Difference between revisions of "mrcImageMultiCTFCompensation"

From EosPedia
Jump to: navigation, search
(Created page with "'''mrcImageMultiCTFCompensation''' is Eos's Command that performs CTF Correction to multiple images. == List of option == === Main option === <table border="1"...")
 
(→‎Case: m=17)
 
(18 intermediate revisions by the same user not shown)
Line 1: Line 1:
−
'''mrcImageMultiCTFCompensation''' is [[Eos]]'s [[Command]] that performs [[CTF Correction]] to multiple images.
+
'''mrcImageMultiCTFCompensation''' is [[Eos]]'s [[Command]] that performs [[CTF Correction]] to multiple images that have each other same field and different [[CTF]]. It outputs the average image of each image after [[CTF Correction]].
  
  
Line 170: Line 170:
 
== Execution example ==
 
== Execution example ==
 
===-i  data===
 
===-i  data===
 +
<div>[[:Media:Input-B120.mrc|Original data]]'s image </div>
 +
<table>
 +
<tr>
 +
<td>[[File:Input-B120.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>
 +
255 (49, 32, 0)<br>
 +
21.0538<br>
 +
47.6709<br>
 +
0.595886<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
 +
Use simulation images that is multiplied each different CTF to above image, as input file.
 
<pre>
 
<pre>
−
/Eos/img/Input0.mrc 27000 2.1 200 0.1
+
/Eos/img/Input-B120-CTF2.mrc 27000 2.1 200 0.1
−
/Eos/img/Input1.mrc 27000 2.1 200 0.1
+
/Eos/img/Input-B120-CTF3.mrc 9000 2.1 200 0.1
−
/Eos/img/Input2.mrc 27000 2.1 200 0.1
+
/Eos/img/Input-B120-CTF4.mrc 27000 2.1 400 0.1
−
/Eos/img/Input3.mrc 27000 2.1 200 0.1
+
/Eos/img/Input-B120-CTF5.mrc 27000 2.1 200 0.3
  
 
</pre>
 
</pre>
  
−
<div>Input0's image</div>
+
<div>[[:Media:Input-B120-CTF2.mrc|Input-B120-CTF2.mrc]]'s image </div>
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
−
<td>[[File:Input0-mrcImageMultiCTFCompensation.png]]</td>  
+
<td>[[File:Input-B120-CTF2.png]]</td>  
 
<td><p align="left">Min<br>  
 
<td><p align="left">Min<br>  
 
Max<br>  
 
Max<br>  
Line 188: Line 208:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0 (0, 0, 0)<br>  
+
<td><p align="left">-67.2449 (35, 36, 0)<br>
−
255 (30, 25, 0)<br>  
+
48.4524 (50, 51, 0)<br>
−
21.8076<br>  
+
-5.60279e-08<br>
−
47.9133<br>  
+
13.2796<br>
−
0.748645<br></p>  
+
0.165995<br></p>
 +
</td>
 +
<td><p align="center">[[File:Input-B120-CTF2-Cnp.png]]<br>
 +
case: CTF Correction at single<br> </p>
 +
</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-49.3218 (28, 26, 0)<br>  
 +
133.566 (37, 38, 0)<br>  
 +
8.98254e-07<br>  
 +
26.7724<br>  
 +
0.334655<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>  
 
</table>  
  
−
<div>Input1's image</div>
+
<div>[[:Media:Input-B120-CTF3.mrc|Input-B120-CTF3.mrc]]'s image </div>
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
−
<td>[[File:Input1-mrcImageMultiCTFCompensation.png]]</td>  
+
<td>[[File:Input-B120-CTF3.png]]</td>  
 
<td><p align="left">Min<br>  
 
<td><p align="left">Min<br>  
 
Max<br>  
 
Max<br>  
Line 207: Line 242:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0 (0, 0, 0)<br>  
+
<td><p align="left">-57.5666 (25, 38, 0)<br>  
−
255 (30, 26, 0)<br>  
+
53.971 (44, 29, 0)<br>  
−
20.6895<br>  
+
-5.02996e-08<br>  
−
47.2143<br>  
+
9.30611<br>  
−
0.737723<br></p>  
+
0.116326<br></p>  
 
</td>  
 
</td>  
−
</tr>  
+
<td><p align="center">[[File:Input-B120-CTF3-Cnp.png]]<br>
 +
case: CTF Correction at single<br> </p>
 +
</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-49.4192 (47, 51, 0)<br>
 +
137.108 (49, 32, 0)<br>
 +
5.49823e-07<br>
 +
19.7161<br>
 +
0.246452<br></p>
 +
</td> 
 +
</tr>
 
</table>  
 
</table>  
  
−
<div>Input2's image</div>
+
<div>[[:Media:Input-B120-CTF4.mrc|Input-B120-CTF4.mrc]]'s image </div>
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
−
<td>[[File:Input2-mrcImageMultiCTFCompensation.png]]</td>  
+
<td>[[File:Input-B120-CTF4.png]]</td>  
 
