pdbRhoFitTm - Revision history

Kinoshita: Created page with "'''pdbRhoFitTm''' is Eos's Command. == List of option == === Main option === ..."
2014-08-11T00:38:16Z
Created page with "'''pdbRhoFitTm''' is Eos's Command. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essential/Optional</th>..."
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'''pdbRhoFitTm''' 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] (原子モデル)</td>
<td>NULL</td>
</tr>
<tr>
<td>-imrc</td>
<td>Essential</td>
<td>Input: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-Sx</td>
<td>Essential</td>
<td>xの回転軸</td>
<td>55</td>
</tr>
<tr>
<td>-Sy</td>
<td>Essential</td>
<td>yの回転軸</td>
<td>110</td>
</tr>
<tr>
<td>-Sz</td>
<td>Essential</td>
<td>zの回転軸</td>
<td>110</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: [テキスト]</td>
<td>NULL</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>xの最小</td>
<td>0</td>
</tr>
<tr>
<td>-xmax</td>
<td>Optional</td>
<td>xの最大</td>
<td>0</td>
</tr>
<tr>
<td>-xd</td>
<td>Optional</td>
<td>xの間隔</td>
<td>1</td>
</tr>
<tr>
<td>-ymin</td>
<td>Optional</td>
<td>yの最小</td>
<td>0</td>
</tr>
<tr>
<td>-ymax</td>
<td>Optional</td>
<td>yの最大</td>
<td>0</td>
</tr>
<tr>
<td>-yd</td>
<td>Optional</td>
<td>yの間隔</td>
<td>1</td>
</tr>
<tr>
<td>-zmin</td>
<td>Optional</td>
<td>zの最小</td>
<td>0</td>
</tr>
<tr>
<td>-zmax</td>
<td>Optional</td>
<td>zの最大</td>
<td>82</td>
</tr>
<tr>
<td>-zd</td>
<td>Optional</td>
<td>zの間隔</td>
<td>1</td>
</tr>
<tr>
<td>-EA</td>
<td>Optional</td>
<td>[[Euler Angle]]の回転Mode</td>
<td>ZOYS</td>
</tr>
<tr>
<td>-phimin</td>
<td>Optional</td>
<td>phiの最小: [degree]</td>
<td>0</td>
</tr>
<tr>
<td>-phimax</td>
<td>Optional</td>
<td>phiの最大: [degree]</td>
<td>194</td>
</tr>
<tr>
<td>-phid</td>
<td>Optional</td>
<td>phiの間隔: [degree]</td>
<td>2</td>
</tr>
<tr>
<td>-psimin</td>
<td>Optional</td>
<td>psiの最小: [degree]</td>
<td>0</td>
</tr>
<tr>
<td>-psimax</td>
<td>Optional</td>
<td>psiの最大: [degree]</td>
<td>0</td>
</tr>
<tr>
<td>-psid</td>
<td>Optional</td>
<td>psiの間隔: [degree]</td>
<td>2</td>
</tr>
<tr>
<td>-thetamin</td>
<td>Optional</td>
<td>thetaの最小: [degree]</td>
<td>0</td>
</tr>
<tr>
<td>-thetamax</td>
<td>Optional</td>
<td>thetaの最大: [degree]</td>
<td>0</td>
</tr>
<tr>
<td>-thetad</td>
<td>Optional</td>
<td>thetaの間隔: [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>黒を高密度とする</td>
<td></td>
</tr>
<tr>
<td>-Zminus</td>
<td>Optional</td>
<td>Shift to -z</td>
<td></td>
</tr>
<tr>
<td>-Tfactor</td>
<td>Optional</td>
<td>Consider T factor</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>可変Input: コンターレベル</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
-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
-Sx : x of rotation axis
-Sy : y of rotation axis
-Sz : z of rotation axis
-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>輪郭内の原子数をカウントする</td>
</tr>
<tr>
<td>1</td>
<td>原子の密度を加える</td>
</tr>
</table>

== Execution example ==
=== Input file's image ===
====pdb image====
<table>
<tr>
<td>[[File:Input(pdb)-pdbRhoFitTm.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)-pdbRhoFitTm.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, Sx=55, Sy=110, Sz=110====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-C-pdbRhoFitTm.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">-4.127895e+01 1.871655e+02 2.597458e+00<br>
3.823911e+01 <br>
21.51 36.99 20.84<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-C-pdbRhoFitTm.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (10, 0, 0)<br>
15519 (32, 8, 0)<br>
125.844<br>
1103.92<br>
7.06681<br></p>
</td>
</tr>
</table>

=== Option -Sx===
====Case: Sx=0, Sy=110, Sz=110, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-Sx-pdbRhoFitTm.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">-4.086051e+01 2.123659e+02 2.597458e+00<br>
3.823867e+01<br>
32.66 29.04 20.84<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-Sx-pdbRhoFitTm.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (15, 0, 0)<br>
12888 (4, 8, 0)<br>
95.5124<br>
842.466<br>
5.39311<br></p>
</td>
</tr>
</table>

=== Option -Sy===
====Case: Sy=0, Sx=55, Sz=110, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-Sy-pdbRhoFitTm.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">2.957797e+00 -1.917446e+01 2.597458e+00<br>
3.823857e+01 <br>
33.06 28.34 20.84<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-Sy-pdbRhoFitTm.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (18, 0, 0)<br>
14125 (93, 8, 0)<br>
119.109<br>
992.326<br>
6.35246<br></p>
</td>
</tr>
</table>

