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Opened 2 years ago
Closed 2 years ago
#10321 closed defect (not a bug)
Fit search results list may show wrong results for subsequent searches.
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.6.1-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202311100228 (2023-11-10 02:28:59 UTC)
Description
There is some bug in fitmap search where clearing the fit list after a bad fit by pressing Clear List, then running a new fit search with more initial placements (100) always fails to find the correct position. But if the fit list panel is closed it always finds the correctly location. It seems like some state is being remembered or an incorrect transform is applied that messes up the results.
Log:
Could not find tool "Tabbed Toolbar"
UCSF ChimeraX version: 1.8.dev202311100228 (2023-11-10)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 12654 format ccp4 fromDatabase emdb
Opened emdb 12654 as #1, grid size 250,250,250, pixel 1.54, shown at level 2,
step 1, values float32, fit PDB 7nyu
> open 7nyu format mmcif fromDatabase pdb
7nyu title:
Respiratory complex I from Escherichia coli - conformation 2 [more info...]
Chain information for 7nyu #2
---
Chain | Description | UniProt
A | NADH-quinone oxidoreductase subunit A | NUOA_ECOLI 1-147
B | NADH-quinone oxidoreductase subunit B | NUOB_ECOLI 1-220
D | NADH-quinone oxidoreductase subunit C/D | NUOCD_ECOLI 1-596
E | NADH-quinone oxidoreductase subunit E | NUOE_ECOLI 1-166
F | NADH-quinone oxidoreductase subunit F | NUOF_ECOLI 1-445
G | NADH-quinone oxidoreductase subunit G | NUOG_ECOLI 1-908
H | NADH-quinone oxidoreductase subunit H | NUOH_ECOLI 1-325
I | NADH-quinone oxidoreductase subunit I | NUOI_ECOLI 1-180
J | NADH-quinone oxidoreductase subunit J | NUOJ_ECOLI 1-184
K | NADH-quinone oxidoreductase subunit K | NUOK_ECOLI 1-100
L | NADH-quinone oxidoreductase subunit L | A0A1V3W1N5_ECOLX 1-613
M | NADH-quinone oxidoreductase subunit M | NUOM_ECOLI 1-509
N | NADH-quinone oxidoreductase subunit N | NUON_ECOLI 1-485
Non-standard residues in 7nyu #2
---
CA — calcium ion
FES — FE2/S2 (inorganic) cluster
FMN — flavin mononucleotide (riboflavin monophosphate)
SF4 — iron/sulfur cluster
> open 3rko format mmcif fromDatabase pdb
3rko title:
Crystal structure of the membrane domain of respiratory complex I from E. coli
at 3.0 angstrom resolution [more info...]
Chain information for 3rko #3
---
Chain | Description | UniProt
A E | NADH-QUINONE OXIDOREDUCTASE SUBUNIT A | C6E9R4_ECOBD 1-147
B L | NADH-QUINONE OXIDOREDUCTASE SUBUNIT L | C6E9S4_ECOBD 1-613
C M | NADH-QUINONE OXIDOREDUCTASE SUBUNIT M | C6E9S5_ECOBD 1-509
D N | NADH-QUINONE OXIDOREDUCTASE SUBUNIT N | C6E9S6_ECOBD 1-485
F J | NADH-QUINONE OXIDOREDUCTASE SUBUNIT J | C6E9S2_ECOBD 1-184
G K | NADH-QUINONE OXIDOREDUCTASE SUBUNIT K | C6E9S3_ECOBD 1-100
Non-standard residues in 3rko #3
---
CA7 — 7-cyclohexylheptyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
LFA — eicosane (lipid fragment)
3rko mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete ~/L
> hide atoms
> show cartoons
> matchmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7nyu, chain L (#2) with 3rko, chain L (#3), sequence alignment
score = 3003.3
RMSD between 575 pruned atom pairs is 1.029 angstroms; (across all 612 pairs:
1.204)
> hide #!1 models
> select :547-1000
1042 atoms, 1058 bonds, 137 residues, 2 models selected
> delete :547-1000
> color #2 #0f988cff
> fitmap #3 inMap #1 search 100 radius 60
Found 94 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (96 of 100).
Average map values and times found:
1.444 (1), 1.236 (1), 1.226 (1), 1.208 (1), 1.2 (1), 1.179 (2), 1.155 (1),
1.155 (1), 1.151 (1), 1.149 (1), 1.134 (1), 1.132 (1), 1.125 (1), 1.124 (1),
1.117 (1), 1.113 (1), 1.109 (1), 1.108 (1), 1.097 (1), 1.093 (1), 1.092 (1),
1.092 (1), 1.087 (1), 1.086 (1), 1.086 (1), 1.082 (1), 1.081 (1), 1.078 (1),
1.077 (1), 1.071 (1), 1.068 (1), 1.066 (1), 1.065 (1), 1.064 (1), 1.063 (1),
1.061 (1), 1.057 (1), 1.056 (1), 1.056 (1), 1.052 (1), 1.051 (1), 1.047 (1),
1.045 (1), 1.044 (1), 1.044 (1), 1.044 (2), 1.041 (1), 1.033 (1), 1.029 (1),
1.025 (1), 1.023 (1), 1.023 (1), 1.022 (1), 1.02 (1), 1.018 (1), 1.013 (1),
1.005 (1), 1.002 (1), 0.9995 (1), 0.9956 (1), 0.9948 (1), 0.9924 (1), 0.9885
(1), 0.9871 (1), 0.9844 (1), 0.9768 (1), 0.9687 (1), 0.9624 (1), 0.96 (1),
0.9586 (1), 0.9547 (1), 0.9472 (1), 0.941 (1), 0.9397 (1), 0.9378 (1), 0.9375
(1), 0.9364 (1), 0.9352 (1), 0.9329 (1), 0.9279 (1), 0.918 (1), 0.918 (1),
0.9176 (1), 0.9069 (1), 0.8914 (1), 0.8621 (1), 0.8612 (1), 0.8312 (1), 0.8023
(1), 0.7812 (1), 0.7203 (1), 0.5597 (1), 0.4846 (1), 0.3311 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 112
shifted from previous position = 4.7
rotated from previous position = 27.4 degrees
atoms outside contour = 2745, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06507240 -0.16047499 -0.98489254 174.07468715
-0.45531137 0.87348046 -0.17240455 117.10198807
0.88795104 0.45965163 -0.01622663 168.11639162
Axis 0.31626670 -0.93712882 -0.14752950
Axis point 26.53661708 0.00000000 177.07941558
Rotation angle (degrees) 92.22574957
Shift along axis -79.48774677
Found 94 fits.
Populating font family aliases took 84 ms. Replace uses of missing font family
"Courier" with one that exists to avoid this cost.
> scalebar 60
> close #4
> fitmap #3 inMap #1 search 100 radius 30
Found 99 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (1), 1.208 (1), 1.2 (1), 1.19 (1), 1.179 (1), 1.175 (1), 1.151 (1),
1.139 (1), 1.139 (1), 1.134 (1), 1.134 (1), 1.132 (1), 1.128 (1), 1.123 (1),
1.123 (1), 1.121 (1), 1.119 (1), 1.113 (1), 1.108 (1), 1.105 (1), 1.103 (1),
1.102 (1), 1.1 (1), 1.099 (1), 1.096 (1), 1.096 (1), 1.093 (1), 1.091 (1),
1.09 (1), 1.088 (1), 1.086 (1), 1.086 (1), 1.085 (1), 1.083 (1), 1.072 (2),
1.067 (1), 1.059 (1), 1.059 (1), 1.058 (1), 1.057 (1), 1.054 (1), 1.052 (1),
1.047 (1), 1.045 (1), 1.044 (1), 1.044 (1), 1.044 (1), 1.044 (1), 1.043 (1),
1.039 (1), 1.038 (1), 1.036 (1), 1.035 (1), 1.035 (1), 1.034 (1), 1.034 (1),
1.034 (1), 1.029 (1), 1.029 (1), 1.028 (1), 1.025 (1), 1.025 (1), 1.021 (1),
1.019 (1), 1.014 (1), 1.013 (1), 1.012 (1), 1.012 (1), 1.012 (1), 1.006 (1),
1.001 (1), 1.001 (1), 1 (1), 0.9983 (1), 0.9963 (1), 0.9812 (1), 0.9764 (1),
0.9752 (1), 0.9742 (1), 0.9692 (1), 0.9691 (1), 0.9561 (1), 0.9534 (1), 0.9472
(1), 0.9462 (1), 0.9349 (1), 0.9294 (1), 0.9206 (1), 0.9008 (1), 0.851 (1),
0.8472 (1), 0.8445 (1), 0.8395 (1), 0.8338 (1), 0.8235 (1), 0.8215 (1), 0.8015
(1), 0.7701 (1), 0.7439 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 156
shifted from previous position = 3.03
rotated from previous position = 59.4 degrees
atoms outside contour = 2738, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06521650 -0.15992190 -0.98497299 174.09299778
-0.45562987 0.87339913 -0.17197446 117.06887740
0.88777708 0.45999875 -0.01590518 168.08359221
Axis 0.31622282 -0.93707504 -0.14796452
Axis point 26.55560692 0.00000000 177.07639512
Rotation angle (degrees) 92.21473415
Shift along axis -79.52055109
Found 99 fits.
> select #3/L:141
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.078486,-0.96171,-0.26259,150.65,0.98392,0.032331,0.17567,139.47,-0.16046,-0.27215,0.94878,111.78
> fitmap #3 inMap #1 search 100 radius 30
Found 96 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (2), 1.291 (2), 1.226 (1), 1.22 (2), 1.207 (1), 1.2 (1), 1.2 (1), 1.19
(1), 1.183 (1), 1.178 (1), 1.171 (1), 1.164 (1), 1.161 (1), 1.161 (1), 1.161
(1), 1.155 (1), 1.152 (2), 1.145 (1), 1.145 (1), 1.137 (1), 1.134 (1), 1.133
(1), 1.132 (1), 1.131 (1), 1.13 (1), 1.123 (1), 1.122 (1), 1.12 (1), 1.108
(1), 1.105 (1), 1.103 (1), 1.099 (1), 1.098 (1), 1.095 (1), 1.093 (1), 1.086
(1), 1.085 (1), 1.083 (1), 1.082 (1), 1.081 (1), 1.081 (1), 1.081 (1), 1.077
(1), 1.076 (1), 1.074 (1), 1.068 (1), 1.066 (1), 1.065 (1), 1.064 (1), 1.063
(1), 1.06 (1), 1.055 (1), 1.052 (1), 1.05 (1), 1.048 (1), 1.046 (1), 1.044
(1), 1.041 (1), 1.041 (1), 1.036 (1), 1.032 (1), 1.03 (1), 1.028 (1), 1.026
(1), 1.025 (1), 1.021 (1), 1.02 (1), 1.019 (1), 1.012 (1), 1.012 (1), 1.009
(1), 1.005 (1), 1.004 (1), 0.9988 (1), 0.9973 (1), 0.9947 (1), 0.994 (1),
0.9903 (1), 0.9863 (1), 0.9834 (1), 0.9763 (1), 0.9754 (1), 0.9676 (1), 0.9535
(1), 0.9534 (1), 0.947 (1), 0.9271 (1), 0.9254 (1), 0.9136 (1), 0.9127 (1),
0.8985 (1), 0.8982 (1), 0.8735 (1), 0.8496 (1), 0.8482 (1), 0.7385 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 92
shifted from previous position = 4.71
rotated from previous position = 14 degrees
atoms outside contour = 2737, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06523183 -0.15995965 -0.98496580 174.09415011
-0.45566132 0.87337481 -0.17201439 117.07105250
0.88775973 0.46003172 -0.01591562 168.08263743
Axis 0.31625944 -0.93706317 -0.14796142
Axis point 26.55870280 0.00000000 177.07711292
Rotation angle (degrees) 92.21529106
Shift along axis -79.51379922
Found 96 fits.
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.127 (1), 1.11 (1), 1.106 (1), 1.087 (1), 1.009 (1), 0.988 (1), 0.9818 (1),
0.9721 (1), 0.9088 (1), 0.898 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.127, steps = 160
shifted from previous position = 14.9
rotated from previous position = 46.4 degrees
atoms outside contour = 2821, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.29298609 -0.95154230 -0.09341400 142.85569864
0.80765384 0.29859826 -0.50846250 176.59015925
0.51171684 0.07352636 0.85600207 100.41584715
Axis 0.29856713 -0.31043924 0.90248831
Axis point -84.97120586 188.64870885 0.00000000
Rotation angle (degrees) 77.06807361
Shift along axis 78.45563002
Found 10 fits.