<td><p align="left">Min<br>  
 
<td><p align="left">Min<br>  
 
Max<br>  
 
Max<br>  
Line 226: Line 276:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0 (0, 0, 0)<br>  
+
<td><p align="left">-68.355 (24, 39, 0)<br>
−
255 (27, 32, 0)<br>  
+
42.4746 (44, 26, 0)<br>
−
19.0078<br>  
+
-3.45941e-08<br>
−
47.768<br>  
+
10.9018<br>
−
0.746374<br></p>  
+
0.136272<br></p>
 +
</td>
 +
<td><p align="center">[[File:Input-B120-CTF4-Cnp.png]]<br>
 +
case: CTF Correction at single<br> </p>
 +
</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-43.0975 (26, 31, 0)<br>  
 +
117.683 (49, 32, 0)<br>  
 +
4.44953e-07<br>  
 +
22.9822<br>  
 +
0.287278<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>  
 
</table>  
  
−
<div>Input3's image</div>
+
<div>[[:Media:Input-B120-CTF5.mrc|Input-B120-CTF5.mrc]]'s image </div>
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
−
<td>[[File:Input3-mrcImageMultiCTFCompensation.png]]</td>  
+
<td>[[File:Input-B120-CTF5.png]]</td>  
 
<td><p align="left">Min<br>  
 
<td><p align="left">Min<br>  
 
Max<br>  
 
Max<br>  
Line 245: Line 310:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0 (0, 0, 0)<br>  
+
<td><p align="left">-44.9091 (37, 36, 0)<br>  
−
255 (28, 33, 0)<br>  
+
26.5736 (28, 28, 0)<br>
−
18.3279<br>  
+
-2.71914e-08<br>
−
45.0774<br>  
+
8.97143<br>
−
0.704334<br></p>  
+
0.112143<br></p>
 +
</td>
 +
<td><p align="center">[[File:Input-B120-CTF5-Cnp.png]]<br>
 +
case: CTF Correction at single<br> </p>
 +
</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-33.0969 (49, 51, 0)<br>
 +
73.3827 (35, 37, 0)<br>  
 +
-1.68364e-08<br>  
 +
15.1195<br>  
 +
0.188993<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
 +
<br>
  
−
 
+
=== Case: Options only essential ===
−
=== Example of options only essential ===
+
 
<div>-o 's image</div>
 
<div>-o 's image</div>
 
<table>  
 
<table>  
Line 266: Line 346:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-950.729 (30, 33, 0)<br>  
+
<td><p align="left">-40.2801 (48, 52, 0)<br>  
−
91.5373 (61, 58, 0)<br>  
+
104.151 (36, 38, 0)<br>  
−
-199.582<br>  
+
1.24049e-07<br>  
−
202.06<br>  
+
18.8015<br>  
−
3.15719<br></p>  
+
0.235019<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 285: Line 365:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0.0117408 (32, 31, 0)<br>  
+
<td><p align="left">7.30857e-06 (75, 37, 0)<br>  
−
12773.2 (0, 0, 0)<br>  
+
378.143 (42, 0, 0)<br>  
−
30.7184<br>  
+
4.45621<br>  
−
365.42<br>  
+
19.8824<br>  
−
5.70969<br></p>  
+
0.24853<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
−
</table>  
+
</table>
−
 
+
  
 
=== Option -W===
 
=== Option -W===
−
====Case: W=0.5====  
+
====Case: W=1====  
 
<div>-o 's image</div>
 
<div>-o 's image</div>
 
<table>  
 
<table>  
Line 307: Line 386:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-178.794 (29, 32, 0)<br>  
+
<td><p align="left">-17.0714 (27, 31, 0)<br>  
−
31.7025 (15, 31, 0)<br>  
+
23.2441 (40, 52, 0)<br>  
−
-7.67623<br>  
+
5.81327e-09<br>  
−
35.9686<br>  
+
4.65713<br>  
−
0.562009<br></p>  
+
0.0582141<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 326: Line 405:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0.000786083 (61, 50, 0)<br>  
+
<td><p align="left">3.22907e-07 (0, 0, 0)<br>  
−
656.031 (1, 0, 0)<br>  
+
62.9461 (46, 78, 0)<br>  
−
5.93815<br>  
+
1.28884<br>  
−
40.2896<br>  
+
4.68843<br>  
−
0.629525<br></p>  
+
0.0586053<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
=== Option -WR===
 