=== Option -Sz===
====Case: Sz=0, Sx=55, Sy=110, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-Sz-pdbRhoFitTm.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">-4.127895e+01 1.871655e+02 2.597458e+00<br>
3.823911e+01 <br>
21.51 36.99 20.84<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-Sz-pdbRhoFitTm.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (10, 0, 0)<br>
15519 (32, 8, 0)<br>
125.844<br>
1103.92<br>
7.06681<br></p>
</td>
</tr>
</table>

=== Option -xmin, -xmax, xd===
====Case: xmin=0, xmax=2, xd=1, Sx=55, Sy=110, Sz=110, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-xminxmaxxd-pdbRhoFitTm.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">-3.366163e+01 1.936936e+02 -1.402542e+00<br>
3.823834e+01<br>
21.46 37.49 20.84<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-xminxmaxxd-pdbRhoFitTm.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (10, 0, 0)<br>
16153 (30, 4, 0)<br>
133.759<br>
1154.61<br>
7.3913<br></p>
</td>
</tr>
</table>

=== Option -ymin, -ymax, yd===
====Case: ymin=10, ymax=30, yd=5, Sx=55, Sy=110, Sz=110, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-yminymaxyd-pdbRhoFitTm.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">-2.960260e+01 2.098140e+02 3.597458e+00<br>
3.823860e+01<br>
22.15 37.81 20.84<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-yminymaxyd-pdbRhoFitTm.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (15, 0, 0)<br>
16212 (28, 9, 0)<br>
145.389<br>
1144.65<br>
7.32756<br></p>
</td>
</tr>
</table>

=== Option -zmin, -zmax, -zd===
====Case: zmin=20, zmax=70, zd=2, Sx=55, Sy=110, Sz=110, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-zminzmaxzd-pdbRhoFitTm.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">-2.960260e+01 1.998140e+02 1.459746e+01<br>
3.823860e+01<br>
22.15 37.81 20.84<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-zminzmaxzd-pdbRhoFitTm.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (10, 0, 0)<br>
7065 (28, 0, 0)<br>
12.826<br>
216.816<br>
2.47988<br></p>
</td>
</tr>
</table>

=== Option -EA===
====Case: EA=YOYS, Sx=55, Sy=110, Sz=110, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-EA-pdbRhoFitTm.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">1.367327e+02 -2.186292e-01 2.095572e+02<br>
3.823908e+01 <br>
34.54 22.99 22.20<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-EA-pdbRhoFitTm.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (9, 0, 0)<br>
11951 (0, 1, 0)<br>
19.1756<br>
362.85<br>
2.32281<br></p>
</td>
</tr>
</table>

=== Option -phimin, -phimax, -phid===
====Case: phimin=0, phimax=360, phid=3, Sx=55, Sy=110, Sz=110, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-phiminphimaxphid-pdbRhoFitTm.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">1.280264e+02 1.054504e+01 2.597458e+00<br>
3.823844e+01 <br>
23.11 37.92 20.84<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-phiminphimaxphid-pdbRhoFitTm.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (7, 0, 0)<br>
15675 (21, 8, 0)<br>
82.6776<br>
875.943<br>
5.04642<br></p>
</td>
</tr>
</table>

=== Option -psimin, -psimax, psid===
====Case: psimin=30, psimax=60, psid=6, Sx=55, Sy=110, Sz=110, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-psiminpsimaxpsid-pdbRhoFitTm.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">-9.654431e+01 8.513753e+01 2.044136e+02<br>
3.823914e+01 <br>
34.74 27.68 23.43<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-psiminpsimaxpsid-pdbRhoFitTm.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>
13241 (32, 24, 0)<br>
217.879<br>
1196.44<br>
7.65912<br></p>
</td>
</tr>
</table>

=== Option -thetamin, -thetamax, -thetad===
====Case: thetamin=30, thetamax=60, thetad=10, Sx=55, Sy=110, Sz=110, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-thetaminthetamaxthetad-pdbRhoFitTm.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">7.654526e+01 1.778230e+02 3.222245e+02<br>
3.823855e+01 <br>
33.84 20.73 30.97<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-thetaminthetamaxthetad-pdbRhoFitTm.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>
17440 (1, 59, 0)<br>
150.133<br>
1133.08<br>
7.25353<br></p>
</td>
</tr>
</table>

=== Option -Centre===
====Case: Centre, Sx=55, Sy=110, Sz=110, C=1====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-Centre-pdbRhoFitTm.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">5.449082e+01 1.100415e+02 1.245975e+02<br>
3.823843e+01<br>
37.79 23.42 20.84<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-Centre-pdbRhoFitTm.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>
28 (68, 20, 0)<br>
0.166913<br>
1.31871<br>
0.00844185<br></p>
</td>
</tr>
</table>

=== Option -m===
====Case: m=1, Sx=55, Sy=110, Sz=110====
=====pdb image=====
<table>
<tr>
<td>[[File:Outdata(pdb)-m1-pdbRhoFitTm.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">-4.127895e+01 1.871655e+02 2.597458e+00<br>
3.823911e+01 <br>
21.51 36.99 20.84<br></p>
</td>
</tr>
</table>

=====[[mrcImage]] image=====
<table>
<tr>
<td>[[File:Outdata(mrc)-m1-pdbRhoFitTm.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (10, 0, 0)<br>
15519 (32, 8, 0)<br>
125.844<br>
1103.92<br>
7.06681<br></p>
</td>
</tr>
</table>

Option Essential/Optional