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.154 (1), 1.107 (1), 1.078 (1), 1.068 (1), 1.035 (1), 1.032 (1), 1.011 (1),
0.9783 (1), 0.9605 (1), 0.8317 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.154, steps = 180
shifted from previous position = 10.7
rotated from previous position = 49.4 degrees
atoms outside contour = 2953, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.07943776 -0.63795916 0.76596174 67.76620603
0.97522859 0.10939505 0.19225450 132.68748550
-0.20644289 0.76226016 0.61346599 94.45287329
Axis 0.28964346 0.49411902 0.81972743
Axis point -9.46204214 48.40265575 0.00000000
Rotation angle (degrees) 100.27007885
Shift along axis 162.61705982
Found 10 fits.
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.178 (1), 1.169 (1), 1.147 (1), 1.111 (1), 1.082 (1), 1.041 (1), 1.031 (1),
1.028 (1), 0.9803 (1), 0.9155 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.178, steps = 140
shifted from previous position = 14.3
rotated from previous position = 15.8 degrees
atoms outside contour = 2876, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.38243718 0.91365198 0.13777453 63.98924846
0.67441480 -0.17409630 -0.71753386 198.94420503
-0.63159022 0.36732895 -0.68276134 185.72949332
Axis 0.80281312 0.56934030 -0.17703874
Axis point 0.00000000 26.14191245 129.94015355
Rotation angle (degrees) 137.49431265
Shift along axis 131.75704600
Found 10 fits.
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.2 (1), 1.174 (1), 1.13 (1), 1.084 (1), 1.061 (1), 1.045 (1), 1.025 (1),
0.9465 (1), 0.9171 (1), 0.9162 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.2, steps = 136
shifted from previous position = 21.2
rotated from previous position = 19 degrees
atoms outside contour = 2801, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.01163033 0.11766181 -0.99298557 171.66178295
-0.98192783 -0.18625408 -0.03357050 132.68853043
-0.18889757 0.97543055 0.11336927 121.06536850
Axis 0.59520700 -0.47432934 -0.64864497
Axis point 190.06068339 -61.17982361 0.00000000
Rotation angle (degrees) 122.04784880
Shift along axis -39.29221084
Found 10 fits.
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.207 (1), 1.174 (1), 1.093 (1), 1.072 (1), 1.045 (1), 1.033 (1), 0.9736 (1),
0.9309 (1), 0.8562 (1), 0.7454 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.207, steps = 216
shifted from previous position = 4.4
rotated from previous position = 49 degrees
atoms outside contour = 2856, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.44679080 -0.21843791 -0.86756133 157.72006625
-0.88122658 0.27473759 0.38465404 99.00915526
0.15432861 0.93637811 -0.31524343 152.69493664
Axis 0.41261458 -0.76423472 -0.49567580
Axis point 78.01074410 0.00000000 92.73521529
Rotation angle (degrees) 138.04314189
Shift along axis -86.27582083
Found 10 fits.
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.272 (1), 1.171 (1), 1.154 (1), 1.087 (1), 1.048 (1), 1.035 (1), 1.024 (1),
0.9722 (1), 0.9709 (1), 0.9447 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.272, steps = 204
shifted from previous position = 24.2
rotated from previous position = 55.1 degrees
atoms outside contour = 2845, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.29372854 -0.26983268 -0.91701346 170.85752001
-0.16926897 0.92948717 -0.32772148 128.42011481
0.94078222 0.25148322 0.22734268 151.67630087
Axis 0.29724326 -0.95340600 0.05160850
Axis point 3.23951305 0.00000000 204.51207708
Rotation angle (degrees) 76.98070164
Shift along axis -63.82247690
Found 10 fits.
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.19 (1), 1.119 (1), 1.062 (1), 1.058 (1), 1.015 (1), 1.007 (1), 0.9578 (1),
0.9167 (1), 0.9138 (1), 0.8616 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.19, steps = 336
shifted from previous position = 9.51
rotated from previous position = 33 degrees
atoms outside contour = 3010, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.70460364 -0.65321573 0.27720484 102.63637029
0.59258760 0.32676365 -0.73625068 188.89463261
0.39035008 0.68303335 0.61732661 108.35346702
Axis 0.75019927 -0.05980584 0.65850157
Axis point 0.00000000 81.64470458 193.03874014
Rotation angle (degrees) 71.07398220
Shift along axis 137.05165535
Found 10 fits.
> time fitmap #3 in #1 search 10 radius 30
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.152 (1), 1.118 (1), 1.091 (1), 1.026 (1), 1.009 (1), 0.9828 (1), 0.9686 (1),
0.937 (1), 0.9025 (1), 0.8994 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.152, steps = 196
shifted from previous position = 20.3
rotated from previous position = 17 degrees
atoms outside contour = 3031, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.61623154 0.64195014 -0.45624376 109.59989159
0.62782141 -0.05065068 0.77670750 98.56756997
0.47549846 -0.76507131 -0.43424262 225.81803342
Axis -0.85582758 -0.51720174 -0.00784273
Axis point 0.00000000 98.59609214 104.05186093
Rotation angle (degrees) 115.74273000
Shift along axis -146.54895923
Found 10 fits.
command time 0.3506 seconds
draw time 0.01984 seconds
> time fitmap #3 in #1 search 10 radius 30
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.159 (1), 1.093 (1), 1.092 (1), 1.074 (1), 1.066 (1), 1.06 (1), 1.06 (1),
1.044 (1), 1.021 (1), 0.9512 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.159, steps = 128
shifted from previous position = 7.01
rotated from previous position = 35.1 degrees
atoms outside contour = 2938, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.05898764 0.99721598 -0.04561134 68.19914832
0.53087238 -0.07003096 -0.84455301 199.15118203
-0.84539609 0.02560454 -0.53352559 193.28024570
Axis 0.68486495 0.62947744 -0.36703972
Axis point 0.00000000 7.93992874 150.37317487
Rotation angle (degrees) 140.55948289
Shift along axis 101.12685382
Found 10 fits.
command time 0.3874 seconds
draw time 0.01954 seconds
> time fitmap #3 in #1 search 10 radius 30
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.208 (1), 1.112 (1), 1.088 (1), 1.084 (1), 1.074 (1), 1.015 (1), 0.9625 (1),
0.9554 (1), 0.9367 (1), 0.9055 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.208, steps = 208
shifted from previous position = 18.7
rotated from previous position = 21.7 degrees
atoms outside contour = 2827, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.55309020 0.82893333 0.08342959 75.34618574
-0.17624167 0.01853984 0.98417218 70.37067167
0.81426637 -0.55903984 0.15634683 174.28596910
Axis -0.77884370 -0.36884603 -0.50730178
Axis point 0.00000000 65.76954351 58.94288260
Rotation angle (degrees) 97.81711851
Shift along axis -173.05442790
Found 10 fits.
command time 0.593 seconds
draw time 0.01897 seconds
> view matrix models
> #3,-0.27959,-0.94391,-0.17565,139.39,0.75312,-0.32909,0.56966,121.1,-0.59551,0.026988,0.80289,106.35
> time fitmap #3 in #1 search 10 radius 30
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.208 (1), 1.151 (1), 1.111 (1), 1.093 (1), 1.046 (1), 1.028 (1), 1.012 (1),
1.007 (1), 0.9736 (1), 0.9173 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.208, steps = 276
shifted from previous position = 23.6
rotated from previous position = 45.5 degrees
atoms outside contour = 2831, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.55393223 0.82842169 0.08292294 75.41663228
-0.17562619 0.01891082 0.98427510 70.34130560
0.81382681 -0.55978532 0.15596769 174.35198526
Axis -0.77922696 -0.36885862 -0.50670373
Axis point 0.00000000 65.83713363 59.01250359
Rotation angle (degrees) 97.79300678
Shift along axis -173.05747071
Found 10 fits.
command time 0.4231 seconds
draw time 0.0191 seconds
> view matrix models
> #3,0.75823,-0.51814,0.39576,99.983,-0.39046,-0.84697,-0.36079,186.77,0.52214,0.11903,-0.84451,231.25
> time fitmap #3 in #1 search 10 radius 30
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.204 (1), 1.136 (1), 1.109 (1), 1.108 (1), 1.079 (1), 1.078 (1), 1.07 (1),
0.9846 (1), 0.9445 (1), 0.936 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.204, steps = 192
shifted from previous position = 15.9
rotated from previous position = 38.6 degrees
atoms outside contour = 2833, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.02677911 0.99617459 -0.08317789 74.53482548
0.99903597 0.02956508 0.03244669 148.57985066
0.03478157 -0.08222878 -0.99600617 224.71733453
Axis -0.69695003 -0.71690880 0.01739027
Axis point -41.48937374 0.00000000 113.20711067
Rotation angle (degrees) 175.28097097
Shift along axis -154.55735731
Found 10 fits.
command time 0.3997 seconds
draw time 0.01259 seconds
> time fitmap #3 in #1 search 5 radius 30
> fitmap #3 inMap #1 search 5 radius 30
Found 5 unique fits from 5 random placements having fraction of points inside
contour >= 0.100 (5 of 5).
Average map values and times found:
1.291 (1), 1.203 (1), 1.053 (1), 1.033 (1), 0.7488 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.291, steps = 92
shifted from previous position = 12.5
rotated from previous position = 18.4 degrees
atoms outside contour = 2804, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.27621960 -0.38895006 -0.87887429 168.33625238
-0.32944121 0.89736834 -0.29359518 125.90375106
0.90286820 0.20844054 -0.37600700 186.10430426
Axis 0.27106640 -0.96202423 0.03213088
Axis point 36.09748584 0.00000000 160.55808685
Rotation angle (degrees) 112.17453205
Shift along axis -69.51246130
Found 5 fits.
command time 0.2056 seconds
draw time 0.01366 seconds
> time fitmap #3 in #1 search 5 radius 30
> fitmap #3 inMap #1 search 5 radius 30
Found 5 unique fits from 5 random placements having fraction of points inside
contour >= 0.100 (5 of 5).
Average map values and times found:
1.444 (1), 1.154 (1), 1.073 (1), 0.9687 (1), 0.95 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 112
shifted from previous position = 5.57
rotated from previous position = 36.8 degrees
atoms outside contour = 2738, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06518205 -0.15995715 -0.98496926 174.09075818
-0.45552836 0.87344854 -0.17199166 117.07058190
0.88783168 0.45989220 -0.01593178 168.08923058
Axis 0.31617824 -0.93710087 -0.14789615
Axis point 26.54862537 0.00000000 177.07761446
Rotation angle (degrees) 92.21506806
Shift along axis -79.52298438
Found 5 fits.
command time 0.1882 seconds
draw time 0.01295 seconds
> time fitmap #3 in #1 search 5 radius 30
> fitmap #3 inMap #1 search 5 radius 30
Found 5 unique fits from 5 random placements having fraction of points inside
contour >= 0.100 (5 of 5).
Average map values and times found:
1.444 (1), 1.161 (1), 1.13 (1), 1.07 (1), 0.9875 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 140
shifted from previous position = 15.3
rotated from previous position = 26.1 degrees
atoms outside contour = 2738, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06521029 -0.15990421 -0.98497600 174.09098037
-0.45561813 0.87340874 -0.17195608 117.06796835
0.88778353 0.45998620 -0.01590000 168.08384916
Axis 0.31620736 -0.93707979 -0.14796750
Axis point 26.55370204 0.00000000 177.07528967
Rotation angle (degrees) 92.21448849
Shift along axis -79.52412465
Found 5 fits.
command time 0.2239 seconds
draw time 0.01405 seconds
> view matrix models
> #3,0.94775,0.22876,0.22235,90.138,0.17133,-0.95294,0.25011,155.65,0.2691,-0.19895,-0.94234,244.97
> time fitmap #3 in #1 search 5 radius 30
> fitmap #3 inMap #1 search 5 radius 30
Found 5 unique fits from 5 random placements having fraction of points inside
contour >= 0.100 (5 of 5).