=== Option -WR===
Line 348: Line 426:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-153.883 (30, 32, 0)<br>  
+
<td><p align="left">-11.5567 (27, 31, 0)<br>  
−
23.7931 (15, 31, 0)<br>  
+
15.7516 (24, 39, 0)<br>  
−
-7.67623<br>  
+
1.23206e-08<br>  
−
31.3292<br>  
+
3.24282<br>  
−
0.489519<br></p>  
+
0.0405352<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 367: Line 445:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">9.05608e-06 (60, 32, 0)<br>  
+
<td><p align="left">2.72506e-08 (75, 37, 0)<br>  
−
587.065 (1, 0, 0)<br>  
+
45.7637 (46, 78, 0)<br>  
−
4.29171<br>  
+
0.700623<br>  
−
35.7021<br>  
+
3.33709<br>  
−
0.557845<br></p>  
+
0.0417136<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
=== Option -SinWin===
 
=== Option -SinWin===
Line 389: Line 466:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-939.931 (30, 33, 0)<br>  
+
<td><p align="left">-39.9332 (48, 52, 0)<br>  
−
82.2886 (61, 59, 0)<br>  
+
102.315 (36, 38, 0)<br>  
−
-199.582<br>  
+
1.52273e-07<br>  
−
201.211<br>  
+
18.7407<br>  
−
3.14392<br></p>  
+
0.234259<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 408: Line 485:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0 (8, 0, 0)<br>  
+
<td><p align="left">0 (40, 1, 0)<br>  
−
12773.2 (0, 0, 0)<br>  
+
378.143 (42, 0, 0)<br>  
−
28.1205<br>  
+
4.1815<br>  
−
365.158<br>  
+
19.8843<br>  
−
5.70559<br></p>  
+
0.248553<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
=== Option -ctfMode===
 
=== Option -ctfMode===
Line 430: Line 506:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-1243.15 (30, 31, 0)<br>  
+
<td><p align="left">-24.2681 (68, 48, 0)<br>  
−
534.543 (1, 0, 0)<br>  
+
207.103 (36, 38, 0)<br>  
−
-7.92556e-07<br>  
+
-1.0943e-09<br>  
−
404.255<br>  
+
45.5848<br>  
−
6.31648<br></p>  
+
0.56981<br></p>  
−
</td>  
+
</td>
 
</tr>  
 
</tr>  
 
</table>
 
</table>
Line 450: Line 526:
 
</td>  
 
</td>  
 
<td><p align="left">0 (0, 0, 0)<br>  
 
<td><p align="left">0 (0, 0, 0)<br>  
−
12267.8 (1, 0, 0)<br>  
+
1280.12 (41, 0, 0)<br>  
−
33.7224<br>  
+
6.47008<br>  
−
477.688<br>  
+
51.7633<br>  
−
7.46387<br></p>  
+
0.647041<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
====Case: ctfMode=256====  
 
====Case: ctfMode=256====  
Line 470: Line 545:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-501.951 (1, 0, 0)<br>  
+
<td><p align="left">-191.228 (36, 38, 0)<br>  
−
1288.01 (33, 32, 0)<br>  
+
26.7763 (67, 30, 0)<br>  
−
-2.09152e-06<br>  
+
-3.91243e-08<br>  
−
404.255<br>  
+
45.3127<br>  
−
6.31648<br></p>  
+
0.566409<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 490: Line 565:
 
</td>  
 
</td>  
 
<td><p align="left">0 (0, 0, 0)<br>  
 
<td><p align="left">0 (0, 0, 0)<br>  
−
12267.8 (1, 0, 0)<br>  
+
1280.12 (41, 0, 0)<br>  
−
33.7224<br>  
+
5.38217<br>  
−
477.688<br>  
+
51.6411<br>  
−
7.46387<br></p>  
+
0.645514<br></p>  
−
</td>  
+
</td>
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
====Case: ctfMode=257====  
 
====Case: ctfMode=257====  
Line 510: Line 584:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-50.4152 (5, 2, 0)<br>  
+
<td><p align="left">-90.5402 (36, 37, 0)<br>  
−
1009.22 (33, 32, 0)<br>  
+
39.3153 (49, 51, 0)<br>  
−
199.582<br>  
+
-1.30477e-07<br>  
−
202.06<br>  
+
18.1267<br>  
−
3.15719<br></p>  
+
0.226584<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 529: Line 603:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0.0117408 (32, 31, 0)<br>  
+
<td><p align="left">1.17451e-06 (75, 37, 0)<br>  
−
12773.2 (0, 0, 0)<br>  
+
378.143 (42, 0, 0)<br>  
−
30.7184<br>  
+
3.33762<br>  
−
365.42<br>  
+
19.4523<br>  
−
5.70969<br></p>  
+
0.243154<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
=== Option -m===
 
