>-phid</td>
<td>Optional</td>
<td>delta phi: [degree]</td>
<td>2</td>
</tr>
<tr>
<td>-psimin</td>
<td>Optional</td>
<td>psimin: [degree]</td>
<td>0</td>
</tr>
<tr>
<td>-psimax</td>
<td>Optional</td>
<td>psimax: [degree]</td>
<td>0</td>
</tr>
<tr>
<td>-psid</td>
<td>Optional</td>
<td>delta psi: [degree]</td>
<td>2</td>
</tr>
<tr>
<td>-thetamin</td>
<td>Optional</td>
<td>thetamin: [degree]</td>
<td>0</td>
</tr>
<tr>
<td>-thetamax</td>
<td>Optional</td>
<td>thetamax [degree]</td>
<td>0</td>
</tr>
<tr>
<td>-thetad</td>
<td>Optional</td>
<td>delta theta: [degree]</td>
<td>2</td>
</tr>
<tr>
<td>-nw</td>
<td>Optional</td>
<td>weight for normalize</td>
<td>100000000.0</td>
</tr>
<tr>
<td>-nC</td>
<td>Optional</td>
<td>Contour Level for Normalize</td>
<td>0.0</td>
</tr>
<tr>
<td>-I</td>
<td>Optional</td>
<td>Black is High Density.</td>
<td></td>
</tr>
<tr>
<td>-Zminus</td>
<td>Optional</td>
<td>Shift to -z</td>
<td></td>
</tr>
<tr>
<td>-Tlim</td>
<td>Optional</td>
<td>The atom will be neglected</td>
<td>60</td>
</tr>
<tr>
<td>-Centre</td>
<td>Optional</td>
<td>Filament-axis is x=0, y=0</td>
<td></td>
</tr>
<tr>
<td>-C</td>
<td>Optional</td>
<td>[[Variable]]: ContourLevel</td>
<td>0.0 ...</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>

<pre>
-ipdb : Filename of pdb file of atomic model
-imrc : Filename of mrc file of contour map
-omrc : Filename of mrc file of fitting results
-otxt : Filename of text file of fitting results
-opar : Filename of text file of fitting results
-opdb : Filename of pdb file with a max score after fitting results
-zmin : Initial value of z (should <= zmax)
-zmax : Final value of z
-zd : Delta z for fitting (should >0)
-phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
-phimax : Final value of phi (should >0)
-phid : Delta phi for fitting (should >0)
-C : Contour level (variable and MUST be last option)
-Inverse: Protein has high density on the image
-Zminus : Atomic model shift to -z while fitting
-Tfactor: Consider temperature factor
-Tlim : The atoms whose T factor is above Tlim will be neglected
-Centre : Filament-axis is x=0, y=0
</pre>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Count the atom number inside the contour.</td>
</tr>
<tr>
<td>1</td>
<td>Add the densities of atoms.</td>
</tr>
</table>

== Execution example ==
=== Input file's image ===
====pdb image====
<table>
<tr>
<td>[[File:Input(pdb)-pdbRhoFit.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>

====[[mrcImage]] image====
<table>
<tr>
<td>[[File:Input(mrc)-pdbRhoFit.png]]</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>
5 (34, 41, 36)<br>
0.00471829<br>
0.0933498<br>
0.000162869<br></p>
</td>
</tr>
</table>

=== Option -C===
====Case: C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-C-pdbRhoFit.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">1.548556e+02 1.552094e+02 9.389075e+01<br>
3.286630e+01 <br>
26.73 23.32 28.04<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-C-pdbRhoFit.png]]</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>
1484 (94, 15, 0)<br>
227.582<br>
415.63<br>
2.66069<br></p>
</td>
</tr>
</table>

=== Option -xmin, -xmax, xd===
====Case: xmin=0, xmax=10, xd=1, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-xminxmaxxd-pdbRhoFit.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">2.041704e+01 1.983455e+01 9.389075e+01<br>
3.286621e+01 <br>
25.81 23.64 28.04<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-xminxmaxxd-pdbRhoFit.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (1, 0, 1)<br>
1547 (1, 43, 0)<br>
231.931<br>
425.602<br>
2.72453<br></p>
</td>
</tr>
</table>