Average map values and times found:
1.238 (1), 1.147 (1), 1.108 (1), 0.9879 (1), 0.9696 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.238, steps = 136
shifted from previous position = 18.6
rotated from previous position = 37.6 degrees
atoms outside contour = 2806, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.21534198 0.88726814 -0.40790008 100.74732723
0.88494035 -0.35392734 -0.30268116 184.68640809
-0.41292649 -0.29578734 -0.86139483 218.83852650
Axis 0.77953165 0.56837124 -0.26321956
Axis point 0.00000000 55.25748542 126.58904581
Rotation angle (degrees) 179.74665025
Shift along axis 125.90359337
Found 5 fits.
command time 0.2039 seconds
draw time 0.01506 seconds
> view matrix models
> #3,0.83989,0.11801,0.52976,71.195,0.22258,0.81532,-0.53451,152.8,-0.49501,0.56685,0.65852,100.06
> time fitmap #3 in #1 search 5 radius 30
> fitmap #3 inMap #1 search 5 radius 30
Found 5 unique fits from 5 random placements having fraction of points inside
contour >= 0.100 (5 of 5).
Average map values and times found:
1.255 (1), 1.078 (1), 0.9895 (1), 0.9749 (1), 0.8799 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.255, steps = 148
shifted from previous position = 9.14
rotated from previous position = 24.4 degrees
atoms outside contour = 2852, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.10049275 0.86209153 -0.49668800 102.66071821
0.98871216 -0.14228842 -0.04692474 160.91248518
-0.11112639 -0.48636596 -0.86665937 234.12030718
Axis -0.73465114 -0.64457603 0.21168243
Axis point 0.00000000 62.66269858 123.78974102
Rotation angle (degrees) 162.59755147
Shift along axis -129.58098798
Found 5 fits.
command time 0.1923 seconds
draw time 0.01413 seconds
> time fitmap #3 in #1 search 5 radius 30
> fitmap #3 inMap #1 search 5 radius 30
Found 5 unique fits from 5 random placements having fraction of points inside
contour >= 0.100 (5 of 5).
Average map values and times found:
1.097 (1), 1.064 (1), 1.023 (1), 0.9603 (1), 0.8834 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.097, steps = 124
shifted from previous position = 16.4
rotated from previous position = 18.2 degrees
atoms outside contour = 2825, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.48202518 -0.77021566 -0.41763527 152.20575110
-0.87201044 0.37541503 0.31410359 100.16146150
-0.08514098 0.51558814 -0.85259557 197.21648945
Axis 0.50135016 -0.82733921 -0.25329400
Axis point 95.23061986 0.00000000 94.35090974
Rotation angle (degrees) 168.40795005
Shift along axis -56.51287953
Found 5 fits.
command time 0.1814 seconds
draw time 0.01297 seconds
> time fitmap #3 in #1 search 5 radius 30
> fitmap #3 inMap #1 search 5 radius 30
Found 5 unique fits from 5 random placements having fraction of points inside
contour >= 0.100 (5 of 5).
Average map values and times found:
1.144 (1), 1.123 (1), 1.119 (1), 1.094 (1), 0.9622 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.144, steps = 108
shifted from previous position = 14.8
rotated from previous position = 25.9 degrees
atoms outside contour = 2746, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.00147787 -0.98054359 -0.19629564 163.67789923
-0.92630760 -0.07261486 0.36970365 106.75075256
-0.37676452 0.18237639 -0.90817767 201.85043842
Axis -0.70500515 0.67919367 0.20411687
Axis point 0.00000000 141.78616942 119.51383694
Rotation angle (degrees) 172.36538073
Shift along axis -1.68824575
Found 5 fits.
command time 0.2059 seconds
draw time 0.008515 seconds
> view matrix models
> #3,-0.0014779,-0.98054,-0.1963,158.36,-0.92631,-0.072615,0.3697,112,-0.37676,0.18238,-0.90818,225.15
> time fitmap #3 in #1 search 10 radius 30
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.059 (1), 1.034 (1), 1.006 (1), 0.9782 (1), 0.9761 (1), 0.9573 (1), 0.9515
(1), 0.9468 (1), 0.9417 (1), 0.8643 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.059, steps = 208
shifted from previous position = 22.3
rotated from previous position = 39.5 degrees
atoms outside contour = 2888, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.98125178 -0.15457742 -0.11511039 132.84874080
-0.02584941 0.48631233 -0.87340225 184.00003985
0.19098774 0.86000349 0.47319936 100.01389770
Axis 0.98214096 -0.17343401 0.07293679
Axis point 0.00000000 25.44124008 216.72794459
Rotation angle (degrees) 61.94091510
Shift along axis 105.85901772
Found 10 fits.
command time 0.364 seconds
draw time 0.01534 seconds
> view matrix models
> #3,0.36208,0.049261,0.93084,57.6,-0.91392,0.21525,0.34411,99.324,-0.18342,-0.97531,0.12296,171.16
> view matrix models
> #3,0.36208,0.049261,0.93084,37.803,-0.91392,0.21525,0.34411,96.855,-0.18342,-0.97531,0.12296,186.38
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 97 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.255 (1), 1.24 (1), 1.233 (1), 1.226 (2), 1.22 (1), 1.22 (1), 1.212 (1),
1.208 (1), 1.203 (1), 1.2 (1), 1.191 (2), 1.183 (1), 1.182 (1), 1.179 (1),
1.178 (1), 1.175 (1), 1.159 (1), 1.146 (1), 1.146 (1), 1.144 (1), 1.142 (1),
1.139 (1), 1.137 (1), 1.135 (1), 1.134 (1), 1.13 (1), 1.13 (1), 1.128 (1),
1.128 (1), 1.126 (1), 1.123 (1), 1.122 (1), 1.121 (1), 1.119 (1), 1.119 (1),
1.114 (1), 1.109 (1), 1.106 (1), 1.104 (1), 1.101 (1), 1.099 (1), 1.099 (1),
1.097 (1), 1.097 (1), 1.096 (1), 1.092 (1), 1.091 (1), 1.09 (1), 1.088 (1),
1.088 (1), 1.087 (1), 1.086 (1), 1.085 (1), 1.084 (1), 1.082 (1), 1.078 (1),
1.078 (1), 1.073 (1), 1.071 (1), 1.07 (1), 1.068 (1), 1.067 (1), 1.064 (1),
1.063 (2), 1.059 (1), 1.043 (1), 1.041 (1), 1.04 (1), 1.037 (1), 1.033 (1),
1.028 (1), 1.028 (1), 1.024 (1), 1.017 (1), 1.014 (1), 1.013 (1), 1.01 (1),
1.01 (1), 1.007 (1), 1.001 (1), 0.9959 (1), 0.9944 (1), 0.9881 (1), 0.9876
(1), 0.9792 (1), 0.978 (1), 0.9592 (1), 0.9492 (1), 0.9476 (1), 0.9455 (1),
0.9437 (1), 0.9163 (1), 0.9153 (1), 0.9098 (1), 0.8989 (1), 0.8204 (1), 0.7672
(1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.255, steps = 196
shifted from previous position = 19.1
rotated from previous position = 43.8 degrees
atoms outside contour = 2853, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.10058329 0.86224349 -0.49640615 102.63808239
0.98870123 -0.14235882 -0.04693922 160.91537606
-0.11114090 -0.48607598 -0.86682029 234.10605064
Axis -0.73469384 -0.64456459 0.21156900
Axis point 0.00000000 62.65183822 123.77808866
Rotation angle (degrees) 162.61103661
Shift along axis -129.59833936
Found 97 fits.
command time 4.719 seconds
draw time 0.01323 seconds
> view matrix models
> #3,-0.18475,-0.92203,0.34019,122.51,-0.88546,0.30635,0.34943,96.375,-0.4264,-0.23667,-0.87302,212.39
> view matrix models
> #3,-0.18475,-0.92203,0.34019,97.261,-0.88546,0.30635,0.34943,94.847,-0.4264,-0.23667,-0.87302,232.14
> view matrix models
> #3,-0.18475,-0.92203,0.34019,102.2,-0.88546,0.30635,0.34943,93.885,-0.4264,-0.23667,-0.87302,236.08
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 93 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (3), 1.272 (1), 1.238 (1), 1.226 (1), 1.226 (1), 1.207 (1), 1.205 (1),
1.2 (1), 1.189 (1), 1.179 (1), 1.169 (1), 1.14 (1), 1.139 (1), 1.131 (1), 1.13
(1), 1.13 (1), 1.126 (1), 1.125 (1), 1.119 (1), 1.117 (1), 1.117 (1), 1.111
(1), 1.111 (1), 1.11 (1), 1.11 (1), 1.109 (1), 1.109 (1), 1.109 (1), 1.103
(2), 1.102 (2), 1.1 (2), 1.098 (1), 1.097 (1), 1.088 (1), 1.087 (1), 1.078
(1), 1.076 (1), 1.074 (1), 1.065 (1), 1.06 (1), 1.05 (1), 1.046 (1), 1.045
(1), 1.044 (2), 1.04 (1), 1.039 (1), 1.037 (1), 1.035 (1), 1.035 (2), 1.034
(1), 1.034 (1), 1.032 (1), 1.032 (1), 1.027 (1), 1.026 (1), 1.026 (1), 1.012
(1), 1.006 (1), 1.003 (1), 1 (1), 0.9998 (1), 0.9956 (1), 0.9946 (1), 0.9944
(1), 0.9917 (1), 0.9909 (1), 0.9881 (1), 0.9878 (1), 0.985 (1), 0.9846 (1),
0.9841 (1), 0.9838 (1), 0.9813 (1), 0.9787 (1), 0.9751 (1), 0.9745 (1), 0.9694
(1), 0.9687 (1), 0.9684 (1), 0.9672 (1), 0.9624 (1), 0.9512 (1), 0.9468 (1),
0.9374 (1), 0.9354 (1), 0.9342 (1), 0.9334 (1), 0.9311 (1), 0.9227 (1), 0.9161
(1), 0.9114 (1), 0.9089 (1), 0.9067 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 188
shifted from previous position = 4.85
rotated from previous position = 47.4 degrees
atoms outside contour = 2744, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06494577 -0.16038638 -0.98491523 174.07258870
-0.45521726 0.87355606 -0.17226928 117.09607227
0.88800822 0.45953861 -0.01627680 168.12440609
Axis 0.31614317 -0.93717088 -0.14752708
Axis point 26.53111407 0.00000000 177.07218877
Rotation angle (degrees) 92.22865150
Shift along axis -79.51007161
Found 93 fits.
command time 4.276 seconds
draw time 0.02062 seconds
> view matrix models
> #3,-0.42039,-0.84433,-0.33223,163.07,-0.50424,0.52181,-0.68808,165.67,0.75433,-0.12174,-0.64511,208.56
> view matrix models
> #3,-0.42039,-0.84433,-0.33223,147.28,-0.50424,0.52181,-0.68808,159.92,0.75433,-0.12174,-0.64511,227.97
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 100 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.291 (1), 1.272 (1), 1.238 (1), 1.22 (1), 1.218 (1), 1.2 (1), 1.183 (1),
1.182 (1), 1.171 (1), 1.168 (1), 1.152 (1), 1.149 (1), 1.143 (1), 1.142 (1),
1.138 (1), 1.129 (1), 1.128 (1), 1.123 (1), 1.12 (1), 1.117 (1), 1.115 (1),
1.11 (1), 1.11 (1), 1.109 (1), 1.108 (1), 1.107 (1), 1.101 (1), 1.097 (1),
1.093 (1), 1.092 (1), 1.09 (1), 1.089 (1), 1.088 (1), 1.088 (1), 1.087 (1),
1.086 (1), 1.082 (1), 1.081 (1), 1.076 (1), 1.074 (1), 1.072 (1), 1.07 (1),
1.07 (1), 1.069 (1), 1.069 (1), 1.065 (1), 1.064 (1), 1.062 (1), 1.06 (1),
1.059 (1), 1.057 (1), 1.057 (1), 1.052 (1), 1.052 (1), 1.05 (1), 1.044 (1),
1.042 (1), 1.04 (1), 1.036 (1), 1.035 (1), 1.035 (1), 1.035 (1), 1.032 (1),
1.031 (1), 1.03 (1), 1.029 (1), 1.026 (1), 1.024 (1), 1.023 (1), 1.021 (1),
1.019 (1), 1.018 (1), 1.018 (1), 1.012 (1), 1.01 (1), 1.009 (1), 1.003 (1),
1.003 (1), 1.001 (1), 1 (1), 0.9981 (1), 0.9939 (1), 0.9925 (1), 0.9923 (1),
0.9914 (1), 0.9858 (1), 0.9835 (1), 0.9736 (1), 0.9732 (1), 0.9684 (1), 0.9624
(1), 0.9474 (1), 0.9464 (1), 0.9411 (1), 0.9401 (1), 0.9312 (1), 0.9277 (1),
0.8935 (1), 0.8748 (1), 0.8588 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.291, steps = 172
shifted from previous position = 18
rotated from previous position = 33.7 degrees
atoms outside contour = 2802, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.27640069 -0.38972269 -0.87847494 168.32365301
-0.32899336 0.89722702 -0.29452807 125.95983342
0.90297601 0.20760445 -0.37621047 186.11551017
Axis 0.27115009 -0.96197828 0.03279366
Axis point 36.10343037 0.00000000 160.58064989
Rotation angle (degrees) 112.19080366
Shift along axis -69.42624167
Found 100 fits.