=== Option -m===
−
====Case: m=1, W=0.5====  
+
====Case: m=1, W=1====  
 
=====Case: No other settings=====
 
=====Case: No other settings=====
 
<div>-o 's image</div>
 
<div>-o 's image</div>
Line 552: Line 625:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-175.249 (29, 32, 0)<br>  
+
<td><p align="left">-9.82557 (48, 51, 0)<br>  
−
49.852 (15, 31, 0)<br>  
+
92.1757 (49, 32, 0)<br>  
−
-1.99391<br>  
+
6.14297<br>  
−
37.3853<br>  
+
14.8838<br>  
−
0.584145<br></p>  
+
0.186048<br></p>  
−
</td>  
+
</td>
 
</tr>  
 
</tr>  
 
</table>
 
</table>
Line 571: Line 644:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0.00642588 (59, 34, 0)<br>  
+
<td><p align="left">0.00108315 (40, 41, 0)<br>  
−
681.324 (34, 0, 0)<br>  
+
491.438 (0, 0, 0)<br>  
−
6.41058<br>  
+
4.1562<br>  
−
40.1134<br>  
+
18.0735<br>  
−
0.626771<br></p>  
+
0.225919<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 582: Line 655:
 
<div>-log 's data</div>
 
<div>-log 's data</div>
 
<pre>
 
<pre>
−
iter          0 : rms   -1.965984e+01 : min    1.000000e+06
+
iter          0 : rms   1.013455e+01 : min    1.000000e+06
 +
iter          1 : rms    1.355871e+00 : min    1.013455e+01
 +
iter          2 : rms    8.647722e-01 : min    1.355871e+00
 +
iter          3 : rms    6.229646e-01 : min    8.647722e-01
 +
iter          4 : rms    4.844930e-01 : min    6.229646e-01
 +
iter          5 : rms    3.971868e-01 : min    4.844930e-01
 +
iter          6 : rms    3.377429e-01 : min    3.971868e-01
 +
iter          7 : rms    2.951728e-01 : min    3.377429e-01
 +
iter          8 : rms    2.629044e-01 : min    2.951728e-01
 +
iter          9 : rms    2.370113e-01 : min    2.629044e-01
 
</pre>
 
</pre>
  
−
====Case: solventMode=1====  
+
=====Case: solventMode=1=====  
 
<div>-o 's image</div>
 
<div>-o 's image</div>
 
<table>  
 
<table>  
Line 596: Line 678:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-220.728 (30, 32, 0)<br>  
+
<td><p align="left">-20.1029 (48, 51, 0)<br>  
−
42.9295 (15, 31, 0)<br>  
+
87.1488 (49, 32, 0)<br>  
−
-9.08899<br>  
+
2.38926<br>  
−
47.6864<br>  
+
14.7396<br>  
−
0.7451<br></p>  
+
0.184245<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 615: Line 697:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0.00745064 (63, 30, 0)<br>  
+
<td><p align="left">0.00627302 (76, 14, 0<br>  
−
916.491 (1, 0, 0)<br>  
+
222.088 (42, 0, 0)<br>  
−
7.81324<br>  
+
4.12707<br>  
−
53.2299<br>  
+
15.7098<br>  
−
0.831717<br></p>  
+
0.196372<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 626: Line 708:
 
<div>-log 's data</div>
 
<div>-log 's data</div>
 
<pre>
 
<pre>
−
iter          0 : rms   -3.997643e+00 : min    1.000000e+06
+
iter          0 : rms   3.709238e+01 : min    1.000000e+06
 +
iter          1 : rms    3.539059e+00 : min    3.709238e+01
 +
iter          2 : rms    1.971014e+00 : min    3.539059e+00
 +
iter          3 : rms    1.314187e+00 : min    1.971014e+00
 +
iter          4 : rms    9.704149e-01 : min    1.314187e+00
 +
iter          5 : rms    7.649823e-01 : min    9.704149e-01
 +
iter          6 : rms    6.304888e-01 : min    7.649823e-01
 +
iter          7 : rms    5.362647e-01 : min    6.304888e-01
 +
iter          8 : rms    4.668152e-01 : min    5.362647e-01
 +
iter          9 : rms    4.135905e-01 : min    4.668152e-01
 
</pre>
 
</pre>
  
−
 
+
=====Case: solventSTD=2.0, solventMode=1=====  
−
====Case: solventSTD=2.0, solventMode=1====  
+
 
<div>-o 's image</div>
 
<div>-o 's image</div>
 
<table>  
 
<table>  
Line 641: Line 731:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">342.42 (29, 32, 0)<br>  
+
<td><p align="left">85.3666 (27, 31, 0)<br>  
−
552.916 (15, 31, 0)<br>  
+
146.065 (58, 33, 0)<br>  
−
513.538<br>  
+
101.654<br>  
−
35.9686<br>  
+
5.9911<br>  
−
0.562009<br></p>  
+
0.0748887<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 660: Line 750:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0.000751982 (61, 50, 0)<br>  
+
<td><p align="left">0.00707058 (78, 44, 0)<br>  
−
32866.4 (0, 0, 0)<br>  
+
8132.32 (0, 0, 0)<br>  
−
21.7463<br>  
+
4.62714<br>  
−
726.986<br>  
+
143.824<br>  
−
11.3592<br></p>  
+
1.7978<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 671: Line 761:
 