=== Option -ymin, -ymax, -yd===
====Case: ymin=10, ymax=20, yd=2, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-yminymaxyd-pdbRhoFit.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">1.475229e+02 2.818824e+01 9.389075e+01<br>
3.286666e+01 <br>
23.76 25.30 28.04<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-yminymaxyd-pdbRhoFit.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (1, 0, 1)<br>
1550 (44, 24, 0)<br>
340.096<br>
555.774<br>
3.55783<br></p>
</td>
</tr>
</table>

=== Option -zmin, -zmax, -zd===
====Case: zmin=20, zmax=70, zd=2, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-zminzmaxzd-pdbRhoFit.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">1.548556e+02 1.552094e+02 8.189075e+01<br>
3.286630e+01<br>
26.73 23.32 28.04<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-zminzmaxzd-pdbRhoFit.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (1, 0, 1)<br>
1484 (94, 0, 0)<br>
231.435<br>
423.41<br>
4.84285<br></p>
</td>
</tr>
</table>

=== Option -EA===
====Case: EA=YOYS, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-EA-pdbRhoFit.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 9.389075e+01<br>
3.286664e+01<br>
24.77 23.85 28.04<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-EA-pdbRhoFit.png]]</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>
1188 (0, 48, 0)<br>
41.5284<br>
155.065<br>
0.992658<br></p>
</td>
</tr>
</table>

=== Option -phimin, -phimax, -phid===
====Case: phimin=0, phimax=360, phid=3, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-phiminphimaxphid-pdbRhoFit.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">1.727132e+01 1.572633e+02 9.389075e+01<br>
3.286635e+01<br>
23.50 26.28 28.04<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-phiminphimaxphid-pdbRhoFit.png]]</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>
1465 (62, 15, 0)<br>
210<br>
387.626<br>
2.23316<br></p>
</td>
</tr>
</table>

=== Option -psimin, -psimax, psid===
====Case: psimin=30, psimax=60, psid=1, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-psiminpsimaxpsid-pdbRhoFit.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">6.009141e+01 1.475229e+02 6.392447e+01<br>
3.286696e+01<br>
26.05 23.76 29.27<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-psiminpsimaxpsid-pdbRhoFit.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (66, 0, 0)<br>
1550 (54, 41, 0)<br>
269.644<br>
502.548<br>
3.2171<br></p>
</td>
</tr>
</table>

=== Option -thetamin, -thetamax, -thetad===
====Case: thetamin=90, thetamax=180, thetad=30, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-thetaminthetamaxthetad-pdbRhoFit.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">1.475229e+02 1.581092e+02 9.018824e+01<br>
3.286666e+01<br>
23.76 28.04 25.30<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-thetaminthetamaxthetad-pdbRhoFit.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (96, 36, 0)<br>
1412 (6, 11, 0)<br>
285.358<br>
511.536<br>
3.27464<br></p>
</td>
</tr>
</table>

=== Option -Centre===
====Case: Centre, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-Centre-pdbRhoFit.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">8.522220e+01 5.908815e+01 1.488908e+02<br>
3.286674e+01<br>
27.86 22.87 28.04<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-Centre-pdbRhoFit.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (1, 0, 1)<br>
1550 (0, 0, 0)<br>
457.617<br>
677.76<br>
4.33874<br></p>
</td>
</tr>
</table>

=== Option -m===
====Case: m=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-m1-pdbRhoFit.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">1.471341e+02 1.621267e+02 9.389075e+01<br>
3.286673e+01 <br>
27.86 22.87 28.04<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-m1-pdbRhoFit.png]]</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>
0 (0, 0, 0)<br>
0<br>
0<br>
0<br></p>
</td>
</tr>
</table>

====Case: m=1, nC=2====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-m1nC-pdbRhoFit.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>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-m1nC-pdbRhoFit.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-0 (14, 0, 0)<br>
194626 (0, 0, 0)<br>
566.611<br>
4738.59<br>
30.3344<br></p>
</td>
</tr>
</table>

====Case: m=1, nC=2, nw=1000====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-m1nw-pdbRhoFit.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>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-m1nw-pdbRhoFit.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-0 (14, 0, 0)<br>
1.94626 (0, 0, 0)<br>
0.00566611<br>
0.0473859<br>
0.000303344<br></p>
</td>
</tr>
</table>

=== Option -I===
====Case: I, m=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-I-pdbRhoFit.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>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-I-pdbRhoFit.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (14, 0, 0)<br>
20.01 (0, 0, 0)<br>
0.0582547<br>
0.487186<br>
0.00311876<br></p>
</td>
</tr>
</table>

Option Essential/Optional