command time 3.685 seconds
draw time 0.01932 seconds
> mmaker #3 to #1
No 'to' model specified
> mmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7nyu, chain L (#2) with 3rko, chain L (#3), sequence alignment
score = 2907.3
RMSD between 508 pruned atom pairs is 1.010 angstroms; (across all 546 pairs:
1.213)
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 95 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.291 (1), 1.272 (2), 1.226 (1), 1.212 (1), 1.208 (1), 1.205 (1), 1.2 (1),
1.189 (1), 1.184 (2), 1.174 (1), 1.168 (1), 1.142 (1), 1.141 (1), 1.134 (1),
1.133 (1), 1.131 (1), 1.131 (1), 1.13 (1), 1.121 (1), 1.113 (1), 1.108 (1),
1.108 (1), 1.106 (1), 1.106 (1), 1.105 (1), 1.105 (1), 1.105 (1), 1.096 (1),
1.092 (1), 1.091 (1), 1.087 (1), 1.082 (1), 1.077 (1), 1.076 (1), 1.073 (1),
1.073 (1), 1.072 (1), 1.071 (1), 1.07 (1), 1.069 (1), 1.069 (1), 1.065 (1),
1.061 (1), 1.06 (2), 1.06 (1), 1.058 (1), 1.056 (1), 1.055 (1), 1.054 (1),
1.052 (1), 1.044 (2), 1.041 (1), 1.04 (1), 1.039 (1), 1.038 (1), 1.035 (1),
1.031 (1), 1.03 (1), 1.026 (1), 1.022 (1), 1.018 (1), 1.015 (1), 1.014 (1),
1.007 (1), 1.007 (1), 1.007 (1), 1.001 (1), 0.9899 (1), 0.9877 (1), 0.9794
(1), 0.9789 (1), 0.9721 (1), 0.9694 (1), 0.9662 (1), 0.9624 (1), 0.9617 (1),
0.9608 (1), 0.9468 (1), 0.9435 (1), 0.943 (2), 0.9404 (1), 0.9369 (1), 0.9368
(1), 0.9291 (1), 0.926 (1), 0.9173 (1), 0.9118 (1), 0.9066 (1), 0.906 (1),
0.9055 (1), 0.8258 (1), 0.8197 (1), 0.7752 (1), 0.7561 (1), 0.7291 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.291, steps = 268
shifted from previous position = 6.24
rotated from previous position = 58 degrees
atoms outside contour = 2802, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.27615412 -0.38949439 -0.87865372 168.35545053
-0.32957934 0.89714950 -0.29410877 125.93097866
0.90283770 0.20836653 -0.37612100 186.09216379
Axis 0.27131975 -0.96194539 0.03235211
Axis point 36.13351387 0.00000000 160.56828560
Rotation angle (degrees) 112.18280581
Shift along axis -69.44009250
Found 95 fits.
command time 3.754 seconds
draw time 0.01215 seconds
> view matrix models
> #3,-0.27615,-0.38949,-0.87865,174.33,-0.32958,0.89715,-0.29411,129.8,0.90284,0.20837,-0.37612,195.15
> view matrix models
> #3,-0.27615,-0.38949,-0.87865,171.76,-0.32958,0.89715,-0.29411,129.1,0.90284,0.20837,-0.37612,200.08
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 96 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (2), 1.291 (1), 1.272 (1), 1.255 (1), 1.238 (1), 1.226 (1), 1.212 (2),
1.207 (2), 1.19 (1), 1.183 (1), 1.179 (1), 1.161 (1), 1.159 (1), 1.152 (1),
1.145 (1), 1.143 (1), 1.139 (1), 1.138 (1), 1.137 (1), 1.134 (2), 1.123 (1),
1.116 (1), 1.115 (1), 1.106 (1), 1.096 (1), 1.096 (1), 1.092 (1), 1.087 (1),
1.082 (1), 1.082 (1), 1.082 (1), 1.082 (1), 1.079 (1), 1.075 (1), 1.072 (1),
1.066 (1), 1.064 (1), 1.062 (1), 1.061 (1), 1.058 (1), 1.058 (1), 1.054 (1),
1.053 (1), 1.052 (1), 1.05 (1), 1.05 (1), 1.044 (1), 1.042 (1), 1.042 (1),
1.042 (1), 1.041 (1), 1.04 (1), 1.038 (1), 1.033 (1), 1.028 (1), 1.027 (1),
1.024 (1), 1.023 (1), 1.021 (1), 1.02 (1), 1.015 (1), 1.011 (1), 1.009 (1),
1.002 (1), 1.001 (1), 0.9963 (1), 0.9959 (1), 0.9931 (1), 0.9894 (1), 0.9815
(1), 0.977 (1), 0.9767 (1), 0.9759 (1), 0.9749 (1), 0.9649 (1), 0.9611 (1),
0.9585 (1), 0.9564 (1), 0.9459 (1), 0.9456 (1), 0.945 (1), 0.9429 (1), 0.9354
(1), 0.93 (1), 0.9235 (1), 0.9205 (1), 0.9141 (1), 0.9136 (1), 0.9082 (1),
0.9039 (1), 0.901 (1), 0.8984 (1), 0.8866 (1), 0.8112 (1), 0.697 (1), 0.6633
(1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 184
shifted from previous position = 19.1
rotated from previous position = 37.7 degrees
atoms outside contour = 2744, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06502978 -0.16044950 -0.98489927 174.07940810
-0.45532298 0.87348284 -0.17236196 117.09976346
0.88794799 0.45965583 -0.01625404 168.11862427
Axis 0.31624800 -0.93713217 -0.14754830
Axis point 26.54026033 0.00000000 177.07797350
Rotation angle (degrees) 92.22768944
Shift along axis -79.49130636
Found 96 fits.
command time 3.723 seconds
draw time 0.05328 seconds
> view matrix models
> #3,0.64168,-0.26618,0.7193,68.046,-0.6115,0.38852,0.68929,71.602,-0.46294,-0.88215,0.086534,186.83
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 96 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (2), 1.238 (1), 1.226 (1), 1.212 (1), 1.208 (1), 1.2 (1), 1.2 (1), 1.193
(1), 1.184 (1), 1.183 (2), 1.182 (1), 1.168 (1), 1.158 (1), 1.153 (1), 1.143
(1), 1.143 (1), 1.142 (1), 1.137 (1), 1.136 (1), 1.133 (1), 1.131 (1), 1.13
(2), 1.123 (1), 1.12 (1), 1.119 (1), 1.115 (1), 1.114 (1), 1.113 (1), 1.111
(1), 1.111 (1), 1.106 (1), 1.104 (1), 1.099 (1), 1.092 (1), 1.092 (1), 1.091
(1), 1.09 (1), 1.089 (1), 1.089 (1), 1.083 (1), 1.083 (1), 1.081 (1), 1.078
(1), 1.078 (1), 1.076 (1), 1.074 (1), 1.074 (1), 1.068 (1), 1.066 (2), 1.065
(1), 1.064 (1), 1.055 (1), 1.055 (1), 1.053 (1), 1.052 (1), 1.045 (1), 1.042
(1), 1.041 (1), 1.041 (1), 1.04 (1), 1.038 (1), 1.037 (1), 1.032 (1), 1.03
(1), 1.03 (1), 1.026 (1), 1.026 (1), 1.025 (1), 1.025 (1), 1.02 (1), 1.014
(1), 1.01 (1), 1.008 (1), 1.004 (1), 0.9913 (1), 0.9837 (1), 0.9808 (1),
0.9767 (1), 0.9767 (1), 0.9651 (1), 0.9622 (1), 0.9613 (1), 0.9594 (1), 0.9576
(1), 0.9531 (1), 0.9468 (1), 0.9448 (1), 0.9445 (1), 0.9417 (1), 0.9411 (1),
0.9372 (1), 0.9342 (1), 0.9087 (1), 0.9063 (1), 0.8893 (1), 0.834 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 284
shifted from previous position = 27.8
rotated from previous position = 76.9 degrees
atoms outside contour = 2745, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06502817 -0.16043482 -0.98490178 174.07281461
-0.45524489 0.87352599 -0.17234962 117.09939932
0.88798812 0.45957901 -0.01623342 168.11933718
Axis 0.31620301 -0.93715237 -0.14751639
Axis point 26.53173612 0.00000000 177.07739353
Rotation angle (degrees) 92.22590750
Shift along axis -79.49799105
Found 96 fits.
command time 3.695 seconds
draw time 0.06088 seconds
> view matrix models
> #3,-0.99112,0.10097,-0.086477,89.952,-0.13103,-0.85182,0.50717,130.72,-0.022453,0.514,0.85749,94.337
> time fitmap #3 in #1 search 10 radius 30
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.131 (1), 1.123 (1), 1.092 (1), 1.042 (1), 1.028 (1), 1.005 (1), 0.9934 (1),
0.9874 (1), 0.9843 (1), 0.9459 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.131, steps = 104
shifted from previous position = 9.43
rotated from previous position = 26.1 degrees
atoms outside contour = 3113, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.79134814 0.50256901 0.34812608 67.45797352
-0.01170182 0.58177106 -0.81326808 170.14460794
-0.61125332 0.63950505 0.46626463 117.80950165
Axis 0.80027923 0.52848680 -0.28329287
Axis point 0.00000000 -82.92769794 180.03137345
Rotation angle (degrees) 65.18485584
Shift along axis 110.52980308
Found 10 fits.
command time 0.3353 seconds
draw time 0.0537 seconds
Drag select of 7 residues
> select #3/L:523
5 atoms, 4 bonds, 1 residue, 1 model selected
> view matrix models
> #3,0.31297,-0.42881,0.84745,57.101,-0.3559,0.77431,0.52324,67.549,-0.88056,-0.46536,0.089725,176.01
> view matrix models
> #3,0.24238,-0.5565,0.79471,63.566,-0.49263,0.63508,0.59497,72.558,-0.83581,-0.5357,-0.12022,185.11
> time fitmap #3 in #1 search 10 radius 30
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.444 (1), 1.291 (1), 1.132 (1), 1.096 (1), 1.09 (1), 1.014 (1), 0.9986 (1),
0.9781 (1), 0.9641 (1), 0.9402 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 136
shifted from previous position = 20.4
rotated from previous position = 21.9 degrees
atoms outside contour = 2740, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06530593 -0.15989107 -0.98497185 174.09624916
-0.45576224 0.87332795 -0.17198568 117.06865346
0.88770227 0.46014457 -0.01583889 168.07310540
Axis 0.31630099 -0.93703579 -0.14804598
Axis point 26.56430186 0.00000000 177.07798106
Rotation angle (degrees) 92.21231095
Shift along axis -79.51325078
Found 10 fits.
command time 0.3578 seconds
draw time 0.0205 seconds
> time fitmap #3 in #1 search 10 radius 30
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.291 (1), 1.114 (1), 1.092 (1), 1.074 (1), 1.069 (1), 1.03 (1), 1.024 (1),
1.005 (1), 0.9892 (1), 0.866 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.291, steps = 276
shifted from previous position = 19.5
rotated from previous position = 41 degrees
atoms outside contour = 2800, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.27627865 -0.38964243 -0.87854921 168.34083049
-0.32932394 0.89716818 -0.29433751 125.94186387
0.90289268 0.20800825 -0.37618700 186.10149032
Axis 0.27126001 -0.96195485 0.03257118
Axis point 36.12249201 0.00000000 160.57224499
Rotation angle (degrees) 112.18811858
Shift along axis -69.42470618
Found 10 fits.