<div>-log 's data</div>
 
<div>-log 's data</div>
 
<pre>
 
<pre>
−
iter          0 : rms    7.485705e-01 : min    1.000000e+06
+
iter          0 : rms    1.424218e+00 : min    1.000000e+06
−
iter          1 : rms    3.354889e-01 : min    7.485705e-01
+
iter          1 : rms    2.156973e-01 : min    1.424218e+00
−
iter          2 : rms    2.279355e-01 : min    3.354889e-01
+
iter          2 : rms    1.394271e-01 : min    2.156973e-01
−
iter          3 : rms    1.763709e-01 : min    2.279355e-01
+
iter          3 : rms    1.043566e-01 : min    1.394271e-01
−
iter          4 : rms    1.463149e-01 : min    1.763709e-01
+
iter          4 : rms    8.473523e-02 : min    1.043566e-01
−
iter          5 : rms    1.267555e-01 : min    1.463149e-01
+
iter          5 : rms    7.243526e-02 : min    8.473523e-02
−
iter          6 : rms    1.130881e-01 : min    1.267555e-01
+
iter          6 : rms    6.412249e-02 : min    7.243526e-02
−
iter          7 : rms    1.030489e-01 : min    1.130881e-01
+
iter          7 : rms    5.819677e-02 : min    6.412249e-02
−
iter          8 : rms    9.539606e-02 : min    1.030489e-01
+
iter          8 : rms    5.380184e-02 : min    5.819677e-02
−
iter          9 : rms    8.939259e-02 : min    9.539606e-02
+
iter          9 : rms    5.044070e-02 : min    5.380184e-02
 
</pre>
 
</pre>
  
−
 
+
=====Case: MaxIter=5, solventSTD=2.0, solventMode=1=====  
−
====Case: MaxIter=5, solventSTD=2.0, solventMode=1====  
+
 
<div>-o 's image</div>
 
<div>-o 's image</div>
 
<table>  
 
<table>  
Line 695: Line 784:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">107.285 (29, 32, 0)<br>  
+
<td><p align="left">35.7164 (27, 31, 0)<br>  
−
317.781 (15, 31, 0)<br>  
+
94.8793 (58, 33, 0)<br>  
−
278.402<br>  
+
52.0534<br>  
−
35.9686<br>  
+
5.94982<br>  
−
0.562009<br></p>  
+
0.0743728<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 714: Line 803:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0.000789315 (61, 50, 0)<br>  
+
<td><p align="left">0.00307367 (71, 39, 0)<br>  
−
17817.7 (0, 0, 0)<br>  
+
4164.28 (0, 0, 0)<br>  
−
14.3983<br>  
+
3.33262<br>  
−
395.41<br>  
+
73.8045<br>  
−
6.17827<br></p>  
+
0.922556<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 725: Line 814:
 
<div>-log 's data</div>
 
<div>-log 's data</div>
 
<pre>
 
<pre>
−
iter          0 : rms    7.485705e-01 : min    1.000000e+06
+
iter          0 : rms    1.424218e+00 : min    1.000000e+06
−
iter          1 : rms    3.354889e-01 : min    7.485705e-01
+
iter          1 : rms    2.156973e-01 : min    1.424218e+00
−
iter          2 : rms    2.279355e-01 : min    3.354889e-01
+
iter          2 : rms    1.394271e-01 : min    2.156973e-01
−
iter          3 : rms    1.763709e-01 : min    2.279355e-01
+
iter          3 : rms    1.043566e-01 : min    1.394271e-01
−
iter          4 : rms    1.463149e-01 : min    1.763709e-01
+
iter          4 : rms    8.473523e-02 : min    1.043566e-01
 
</pre>
 
</pre>
−
 
  
 
====Case: m=16====  
 
====Case: m=16====  
Line 744: Line 832:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-50.4152 (5, 2, 0)<br>  
+
<td><p align="left">-90.5402 (36, 37, 0)<br>  
−
1009.22 (33, 32, 0)<br>  
+
39.3153 (49, 51, 0)<br>  
−
199.582<br>  
+
-1.13944e-07<br>  
−
202.06<br>  
+
18.1267<br>  
−
3.15719<br></p>  
+
0.226584<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 763: Line 851:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0.0117408 (32, 31, 0)<br>  
+
<td><p align="left">1.17451e-06 (75, 37, 0)<br>  
−
12773.2 (0, 0, 0)<br>  
+
378.143 (42, 0, 0)<br>  
−
30.7184<br>  
+
3.33762<br>  
−
365.42<br>  
+
19.4523<br>  
−
5.70969<br></p>  
+
0.243154<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
====Case: m=17====  
 