command time 0.4769 seconds
draw time 0.04954 seconds
> view matrix models
> #3,-0.45612,-0.52873,-0.71582,153.5,-0.51902,0.81145,-0.26865,120.78,0.72289,0.24899,-0.64454,212.13
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 95 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (3), 1.291 (1), 1.238 (1), 1.233 (1), 1.204 (1), 1.202 (1), 1.2 (2),
1.178 (2), 1.168 (1), 1.161 (1), 1.161 (1), 1.159 (1), 1.158 (1), 1.145 (1),
1.144 (1), 1.144 (1), 1.143 (1), 1.141 (1), 1.141 (1), 1.139 (1), 1.131 (1),
1.13 (2), 1.128 (1), 1.128 (1), 1.125 (1), 1.124 (1), 1.124 (1), 1.123 (1),
1.12 (1), 1.114 (1), 1.111 (1), 1.109 (1), 1.108 (1), 1.106 (1), 1.106 (1),
1.102 (1), 1.101 (1), 1.097 (1), 1.094 (1), 1.093 (1), 1.088 (1), 1.088 (1),
1.086 (1), 1.082 (1), 1.081 (1), 1.069 (1), 1.065 (1), 1.062 (1), 1.058 (1),
1.055 (1), 1.052 (1), 1.051 (1), 1.05 (1), 1.048 (1), 1.048 (1), 1.048 (1),
1.047 (1), 1.046 (1), 1.046 (1), 1.035 (1), 1.035 (1), 1.032 (1), 1.028 (1),
1.018 (1), 1.017 (1), 1.016 (1), 1.012 (1), 1.011 (1), 1.011 (1), 1.006 (1),
1.004 (1), 1.003 (1), 0.9989 (1), 0.9931 (1), 0.9876 (1), 0.9843 (1), 0.9801
(1), 0.9791 (1), 0.9742 (1), 0.9692 (1), 0.9654 (1), 0.9653 (1), 0.9549 (1),
0.9526 (1), 0.9518 (1), 0.9512 (1), 0.9507 (1), 0.9447 (1), 0.9309 (1), 0.9077
(1), 0.8495 (1), 0.844 (1), 0.8368 (1), 0.8344 (1), 0.781 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 96
shifted from previous position = 7.81
rotated from previous position = 23.7 degrees
atoms outside contour = 2743, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06508862 -0.16043832 -0.98489738 174.07881360
-0.45555955 0.87335654 -0.17237531 117.10043797
0.88782221 0.45989916 -0.01624345 168.10948941
Axis 0.31637674 -0.93706917 -0.14767240
Axis point 26.55537315 0.00000000 177.07235305
Rotation angle (degrees) 92.22931972
Shift along axis -79.48185514
Found 95 fits.
command time 4.004 seconds
draw time 0.06865 seconds
> view matrix models
> #3,0.57705,-0.66498,0.47415,96.984,-0.28702,0.37841,0.88002,63.103,-0.76461,-0.6439,0.027493,179.18
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 96 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (2), 1.255 (1), 1.24 (1), 1.208 (1), 1.189 (1), 1.179 (1), 1.178 (1),
1.174 (1), 1.168 (1), 1.166 (1), 1.159 (2), 1.155 (1), 1.155 (1), 1.153 (1),
1.151 (1), 1.15 (1), 1.144 (1), 1.143 (1), 1.142 (1), 1.131 (1), 1.13 (2),
1.123 (1), 1.123 (2), 1.12 (1), 1.118 (1), 1.116 (1), 1.113 (1), 1.109 (1),
1.109 (1), 1.108 (1), 1.107 (1), 1.106 (1), 1.106 (1), 1.104 (1), 1.102 (1),
1.099 (1), 1.098 (1), 1.094 (1), 1.094 (1), 1.089 (1), 1.088 (1), 1.082 (1),
1.078 (1), 1.07 (1), 1.064 (1), 1.062 (1), 1.058 (1), 1.057 (1), 1.055 (1),
1.054 (1), 1.05 (1), 1.048 (1), 1.048 (1), 1.046 (1), 1.045 (1), 1.04 (1),
1.039 (1), 1.036 (1), 1.035 (1), 1.035 (1), 1.034 (1), 1.028 (1), 1.026 (1),
1.026 (1), 1.023 (1), 1.022 (1), 1.017 (1), 1.017 (1), 1.017 (1), 1.013 (1),
1.01 (1), 1.003 (1), 1.001 (1), 1 (1), 0.9974 (1), 0.9932 (1), 0.9888 (1),
0.9883 (1), 0.982 (1), 0.9781 (1), 0.9773 (1), 0.9754 (1), 0.9746 (1), 0.9724
(1), 0.9661 (1), 0.9641 (1), 0.956 (1), 0.9526 (1), 0.9449 (1), 0.9396 (1),
0.9305 (1), 0.9156 (1), 0.9068 (1), 0.8804 (1), 0.8786 (1), 0.8195 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 188
shifted from previous position = 0.279
rotated from previous position = 49.8 degrees
atoms outside contour = 2743, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06501812 -0.16037162 -0.98491287 174.07300224
-0.45534950 0.87348332 -0.17228766 117.09743317
0.88793509 0.45968151 -0.01623272 168.11765680
Axis 0.31622356 -0.93713220 -0.14760049
Axis point 26.53832123 0.00000000 177.07271068
Rotation angle (degrees) 92.22739852
Shift along axis -79.50403809
Found 96 fits.
command time 3.898 seconds
draw time 0.05265 seconds
> view matrix models
> #3,-0.98215,0.14687,0.11754,74.567,-0.05428,-0.81951,0.57049,126.34,0.18011,0.55392,0.81285,98.778
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 99 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (1), 1.208 (1), 1.2 (1), 1.19 (2), 1.186 (1), 1.185 (1), 1.184 (1),
1.183 (1), 1.182 (1), 1.178 (1), 1.169 (1), 1.165 (1), 1.164 (1), 1.161 (1),
1.155 (1), 1.154 (1), 1.151 (1), 1.151 (1), 1.151 (1), 1.147 (1), 1.144 (1),
1.144 (1), 1.141 (1), 1.128 (1), 1.117 (1), 1.112 (1), 1.11 (1), 1.105 (1),
1.103 (1), 1.101 (1), 1.091 (1), 1.09 (1), 1.089 (1), 1.087 (1), 1.087 (1),
1.082 (1), 1.073 (1), 1.071 (1), 1.066 (1), 1.065 (1), 1.062 (1), 1.061 (1),
1.058 (1), 1.058 (1), 1.055 (1), 1.054 (1), 1.054 (1), 1.052 (1), 1.05 (1),
1.048 (1), 1.048 (1), 1.046 (1), 1.044 (1), 1.041 (1), 1.04 (1), 1.038 (1),
1.037 (1), 1.036 (1), 1.032 (1), 1.031 (1), 1.03 (1), 1.026 (1), 1.025 (1),
1.02 (1), 1.019 (1), 1.017 (1), 1.017 (1), 1.014 (1), 1.012 (1), 1.011 (1),
1.01 (1), 1.004 (1), 1.003 (1), 0.9995 (1), 0.9894 (1), 0.9868 (1), 0.9827
(1), 0.9801 (1), 0.9792 (1), 0.9673 (1), 0.9657 (1), 0.9623 (1), 0.96 (1),
0.9572 (1), 0.9564 (1), 0.9538 (1), 0.9526 (1), 0.9511 (1), 0.9396 (1), 0.9313
(1), 0.9264 (1), 0.9261 (1), 0.9083 (1), 0.9043 (1), 0.898 (1), 0.8946 (1),
0.8935 (1), 0.8878 (1), 0.8291 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 200
shifted from previous position = 19.9
rotated from previous position = 50.1 degrees
atoms outside contour = 2744, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06505439 -0.16033216 -0.98491689 174.07187135
-0.45539222 0.87346482 -0.17226852 117.09485877
0.88791051 0.45973044 -0.01619111 168.11198264
Axis 0.31623811 -0.93712084 -0.14764144
Axis point 26.53970349 0.00000000 177.07171916
Rotation angle (degrees) 92.22569626
Shift along axis -79.50416895
Found 99 fits.
command time 3.686 seconds
draw time 0.06496 seconds
> view matrix models
> #3,0.028537,-0.2479,0.96837,42.259,-0.93209,0.34335,0.11536,108.27,-0.36109,-0.9059,-0.22126,210.09
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 95 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (2), 1.22 (1), 1.207 (1), 1.184 (1), 1.18 (2), 1.169 (1), 1.168 (1),
1.161 (1), 1.151 (1), 1.151 (1), 1.147 (1), 1.141 (2), 1.141 (1), 1.137 (1),
1.129 (1), 1.128 (1), 1.121 (1), 1.12 (1), 1.12 (1), 1.117 (2), 1.117 (1),
1.115 (1), 1.114 (1), 1.114 (1), 1.111 (1), 1.11 (1), 1.098 (1), 1.096 (1),
1.095 (1), 1.093 (1), 1.091 (1), 1.078 (1), 1.077 (1), 1.074 (1), 1.072 (1),
1.069 (1), 1.066 (1), 1.065 (1), 1.065 (1), 1.064 (1), 1.06 (1), 1.06 (1),
1.057 (1), 1.053 (1), 1.053 (1), 1.049 (1), 1.047 (1), 1.046 (1), 1.042 (1),
1.04 (1), 1.039 (1), 1.038 (1), 1.037 (1), 1.029 (1), 1.026 (1), 1.025 (1),
1.018 (1), 1.018 (1), 1.015 (1), 1.013 (1), 1.013 (1), 1.013 (1), 1.009 (1),
1.008 (1), 1.005 (1), 1.003 (1), 1.003 (1), 0.9984 (1), 0.9909 (2), 0.9833
(1), 0.9821 (1), 0.9818 (1), 0.9794 (1), 0.9771 (1), 0.9753 (1), 0.9732 (1),
0.9724 (1), 0.9694 (1), 0.9668 (1), 0.9614 (1), 0.9603 (1), 0.9566 (1), 0.9549
(1), 0.9514 (1), 0.9501 (1), 0.9375 (1), 0.9342 (1), 0.9327 (1), 0.9187 (1),
0.9073 (1), 0.8982 (1), 0.8856 (1), 0.8778 (1), 0.8743 (1), 0.7802 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 124
shifted from previous position = 1.17
rotated from previous position = 29.2 degrees
atoms outside contour = 2745, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06502106 -0.16045924 -0.98489840 174.07439524
-0.45530658 0.87348997 -0.17236746 117.10094255
0.88795689 0.45963835 -0.01626272 168.11996419
Axis 0.31624203 -0.93713624 -0.14753522
Axis point 26.53720111 0.00000000 177.07597961
Rotation angle (degrees) 92.22798364
Shift along axis -79.49351351
Found 95 fits.
command time 3.667 seconds
draw time 0.05369 seconds
> rmsd #3@CA to #2@CA
RMSD between 546 atom pairs is 1.693
> select clear
> color bychain
> undo
> show atoms
> style stick
Changed 7796 atom styles
> hide cartoons
> select :50
14 atoms, 12 bonds, 2 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> show cartoons
> hide atoms
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 95 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (1), 1.272 (3), 1.255 (1), 1.226 (1), 1.22 (1), 1.203 (1), 1.182 (1),
1.181 (1), 1.161 (1), 1.161 (1), 1.158 (1), 1.149 (1), 1.147 (1), 1.146 (1),
1.142 (1), 1.139 (1), 1.131 (1), 1.13 (1), 1.13 (1), 1.129 (1), 1.119 (1),
1.119 (1), 1.115 (1), 1.114 (1), 1.107 (1), 1.106 (2), 1.103 (2), 1.102 (1),
1.099 (1), 1.093 (1), 1.088 (1), 1.086 (1), 1.085 (1), 1.082 (1), 1.079 (1),
1.069 (1), 1.065 (1), 1.065 (1), 1.064 (1), 1.063 (1), 1.057 (1), 1.055 (1),
1.054 (1), 1.048 (1), 1.04 (2), 1.039 (1), 1.038 (1), 1.038 (1), 1.035 (1),
1.034 (1), 1.033 (1), 1.032 (1), 1.028 (1), 1.021 (1), 1.017 (1), 1.017 (1),
1.017 (1), 1.013 (1), 1.009 (1), 1.009 (1), 1.006 (1), 1.005 (1), 1.003 (1),
1.003 (1), 1.001 (1), 0.997 (1), 0.9941 (1), 0.9931 (1), 0.9923 (1), 0.9912
(1), 0.9858 (1), 0.9853 (1), 0.9848 (1), 0.9846 (1), 0.9846 (1), 0.9779 (1),
0.977 (1), 0.97 (1), 0.9627 (1), 0.9549 (1), 0.9548 (1), 0.9523 (1), 0.951
(1), 0.9473 (1), 0.936 (1), 0.9315 (1), 0.9226 (1), 0.9202 (1), 0.888 (1),
0.8664 (1), 0.8569 (1), 0.8545 (1), 0.8426 (1), 0.8388 (1), 0.8332 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 136
shifted from previous position = 10.5
rotated from previous position = 38.8 degrees
atoms outside contour = 2740, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06515237 -0.15996724 -0.98496976 174.08508497
-0.45534194 0.87354578 -0.17199078 117.07069886
0.88792914 0.45970377 -0.01592604 168.09564338
Axis 0.31608306 -0.93714853 -0.14779761
Axis point 26.53331988 0.00000000 177.08056073
Rotation angle (degrees) 92.21296660
Shift along axis -79.53142081
Found 95 fits.
command time 3.78 seconds
draw time 0.05205 seconds
> select #3/L:39
4 atoms, 3 bonds, 1 residue, 1 model selected
> view matrix models
> #3,0.36252,0.9285,0.080438,69.471,-0.026383,0.096499,-0.99498,204.49,-0.9316,0.35858,0.059479,142.22
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 99 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (1), 1.255 (1), 1.238 (1), 1.22 (1), 1.22 (1), 1.212 (1), 1.208 (1), 1.2
(1), 1.184 (1), 1.182 (1), 1.166 (1), 1.16 (1), 1.148 (1), 1.145 (1), 1.142
(1), 1.139 (1), 1.138 (2), 1.134 (1), 1.134 (1), 1.131 (1), 1.13 (1), 1.129
(1), 1.128 (1), 1.126 (1), 1.12 (1), 1.113 (1), 1.106 (1), 1.105 (1), 1.105
(1), 1.102 (1), 1.099 (1), 1.098 (1), 1.096 (1), 1.096 (1), 1.095 (1), 1.093
(1), 1.092 (1), 1.091 (1), 1.088 (1), 1.087 (1), 1.086 (1), 1.086 (1), 1.082
(1), 1.081 (1), 1.078 (1), 1.077 (1), 1.077 (1), 1.074 (1), 1.072 (1), 1.072
(1), 1.072 (1), 1.07 (1), 1.07 (1), 1.067 (1), 1.066 (1), 1.055 (1), 1.055
(1), 1.055 (1), 1.054 (1), 1.053 (1), 1.048 (1), 1.048 (1), 1.048 (1), 1.043
(1), 1.041 (1), 1.041 (1), 1.041 (1), 1.04 (1), 1.04 (1), 1.028 (1), 1.027
(1), 1.025 (1), 1.023 (1), 1.02 (1), 1.02 (1), 1.019 (1), 1.015 (1), 1.014
(1), 1.005 (1), 0.9997 (1), 0.9881 (1), 0.9822 (1), 0.9817 (1), 0.9778 (1),
0.9772 (1), 0.9716 (1), 0.9689 (1), 0.9673 (1), 0.9626 (1), 0.9612 (1), 0.9595
(1), 0.9515 (1), 0.9452 (1), 0.9216 (1), 0.9124 (1), 0.8821 (1), 0.8553 (1),
0.8503 (1), 0.8382 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 152
shifted from previous position = 19.7
rotated from previous position = 12.7 degrees
atoms outside contour = 2739, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06517967 -0.16005009 -0.98495445 174.09097887
-0.45550097 0.87344649 -0.17207393 117.07586222
0.88784556 0.45986353 -0.01597184 168.09230101
Axis 0.31620534 -0.93710121 -0.14783606
Axis point 26.54838334 0.00000000 177.07986042
Rotation angle (degrees) 92.21634371
Shift along axis -79.51353941
Found 99 fits.
command time 3.563 seconds
draw time 0.06927 seconds
> view matrix models
> #3,-0.27973,-0.82605,0.48928,89.906,0.29498,0.41102,0.86258,70.909,-0.91364,0.38562,0.1287,136.83
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 99 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (1), 1.272 (1), 1.226 (1), 1.207 (1), 1.202 (1), 1.2 (1), 1.175 (1),
1.166 (1), 1.152 (2), 1.15 (1), 1.147 (1), 1.147 (1), 1.138 (1), 1.124 (1),
1.123 (1), 1.122 (1), 1.12 (1), 1.12 (1), 1.115 (1), 1.115 (1), 1.114 (1),
1.113 (1), 1.109 (1), 1.108 (1), 1.107 (1), 1.105 (1), 1.102 (1), 1.1 (1),
1.099 (1), 1.099 (1), 1.095 (1), 1.093 (1), 1.091 (1), 1.087 (1), 1.084 (1),
1.084 (1), 1.079 (1), 1.077 (1), 1.075 (1), 1.074 (1), 1.073 (1), 1.071 (1),
1.071 (1), 1.066 (1), 1.064 (1), 1.063 (1), 1.062 (1), 1.062 (1), 1.058 (1),
1.056 (1), 1.054 (1), 1.053 (1), 1.053 (1), 1.05 (1), 1.05 (1), 1.043 (1),
1.042 (1), 1.041 (1), 1.039 (1), 1.037 (1), 1.036 (1), 1.036 (1), 1.035 (1),
1.033 (1), 1.033 (1), 1.032 (1), 1.031 (1), 1.031 (1), 1.031 (1), 1.028 (1),
1.025 (1), 1.02 (1), 1.018 (1), 1.014 (1), 1.01 (1), 1.009 (1), 1.007 (1),
1.006 (1), 0.9977 (1), 0.9969 (1), 0.992 (1), 0.9865 (1), 0.986 (1), 0.9857
(1), 0.9747 (1), 0.9692 (1), 0.9666 (1), 0.958 (1), 0.9555 (1), 0.9526 (1),
0.9515 (1), 0.9415 (1), 0.9385 (1), 0.911 (1), 0.9099 (1), 0.898 (1), 0.8905
(1), 0.8845 (1), 0.3993 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 104
shifted from previous position = 9.66
rotated from previous position = 32.5 degrees
atoms outside contour = 2746, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06485799 -0.16055652 -0.98489332 174.07090726
-0.45494032 0.87367721 -0.17238566 117.10129749
0.88815656 0.45924836 -0.01637847 168.14180651
Axis 0.31605654 -0.93723526 -0.14730354
Axis point 26.51406754 0.00000000 177.07903148
Rotation angle (degrees) 92.23060892
Shift along axis -79.50309792
Found 99 fits.
command time 4.299 seconds
draw time 0.0526 seconds
> view matrix models
> #3,0.13949,0.66902,-0.73004,130.61,0.95288,-0.29125,-0.084842,167.47,-0.26938,-0.6838,-0.67812,235.47
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 96 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (1), 1.207 (1), 1.2 (4), 1.19 (1), 1.185 (1), 1.184 (1), 1.182 (1),
1.174 (1), 1.161 (1), 1.16 (1), 1.151 (2), 1.147 (1), 1.147 (1), 1.145 (1),
1.143 (1), 1.142 (1), 1.14 (1), 1.139 (1), 1.134 (1), 1.125 (1), 1.123 (1),
1.115 (1), 1.114 (1), 1.113 (1), 1.11 (1), 1.109 (1), 1.108 (1), 1.106 (1),
1.102 (1), 1.099 (1), 1.096 (1), 1.093 (1), 1.093 (1), 1.091 (1), 1.09 (1),
1.087 (1), 1.086 (1), 1.082 (1), 1.08 (1), 1.077 (1), 1.074 (1), 1.074 (1),
1.07 (1), 1.067 (1), 1.066 (1), 1.066 (1), 1.065 (1), 1.065 (1), 1.06 (1),
1.052 (1), 1.052 (1), 1.048 (1), 1.048 (1), 1.048 (1), 1.048 (1), 1.047 (1),
1.044 (1), 1.043 (1), 1.042 (1), 1.042 (1), 1.039 (1), 1.034 (1), 1.034 (1),
1.028 (1), 1.027 (1), 1.024 (1), 1.019 (1), 1.016 (1), 1.014 (1), 1.012 (1),
1.011 (1), 1.009 (1), 1.004 (1), 1.003 (1), 1 (1), 1 (1), 0.9953 (1), 0.994
(1), 0.9836 (1), 0.9826 (1), 0.9791 (1), 0.9787 (1), 0.9787 (1), 0.9725 (1),
0.9687 (1), 0.9648 (1), 0.962 (1), 0.9583 (1), 0.9507 (1), 0.9294 (1), 0.9251
(1), 0.8996 (1), 0.8969 (1), 0.8816 (1), 0.8291 (1), 0.7858 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 120
shifted from previous position = 1.16
rotated from previous position = 30.7 degrees
atoms outside contour = 2743, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06502532 -0.16046006 -0.98489804 174.07759425
-0.45528760 0.87349928 -0.17237045 117.10077231
0.88796639 0.45962039 -0.01625567 168.11986641
Axis 0.31623440 -0.93714039 -0.14752525
Axis point 26.53729824 0.00000000 177.07837124
Rotation angle (degrees) 92.22739258
Shift along axis -79.49246630
Found 96 fits.
command time 4.32 seconds
draw time 0.06703 seconds
> time fitmap #3 in #1 search 10 radius 30
> fitmap #3 inMap #1 search 10 radius 30
Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).
Average map values and times found:
1.272 (1), 1.115 (1), 1.094 (1), 1.078 (1), 1.053 (1), 1.016 (1), 1.012 (1),
0.9478 (1), 0.8918 (1), 0.7917 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.272, steps = 100
shifted from previous position = 8.95
rotated from previous position = 20.8 degrees
atoms outside contour = 2844, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.29368160 -0.26969792 -0.91706806 170.85831934
-0.16942223 0.92949856 -0.32760967 128.41799633
0.94076920 0.25158466 0.22728419 151.66917528
Axis 0.29723463 -0.95341672 0.05146011
Axis point 3.25513484 0.00000000 204.49558155
Rotation angle (degrees) 76.98346642
Shift along axis -63.84594244
Found 10 fits.
command time 0.3726 seconds
draw time 0.01254 seconds
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 97 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (1), 1.291 (2), 1.255 (1), 1.24 (1), 1.238 (1), 1.238 (1), 1.221 (1),
1.208 (1), 1.203 (1), 1.202 (1), 1.202 (1), 1.2 (2), 1.182 (1), 1.169 (1),
1.165 (1), 1.16 (1), 1.159 (1), 1.158 (1), 1.152 (1), 1.146 (1), 1.143 (2),
1.14 (1), 1.137 (1), 1.137 (1), 1.137 (1), 1.131 (1), 1.131 (1), 1.131 (1),
1.13 (1), 1.13 (1), 1.123 (1), 1.123 (1), 1.12 (1), 1.115 (1), 1.113 (1),
1.105 (1), 1.104 (1), 1.1 (1), 1.099 (1), 1.098 (1), 1.09 (1), 1.089 (1),
1.082 (1), 1.081 (1), 1.076 (1), 1.076 (1), 1.072 (1), 1.072 (1), 1.069 (1),
1.069 (1), 1.066 (1), 1.058 (1), 1.058 (1), 1.05 (1), 1.048 (1), 1.046 (1),
1.045 (1), 1.043 (1), 1.042 (1), 1.039 (1), 1.037 (1), 1.035 (1), 1.035 (1),
1.032 (1), 1.032 (1), 1.031 (1), 1.03 (1), 1.029 (1), 1.028 (1), 1.028 (1),
1.02 (1), 1.019 (1), 1.018 (1), 1.005 (1), 0.9994 (1), 0.9985 (1), 0.9974 (1),
0.9932 (1), 0.9917 (1), 0.9866 (1), 0.984 (1), 0.9804 (1), 0.9653 (1), 0.9648
(1), 0.9509 (1), 0.9491 (1), 0.9485 (1), 0.9485 (1), 0.9439 (1), 0.9315 (1),
0.921 (1), 0.9136 (1), 0.9106 (1), 0.8831 (1), 0.8738 (1), 0.7931 (1), 0.7884
(1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 236
shifted from previous position = 16
rotated from previous position = 60.4 degrees
atoms outside contour = 2741, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06513234 -0.15999436 -0.98496674 174.08959327
-0.45531112 0.87355891 -0.17200615 117.07196012
0.88794654 0.45966953 -0.01595006 168.09843584
Axis 0.31607378 -0.93715622 -0.14776869
Axis point 26.53416680 0.00000000 177.08290024
Rotation angle (degrees) 92.21385267
Shift along axis -79.52924395
Found 97 fits.