====Case: m=17====  
Line 784: Line 871:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">161250 (60, 60, 0)<br>  
+
<td><p align="left">-363.432 (24, 39, 0)<br>  
−
1.85064e+06 (29, 32, 0)<br>  
+
64206.9 (50, 53, 0)<br>  
−
432887<br>  
+
12232.5<br>  
−
388639<br>  
+
12224.9<br>  
−
6072.49<br></p>  
+
152.812<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 803: Line 890:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0.00899138 (31, 33, 0)<br>  
+
<td><p align="left">0.000769818 (62, 30, 0)<br>  
−
2.77048e+07 (0, 0, 0)<br>  
+
978599 (0, 0, 0)<br>  
−
51930<br>  
+
2152.97<br>  
−
757226<br>  
+
21751<br>  
−
11831.7<br></p>  
+
271.888<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 814: Line 901:
 
<div>-log 's data</div>
 
<div>-log 's data</div>
 
<pre>
 
<pre>
−
iter          0 : rms    9.051428e-01 : min    1.000000e+06
+
iter          0 : rms    2.228456e+00 : min    1.000000e+06
−
iter          1 : rms    7.732108e-01 : min    9.051428e-01
+
iter          1 : rms    1.072463e+00 : min    2.228456e+00
−
iter          2 : rms    7.194946e-01 : min    7.732108e-01
+
iter          2 : rms    8.595473e-01 : min    1.072463e+00
−
iter          3 : rms    6.952064e-01 : min    7.194946e-01
+
iter          3 : rms    7.822678e-01 : min    8.595473e-01
−
iter          4 : rms    6.840820e-01 : min    6.952064e-01
+
iter          4 : rms    7.485957e-01 : min    7.822678e-01
−
iter          5 : rms    6.782160e-01 : min    6.840820e-01
+
iter          5 : rms    7.339871e-01 : min    7.485957e-01
−
iter          6 : rms    6.752780e-01 : min    6.782160e-01
+
iter          6 : rms    7.188863e-01 : min    7.339871e-01
−
iter          7 : rms    6.739355e-01 : min    6.752780e-01
+
iter          7 : rms    7.127621e-01 : min    7.188863e-01
−
iter          8 : rms    6.730211e-01 : min    6.739355e-01
+
iter          8 : rms    7.096454e-01 : min    7.127621e-01
−
iter          9 : rms    6.722654e-01 : min    6.730211e-01
+
iter          9 : rms    7.069848e-01 : min    7.096454e-01
 
</pre>
 
</pre>

Latest revision as of 08:10, 22 September 2014

mrcImageMultiCTFCompensation is Eos's Command that performs CTF Correction to multiple images that have each other same field and different CTF. It outputs the average image of each image after CTF Correction.


List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: ASCII(File List) stdin
-info2 Optional Input: ASCII(File List) stdin
-o Essential Output(average): mrcImage stdout
-f Optional Output(average): mrcImage(FFT) stdout
-W Optional WhiteNoise(Noise/Signal) 1.0
-WR Optional WhiteNoiseRaising 1.0
-SinWin Optional sin Windowing (R[/A]): (SinWinRmin, SinWinRmax) (0.1, 1.0)
-MaxIter Optional Max Iteration 10
-ctfMode Optional CTFMode 1
-solventMode Optional If solvent flatterning is used, NEED 0
-solventSTD Optional If solvent flatterning is used as mode=1, NEED -1.0
-Log Optional Log File Name stderr
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help 　

-ctfMode details

Value Description
0 Phase Only
1 Phase and Amplitude
+32 With Illumination Angle
+256 As Absolute Value

-m details

Value Description
0 CTF-weighted compensation, CTF/(SQR(CTF) + (NS)^2)
+1 Adding solvent-flattening process
+16 Without phase flipping, in case of images after phase only correction.

-i format

filename0 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
filename1 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
     .                .            .           .                   .
     .                .            .           .                   .
     .                .            .           .                   .

-Info2 format

filename0.ctfinfo 
filename1.ctfinfo 
          .
          .
          .


Execution example

-i data

Original data's image
Input-B120.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

255 (49, 32, 0)
21.0538
47.6709

0.595886

Use simulation images that is multiplied each different CTF to above image, as input file. 