command time 3.688 seconds
draw time 0.0194 seconds
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 92 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.291 (1), 1.238 (1), 1.238 (1), 1.22 (1), 1.212 (1), 1.207 (1), 1.2 (2),
1.184 (1), 1.179 (1), 1.178 (1), 1.178 (1), 1.174 (1), 1.171 (1), 1.165 (1),
1.162 (1), 1.161 (1), 1.16 (1), 1.158 (1), 1.155 (1), 1.155 (1), 1.153 (1),
1.151 (1), 1.146 (1), 1.145 (2), 1.141 (2), 1.137 (1), 1.134 (1), 1.131 (1),
1.13 (1), 1.13 (2), 1.123 (1), 1.121 (1), 1.12 (1), 1.119 (1), 1.117 (1),
1.115 (1), 1.109 (3), 1.108 (1), 1.103 (1), 1.102 (1), 1.102 (1), 1.101 (1),
1.099 (2), 1.089 (1), 1.084 (1), 1.082 (1), 1.082 (1), 1.08 (1), 1.076 (1),
1.072 (1), 1.072 (1), 1.07 (1), 1.069 (1), 1.06 (1), 1.059 (1), 1.053 (1),
1.05 (1), 1.041 (1), 1.036 (1), 1.035 (1), 1.035 (1), 1.035 (1), 1.03 (1),
1.026 (1), 1.021 (1), 1.019 (1), 1.017 (1), 1.008 (1), 1.005 (1), 1.001 (1),
0.9997 (1), 0.9969 (1), 0.9895 (1), 0.9868 (1), 0.9858 (1), 0.9846 (1), 0.981
(1), 0.9758 (1), 0.9714 (1), 0.97 (1), 0.9679 (1), 0.9647 (1), 0.9573 (1),
0.9507 (1), 0.9383 (1), 0.936 (1), 0.9325 (2), 0.9215 (1), 0.9077 (1), 0.874
(1), 0.8722 (1), 0.8665 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.291, steps = 184
shifted from previous position = 26.3
rotated from previous position = 24.2 degrees
atoms outside contour = 2801, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.27651511 -0.38963786 -0.87847697 168.33611025
-0.32944004 0.89716128 -0.29422868 125.93781456
0.90277800 0.20804692 -0.37644110 186.10620065
Axis 0.27125182 -0.96195924 0.03250958
Axis point 36.13805900 0.00000000 160.55038444
Rotation angle (degrees) 112.20350808
Shift along axis -69.43533388
Found 92 fits.
command time 4.346 seconds
draw time 0.01468 seconds
> view matrix models
> #3,0.3809,-0.18686,-0.90553,172.27,-0.40156,0.84875,-0.34406,129.98,0.83286,0.49468,0.24825,132.96
> view matrix models
> #3,0.3809,-0.18686,-0.90553,173.18,-0.40156,0.84875,-0.34406,129.24,0.83286,0.49468,0.24825,146.7
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 98 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (3), 1.291 (1), 1.272 (1), 1.24 (1), 1.216 (1), 1.182 (1), 1.182 (1),
1.178 (1), 1.174 (1), 1.169 (1), 1.168 (1), 1.166 (1), 1.158 (1), 1.158 (1),
1.155 (1), 1.154 (1), 1.152 (1), 1.131 (1), 1.123 (1), 1.123 (1), 1.118 (1),
1.117 (1), 1.114 (1), 1.113 (1), 1.109 (1), 1.105 (1), 1.105 (1), 1.102 (1),
1.102 (1), 1.099 (1), 1.097 (1), 1.096 (1), 1.087 (1), 1.087 (1), 1.084 (1),
1.083 (1), 1.081 (1), 1.078 (1), 1.077 (1), 1.074 (1), 1.07 (1), 1.06 (1),
1.06 (1), 1.054 (1), 1.052 (1), 1.051 (1), 1.048 (1), 1.041 (1), 1.038 (1),
1.036 (1), 1.032 (1), 1.031 (1), 1.026 (1), 1.022 (1), 1.022 (1), 1.02 (1),
1.018 (1), 1.017 (1), 1.017 (1), 1.017 (1), 1.014 (1), 1.014 (1), 1.013 (1),
1.012 (1), 1.01 (1), 1.008 (1), 1.003 (1), 0.9994 (1), 0.9945 (1), 0.9919 (1),
0.9909 (1), 0.9887 (1), 0.9876 (1), 0.9875 (1), 0.9864 (1), 0.9796 (1), 0.9792
(1), 0.9785 (1), 0.976 (1), 0.9758 (1), 0.9756 (1), 0.9728 (1), 0.9724 (1),
0.9697 (1), 0.9674 (1), 0.9654 (1), 0.9647 (1), 0.948 (1), 0.9227 (1), 0.9196
(1), 0.9014 (1), 0.8995 (1), 0.8849 (1), 0.8726 (1), 0.8708 (1), 0.8129 (1),
0.8035 (1), 0.6605 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 148
shifted from previous position = 19.6
rotated from previous position = 44.5 degrees
atoms outside contour = 2745, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06502828 -0.16053171 -0.98488629 174.07632259
-0.45535292 0.87345278 -0.17243408 117.10527873
0.88793272 0.45968399 -0.01629937 168.12077083
Axis 0.31629857 -0.93711919 -0.14752233
Axis point 26.54227546 0.00000000 177.07673159
Rotation angle (degrees) 92.22989339
Shift along axis -79.48307963
Found 98 fits.
command time 3.894 seconds
draw time 0.01558 seconds
> view matrix models
> #3,0.065028,-0.16053,-0.98489,173.35,-0.45535,0.87345,-0.17243,117.45,0.88793,0.45968,-0.016299,169.09
> view matrix models
> #3,-0.6271,-0.56495,0.53626,72.869,0.58897,-0.79445,-0.14822,183.71,0.50976,0.22289,0.83094,113.6
> view matrix models
> #3,-0.6271,-0.56495,0.53626,74.262,0.58897,-0.79445,-0.14822,175.55,0.50976,0.22289,0.83094,112.58
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 98 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (1), 1.291 (1), 1.255 (1), 1.226 (1), 1.204 (1), 1.202 (1), 1.2 (1),
1.191 (1), 1.189 (1), 1.182 (1), 1.178 (1), 1.158 (1), 1.143 (1), 1.142 (1),
1.141 (1), 1.141 (1), 1.141 (1), 1.138 (1), 1.135 (1), 1.128 (1), 1.125 (1),
1.123 (1), 1.119 (1), 1.115 (1), 1.11 (1), 1.109 (2), 1.109 (1), 1.108 (1),
1.107 (1), 1.105 (1), 1.103 (1), 1.103 (1), 1.102 (1), 1.101 (1), 1.099 (1),
1.088 (1), 1.085 (1), 1.084 (1), 1.081 (1), 1.078 (1), 1.078 (1), 1.074 (1),
1.069 (1), 1.067 (1), 1.065 (1), 1.064 (1), 1.064 (1), 1.059 (1), 1.058 (1),
1.057 (1), 1.055 (1), 1.055 (1), 1.051 (1), 1.05 (1), 1.048 (1), 1.046 (1),
1.046 (1), 1.045 (1), 1.044 (1), 1.043 (1), 1.042 (1), 1.04 (1), 1.032 (1),
1.032 (1), 1.032 (1), 1.03 (1), 1.03 (1), 1.027 (1), 1.025 (1), 1.024 (1),
1.024 (1), 1.018 (1), 1.016 (1), 1.016 (2), 1.014 (1), 1.011 (1), 1.01 (1),
1.009 (1), 0.9963 (1), 0.9933 (1), 0.9931 (1), 0.9867 (1), 0.9823 (1), 0.9763
(1), 0.9687 (1), 0.9556 (1), 0.9492 (1), 0.9455 (1), 0.9437 (1), 0.9401 (1),
0.9279 (1), 0.9202 (1), 0.9146 (1), 0.8717 (1), 0.8546 (1), 0.8478 (1), 0.8411
(1), 0.8143 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 96
shifted from previous position = 6.35
rotated from previous position = 22.1 degrees
atoms outside contour = 2743, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06484895 -0.16062678 -0.98488259 174.06768179
-0.45494887 0.87366141 -0.17244358 117.10843964
0.88815291 0.45925410 -0.01642088 168.14518801
Axis 0.31608879 -0.93722921 -0.14727284
Axis point 26.51475155 0.00000000 177.07836673
Rotation angle (degrees) 92.23253703
Shift along axis -79.49982716
Found 98 fits.
command time 3.428 seconds
draw time 0.01623 seconds
> time fitmap #3 in #1 search 1 radius 30
> fitmap #3 inMap #1 search 1 radius 30
Found 1 unique fits from 1 random placements having fraction of points inside
contour >= 0.100 (1 of 1).
Average map values and times found:
1.144 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.144, steps = 232
shifted from previous position = 6.34
rotated from previous position = 40.2 degrees
atoms outside contour = 2975, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.86027714 -0.05435218 0.50692064 54.59507080
0.33099445 -0.81580029 0.47424917 136.27984670
0.38776969 0.57577359 0.71980506 101.98477573
Axis 0.24409128 0.28647006 0.92647415
Axis point 8.51766948 53.43664794 0.00000000
Rotation angle (degrees) 167.99692971
Shift along axis 146.85253472
Found 1 fits.
command time 0.06972 seconds
draw time 0.00772 seconds
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 93 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (2), 1.243 (1), 1.238 (1), 1.226 (1), 1.212 (2), 1.208 (2), 1.207 (1),
1.2 (1), 1.2 (1), 1.19 (1), 1.182 (1), 1.174 (1), 1.169 (1), 1.167 (1), 1.161
(1), 1.16 (1), 1.152 (2), 1.147 (1), 1.146 (1), 1.146 (1), 1.141 (1), 1.134
(1), 1.123 (1), 1.121 (2), 1.121 (1), 1.119 (1), 1.117 (1), 1.114 (1), 1.111
(1), 1.111 (1), 1.108 (1), 1.107 (1), 1.103 (1), 1.096 (1), 1.091 (2), 1.091
(1), 1.091 (1), 1.089 (1), 1.077 (1), 1.076 (1), 1.075 (1), 1.072 (1), 1.07
(1), 1.068 (1), 1.068 (1), 1.064 (1), 1.064 (1), 1.058 (1), 1.055 (1), 1.055
(1), 1.051 (1), 1.048 (1), 1.044 (1), 1.041 (1), 1.041 (2), 1.04 (1), 1.039
(1), 1.037 (1), 1.034 (1), 1.033 (1), 1.032 (1), 1.031 (1), 1.031 (1), 1.03
(1), 1.029 (1), 1.026 (1), 1.023 (1), 1.019 (1), 1.019 (1), 1.018 (1), 1.016
(1), 1.015 (1), 1.012 (1), 1.011 (1), 1.007 (1), 1.007 (1), 1 (1), 0.9954 (1),
0.989 (1), 0.9889 (1), 0.9831 (1), 0.983 (1), 0.9829 (1), 0.9654 (1), 0.9628
(1), 0.9587 (1), 0.9585 (1), 0.956 (1), 0.9555 (1), 0.9553 (1), 0.9502 (1),
0.9344 (1), 0.9024 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 128
shifted from previous position = 18.3
rotated from previous position = 22.9 degrees
atoms outside contour = 2737, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06522764 -0.15995190 -0.98496744 174.09370714
-0.45566842 0.87337266 -0.17200579 117.07077869
0.88775621 0.46003819 -0.01591690 168.08263309
Axis 0.31625841 -0.93706234 -0.14796888
Axis point 26.55902250 0.00000000 177.07628711
Rotation angle (degrees) 92.21550961
Shift along axis -79.51501641
Found 93 fits.