/Eos/img/Input-B120-CTF2.mrc 27000 2.1 200 0.1
/Eos/img/Input-B120-CTF3.mrc 9000 2.1 200 0.1
/Eos/img/Input-B120-CTF4.mrc 27000 2.1 400 0.1
/Eos/img/Input-B120-CTF5.mrc 27000 2.1 200 0.3
Input-B120-CTF2.mrc's image
Input-B120-CTF2.png

Min

Max
Mean
SD

SE

-67.2449 (35, 36, 0)

48.4524 (50, 51, 0)
-5.60279e-08
13.2796

0.165995

Input-B120-CTF2-Cnp.png
case: CTF Correction at single

Min

Max
Mean
SD

SE

-49.3218 (28, 26, 0)

133.566 (37, 38, 0)
8.98254e-07
26.7724

0.334655
Input-B120-CTF3.mrc's image
Input-B120-CTF3.png

Min

Max
Mean
SD

SE

-57.5666 (25, 38, 0)

53.971 (44, 29, 0)
-5.02996e-08
9.30611

0.116326

Input-B120-CTF3-Cnp.png
case: CTF Correction at single

Min

Max
Mean
SD

SE

-49.4192 (47, 51, 0)

137.108 (49, 32, 0)
5.49823e-07
19.7161

0.246452
Input-B120-CTF4.mrc's image
Input-B120-CTF4.png

Min

Max
Mean
SD

SE

-68.355 (24, 39, 0)

42.4746 (44, 26, 0)
-3.45941e-08
10.9018

0.136272

Input-B120-CTF4-Cnp.png
case: CTF Correction at single

Min

Max
Mean
SD

SE

-43.0975 (26, 31, 0)

117.683 (49, 32, 0)
4.44953e-07
22.9822

0.287278
Input-B120-CTF5.mrc's image
Input-B120-CTF5.png

Min

Max
Mean
SD

SE

-44.9091 (37, 36, 0)

26.5736 (28, 28, 0)
-2.71914e-08
8.97143

0.112143

Input-B120-CTF5-Cnp.png
case: CTF Correction at single

Min

Max
Mean
SD

SE

-33.0969 (49, 51, 0)

73.3827 (35, 37, 0)
-1.68364e-08
15.1195

0.188993


Case: Options only essential

-o 's image
Outdata-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-40.2801 (48, 52, 0)

104.151 (36, 38, 0)
1.24049e-07
18.8015

0.235019
-f 's image
Outdata2-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

7.30857e-06 (75, 37, 0)

378.143 (42, 0, 0)
4.45621
19.8824

0.24853

Option -W

Case: W=1

-o 's image
Outdata-W-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-17.0714 (27, 31, 0)

23.2441 (40, 52, 0)
5.81327e-09
4.65713

0.0582141
-f 's image
Outdata2-W-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

3.22907e-07 (0, 0, 0)

62.9461 (46, 78, 0)
1.28884
4.68843

0.0586053

Option -WR

Case: WR=10.0, W=0.5

-o 's image
Outdata-WR-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-11.5567 (27, 31, 0)

15.7516 (24, 39, 0)
1.23206e-08
3.24282

0.0405352
-f 's image
Outdata2-WR-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

2.72506e-08 (75, 37, 0)

45.7637 (46, 78, 0)
0.700623
3.33709

0.0417136

Option -SinWin

Case: SinWin=(0.05, 0.2)

-o 's image
Outdata-SinWin-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-39.9332 (48, 52, 0)

102.315 (36, 38, 0)
1.52273e-07
18.7407

0.234259
-f 's image
Outdata2-SinWin-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (40, 1, 0)

378.143 (42, 0, 0)
4.1815
19.8843

0.248553

Option -ctfMode

Case: ctfMode=32

-o 's image
Outdata-ctfMode32-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-24.2681 (68, 48, 0)

207.103 (36, 38, 0)
-1.0943e-09
45.5848

0.56981
-f 's image
Outdata2-ctfMode32-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1280.12 (41, 0, 0)
6.47008
51.7633

0.647041

Case: ctfMode=256

-o 's image
Outdata-ctfMode256-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-191.228 (36, 38, 0)

26.7763 (67, 30, 0)
-3.91243e-08
45.3127

0.566409
-f 's image
Outdata2-ctfMode256-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1280.12 (41, 0, 0)
5.38217
51.6411

0.645514

Case: ctfMode=257

-o 's image
Outdata-ctfMode257-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-90.5402 (36, 37, 0)

39.3153 (49, 51, 0)
-1.30477e-07
18.1267

0.226584
-f 's image
Outdata2-ctfMode257-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

1.17451e-06 (75, 37, 0)

378.143 (42, 0, 0)
3.33762
19.4523

0.243154

Option -m

Case: m=1, W=1

Case: No other settings
-o 's image
Outdata-m1-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-9.82557 (48, 51, 0)

92.1757 (49, 32, 0)
6.14297
14.8838

0.186048
-f 's image
Outdata2-m1-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00108315 (40, 41, 0)

491.438 (0, 0, 0)
4.1562
18.0735

0.225919
-log 's data
iter          0 : rms    1.013455e+01 : min    1.000000e+06
iter          1 : rms    1.355871e+00 : min    1.013455e+01
iter          2 : rms    8.647722e-01 : min    1.355871e+00
iter          3 : rms    6.229646e-01 : min    8.647722e-01
iter          4 : rms    4.844930e-01 : min    6.229646e-01
iter          5 : rms    3.971868e-01 : min    4.844930e-01
iter          6 : rms    3.377429e-01 : min    3.971868e-01
iter          7 : rms    2.951728e-01 : min    3.377429e-01
iter          8 : rms    2.629044e-01 : min    2.951728e-01
iter          9 : rms    2.370113e-01 : min    2.629044e-01
Case: solventMode=1
-o 's image
Outdata-m1solventMode-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-20.1029 (48, 51, 0)

87.1488 (49, 32, 0)
2.38926
14.7396

0.184245
-f 's image
Outdata2-m1solventMode-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00627302 (76, 14, 0

222.088 (42, 0, 0)
4.12707
15.7098

0.196372
-log 's data
iter          0 : rms    3.709238e+01 : min    1.000000e+06
iter          1 : rms    3.539059e+00 : min    3.709238e+01
iter          2 : rms    1.971014e+00 : min    3.539059e+00
iter          3 : rms    1.314187e+00 : min    1.971014e+00
iter          4 : rms    9.704149e-01 : min    1.314187e+00
iter          5 : rms    7.649823e-01 : min    9.704149e-01
iter          6 : rms    6.304888e-01 : min    7.649823e-01
iter          7 : rms    5.362647e-01 : min    6.304888e-01
iter          8 : rms    4.668152e-01 : min    5.362647e-01
iter          9 : rms    4.135905e-01 : min    4.668152e-01
Case: solventSTD=2.0, solventMode=1
-o 's image
Outdata-m1solventSTD-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

85.3666 (27, 31, 0)

146.065 (58, 33, 0)
101.654
5.9911

0.0748887
-f 's image
Outdata2-m1solventSTD-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00707058 (78, 44, 0)

8132.32 (0, 0, 0)
4.62714
143.824

1.7978
-log 's data
iter          0 : rms    1.424218e+00 : min    1.000000e+06
iter          1 : rms    2.156973e-01 : min    1.424218e+00
iter          2 : rms    1.394271e-01 : min    2.156973e-01
iter          3 : rms    1.043566e-01 : min    1.394271e-01
iter          4 : rms    8.473523e-02 : min    1.043566e-01
iter          5 : rms    7.243526e-02 : min    8.473523e-02
iter          6 : rms    6.412249e-02 : min    7.243526e-02
iter          7 : rms    5.819677e-02 : min    6.412249e-02
iter          8 : rms    5.380184e-02 : min    5.819677e-02
iter          9 : rms    5.044070e-02 : min    5.380184e-02
Case: MaxIter=5, solventSTD=2.0, solventMode=1
-o 's image
Outdata-m1MaxIter-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

35.7164 (27, 31, 0)

94.8793 (58, 33, 0)
52.0534
5.94982

0.0743728
-f 's image
Outdata2-m1MaxIter-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00307367 (71, 39, 0)

4164.28 (0, 0, 0)
3.33262
73.8045

0.922556
-log 's data
iter          0 : rms    1.424218e+00 : min    1.000000e+06
iter          1 : rms    2.156973e-01 : min    1.424218e+00
iter          2 : rms    1.394271e-01 : min    2.156973e-01
iter          3 : rms    1.043566e-01 : min    1.394271e-01
iter          4 : rms    8.473523e-02 : min    1.043566e-01

Case: m=16

-o 's image
Outdata-m16-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-90.5402 (36, 37, 0)

39.3153 (49, 51, 0)
-1.13944e-07
18.1267

0.226584
-f 's image
Outdata2-m16-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

1.17451e-06 (75, 37, 0)

378.143 (42, 0, 0)
3.33762
19.4523

0.243154

Case: m=17

-o 's image
Outdata-m17-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-363.432 (24, 39, 0)

64206.9 (50, 53, 0)
12232.5
12224.9

152.812
-f 's image
Outdata2-m17-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.000769818 (62, 30, 0)

978599 (0, 0, 0)
2152.97
21751

271.888
-log 's data
iter          0 : rms    2.228456e+00 : min    1.000000e+06
iter          1 : rms    1.072463e+00 : min    2.228456e+00
iter          2 : rms    8.595473e-01 : min    1.072463e+00
iter          3 : rms    7.822678e-01 : min    8.595473e-01
iter          4 : rms    7.485957e-01 : min    7.822678e-01
iter          5 : rms    7.339871e-01 : min    7.485957e-01
iter          6 : rms    7.188863e-01 : min    7.339871e-01
iter          7 : rms    7.127621e-01 : min    7.188863e-01
iter          8 : rms    7.096454e-01 : min    7.127621e-01
iter          9 : rms    7.069848e-01 : min    7.096454e-01
Retrieved from "http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImageMultiCTFCompensation&oldid=4044"