command time 3.638 seconds
draw time 0.0217 seconds
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 92 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.291 (2), 1.238 (1), 1.226 (1), 1.22 (4), 1.208 (1), 1.207 (1), 1.203 (1),
1.19 (1), 1.181 (1), 1.175 (1), 1.168 (1), 1.166 (1), 1.153 (1), 1.151 (2),
1.141 (1), 1.133 (1), 1.132 (1), 1.132 (1), 1.13 (1), 1.13 (2), 1.128 (1),
1.126 (1), 1.125 (1), 1.123 (1), 1.121 (1), 1.119 (1), 1.115 (1), 1.115 (1),
1.114 (1), 1.113 (1), 1.113 (1), 1.11 (1), 1.11 (1), 1.108 (1), 1.106 (2),
1.105 (1), 1.102 (1), 1.096 (2), 1.095 (1), 1.093 (1), 1.087 (1), 1.087 (1),
1.084 (1), 1.079 (1), 1.078 (1), 1.077 (1), 1.073 (1), 1.068 (1), 1.066 (1),
1.065 (1), 1.062 (1), 1.06 (1), 1.06 (1), 1.058 (1), 1.047 (1), 1.046 (1),
1.045 (1), 1.043 (1), 1.042 (1), 1.041 (1), 1.041 (1), 1.036 (1), 1.036 (1),
1.034 (1), 1.032 (1), 1.032 (1), 1.031 (1), 1.031 (1), 1.023 (1), 1.02 (1),
1.019 (1), 1.018 (1), 1.012 (1), 0.9917 (1), 0.9851 (1), 0.9846 (1), 0.982
(1), 0.9772 (1), 0.9708 (1), 0.9611 (1), 0.9545 (1), 0.9522 (1), 0.9418 (1),
0.9415 (1), 0.9338 (1), 0.9198 (1), 0.916 (1), 0.9079 (1), 0.8962 (1), 0.8946
(1), 0.837 (1), 0.8051 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.291, steps = 128
shifted from previous position = 6.59
rotated from previous position = 37 degrees
atoms outside contour = 2802, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.27608116 -0.38935212 -0.87873986 168.36676718
-0.32961627 0.89718270 -0.29396561 125.91863802
0.90284675 0.20848888 -0.37603238 186.08696492
Axis 0.27129678 -0.96195517 0.03225395
Axis point 36.13303470 0.00000000 160.57001748
Rotation angle (degrees) 112.17677242
Shift along axis -69.44868380
Found 92 fits.
command time 3.898 seconds
draw time 0.02469 seconds
> view matrix models
> #3,-0.54519,-0.30149,-0.78222,155.34,-0.18409,0.95337,-0.23915,122.25,0.81785,0.013615,-0.57527,204.98
> view matrix models
> #3,-0.54519,-0.30149,-0.78222,157.65,-0.18409,0.95337,-0.23915,120.74,0.81785,0.013615,-0.57527,218.58
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 97 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (1), 1.272 (1), 1.238 (1), 1.226 (2), 1.207 (1), 1.203 (1), 1.184 (1),
1.18 (1), 1.179 (1), 1.164 (1), 1.158 (1), 1.149 (1), 1.146 (2), 1.144 (1),
1.144 (1), 1.133 (1), 1.131 (1), 1.129 (1), 1.123 (1), 1.122 (1), 1.12 (1),
1.115 (1), 1.114 (1), 1.109 (1), 1.109 (1), 1.107 (1), 1.107 (1), 1.104 (1),
1.104 (1), 1.099 (1), 1.099 (1), 1.096 (1), 1.096 (1), 1.094 (1), 1.087 (1),
1.078 (1), 1.078 (1), 1.077 (1), 1.076 (1), 1.073 (1), 1.072 (1), 1.068 (1),
1.068 (1), 1.065 (1), 1.062 (1), 1.061 (1), 1.055 (1), 1.055 (1), 1.052 (2),
1.052 (1), 1.051 (1), 1.05 (1), 1.049 (1), 1.048 (1), 1.046 (1), 1.043 (1),
1.039 (1), 1.036 (1), 1.032 (1), 1.03 (1), 1.026 (1), 1.02 (1), 1.016 (1),
1.015 (1), 1.013 (1), 1.013 (1), 1.013 (1), 1.012 (1), 1.007 (1), 1.004 (1),
1.001 (1), 0.9966 (1), 0.996 (1), 0.9867 (1), 0.9813 (1), 0.9804 (1), 0.9798
(1), 0.9709 (1), 0.9689 (1), 0.9607 (1), 0.9587 (1), 0.9574 (1), 0.9564 (1),
0.9545 (1), 0.9522 (1), 0.9518 (1), 0.9502 (1), 0.9468 (1), 0.9428 (1), 0.9421
(1), 0.9354 (1), 0.9268 (1), 0.914 (1), 0.901 (1), 0.8905 (1), 0.8882 (1),
0.878 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 156
shifted from previous position = 21.3
rotated from previous position = 51.6 degrees
atoms outside contour = 2743, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06489544 -0.16059151 -0.98488513 174.07079232
-0.45500436 0.87363462 -0.17243249 117.10678637
0.88812134 0.45931727 -0.01637525 168.13974307
Axis 0.31611443 -0.93721345 -0.14731806
Axis point 26.51847114 0.00000000 177.08016732
Rotation angle (degrees) 92.23066408
Shift along axis -79.49778772
Found 97 fits.
command time 3.983 seconds
draw time 0.02498 seconds
> time fitmap #3 in #1 search 1 radius 30
> fitmap #3 inMap #1 search 1 radius 30
Found 1 unique fits from 1 random placements having fraction of points inside
contour >= 0.100 (1 of 1).
Average map values and times found:
0.9639 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 0.9639, steps = 160
shifted from previous position = 20.8
rotated from previous position = 30.3 degrees
atoms outside contour = 3236, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.13647137 0.77444692 -0.61774370 107.34326005
-0.96796667 -0.23690683 -0.08316034 141.71782980
-0.21075105 0.58660599 0.78196986 96.82872840
Axis 0.35056043 -0.21302283 -0.91199159
Axis point 122.60198283 4.70280093 0.00000000
Rotation angle (degrees) 107.19976957
Shift along axis -80.86581974
Found 1 fits.
command time 0.05219 seconds
draw time 0.007817 seconds
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 96 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.291 (1), 1.255 (2), 1.22 (1), 1.208 (1), 1.207 (1), 1.19 (1), 1.186 (1),
1.178 (1), 1.17 (1), 1.167 (1), 1.158 (1), 1.153 (1), 1.152 (1), 1.146 (1),
1.139 (1), 1.139 (1), 1.139 (1), 1.138 (1), 1.137 (1), 1.13 (1), 1.119 (1),
1.115 (1), 1.114 (1), 1.114 (1), 1.11 (1), 1.11 (1), 1.108 (1), 1.106 (1),
1.106 (1), 1.106 (1), 1.105 (1), 1.1 (1), 1.099 (1), 1.096 (1), 1.095 (1),
1.093 (1), 1.091 (1), 1.091 (1), 1.089 (1), 1.088 (1), 1.078 (1), 1.074 (1),
1.067 (1), 1.063 (1), 1.062 (1), 1.058 (1), 1.053 (1), 1.052 (1), 1.052 (1),
1.05 (1), 1.05 (1), 1.047 (1), 1.044 (1), 1.042 (1), 1.042 (1), 1.041 (2),
1.041 (1), 1.04 (1), 1.04 (1), 1.033 (1), 1.024 (1), 1.02 (1), 1.016 (1),
1.012 (2), 1.012 (1), 1.009 (1), 1.007 (1), 1.001 (1), 1.001 (1), 1 (1),
0.9998 (1), 0.9983 (1), 0.9972 (1), 0.9971 (1), 0.997 (1), 0.9965 (1), 0.9947
(1), 0.9924 (1), 0.9867 (1), 0.9836 (1), 0.9749 (1), 0.9737 (1), 0.9613 (1),
0.9476 (1), 0.931 (1), 0.929 (2), 0.9216 (1), 0.9098 (1), 0.9079 (1), 0.8979
(1), 0.897 (1), 0.894 (1), 0.8849 (1), 0.8731 (1), 0.867 (1), 0.8445 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.291, steps = 180
shifted from previous position = 6.86
rotated from previous position = 48.5 degrees
atoms outside contour = 2803, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.27635021 -0.38930401 -0.87867656 168.32948697
-0.32937008 0.89727637 -0.29395568 125.92350877
0.90285430 0.20817533 -0.37618790 186.10425033
Axis 0.27114187 -0.96199517 0.03236326
Axis point 36.11066394 0.00000000 160.55605472
Rotation angle (degrees) 112.18700981
Shift along axis -69.47369468
Found 96 fits.
command time 3.915 seconds
draw time 0.02117 seconds
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 95 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (2), 1.243 (1), 1.207 (1), 1.2 (1), 1.192 (1), 1.19 (1), 1.184 (1),
1.179 (1), 1.175 (1), 1.174 (1), 1.162 (1), 1.161 (1), 1.158 (1), 1.152 (1),
1.152 (1), 1.151 (1), 1.141 (1), 1.139 (2), 1.131 (2), 1.128 (1), 1.127 (1),
1.115 (2), 1.114 (1), 1.114 (2), 1.111 (1), 1.111 (1), 1.11 (1), 1.11 (1),
1.107 (1), 1.106 (1), 1.102 (1), 1.098 (1), 1.096 (1), 1.093 (1), 1.091 (1),
1.089 (1), 1.086 (1), 1.082 (1), 1.073 (1), 1.072 (1), 1.071 (1), 1.069 (1),
1.069 (1), 1.069 (1), 1.065 (1), 1.064 (1), 1.061 (1), 1.06 (1), 1.06 (1),
1.058 (1), 1.057 (1), 1.051 (1), 1.047 (1), 1.044 (1), 1.043 (1), 1.043 (1),
1.031 (1), 1.031 (1), 1.026 (1), 1.024 (1), 1.023 (1), 1.02 (1), 1.019 (1),
1.013 (1), 1.007 (1), 1.003 (1), 0.997 (1), 0.997 (1), 0.9937 (1), 0.9935 (1),
0.9924 (1), 0.9909 (1), 0.9803 (1), 0.9775 (1), 0.9753 (1), 0.9708 (1), 0.9635
(1), 0.9596 (1), 0.958 (1), 0.9561 (1), 0.9514 (1), 0.9507 (1), 0.9494 (1),
0.9458 (1), 0.9309 (1), 0.9217 (1), 0.9214 (1), 0.9201 (1), 0.9071 (1), 0.8907
(1), 0.8813 (1), 0.8522 (1), 0.8398 (1), 0.8211 (1), 0.7031 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 224
shifted from previous position = 18.6
rotated from previous position = 63.7 degrees
atoms outside contour = 2744, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06506029 -0.16037243 -0.98491007 174.07167687
-0.45534890 0.87348010 -0.17230704 117.09662504
0.88793253 0.45968783 -0.01619657 168.11345846
Axis 0.31623597 -0.93712816 -0.14759956
Axis point 26.53685156 0.00000000 177.07419646
Rotation angle (degrees) 92.22524559
Shift along axis -79.50029275
Found 95 fits.
command time 3.979 seconds
draw time 0.02122 seconds
> time fitmap #3 in #1 search 1 radius 30
> fitmap #3 inMap #1 search 1 radius 30
Found 1 unique fits from 1 random placements having fraction of points inside
contour >= 0.100 (1 of 1).
Average map values and times found:
0.981 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 0.981, steps = 152
shifted from previous position = 5.01
rotated from previous position = 23 degrees
atoms outside contour = 3107, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.79286501 0.60928669 0.01158694 90.84044570
-0.33700919 0.42255001 0.84135399 59.00811417
0.50772984 -0.67098509 0.54036020 160.10236816
Axis -0.81672885 -0.26793874 -0.51104092
Axis point 0.00000000 80.47072684 39.81361074
Rotation angle (degrees) 67.79710065
Shift along axis -171.82143322
Found 1 fits.
command time 0.04985 seconds
draw time 0.007817 seconds
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 95 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.444 (3), 1.291 (1), 1.207 (1), 1.2 (2), 1.19 (1), 1.187 (2), 1.183 (1),
1.174 (1), 1.166 (1), 1.16 (1), 1.158 (1), 1.15 (1), 1.149 (1), 1.142 (1),
1.134 (1), 1.133 (1), 1.131 (1), 1.131 (1), 1.13 (1), 1.127 (1), 1.117 (1),
1.115 (1), 1.114 (1), 1.109 (1), 1.108 (1), 1.108 (1), 1.108 (1), 1.106 (1),
1.106 (1), 1.105 (1), 1.103 (1), 1.102 (1), 1.096 (1), 1.09 (1), 1.088 (1),
1.082 (1), 1.081 (1), 1.081 (1), 1.079 (1), 1.078 (1), 1.073 (1), 1.073 (1),
1.069 (1), 1.068 (1), 1.065 (1), 1.064 (2), 1.061 (1), 1.06 (1), 1.059 (1),
1.057 (1), 1.056 (1), 1.052 (1), 1.05 (1), 1.048 (1), 1.048 (1), 1.048 (1),
1.046 (1), 1.041 (1), 1.038 (1), 1.036 (1), 1.036 (1), 1.035 (1), 1.033 (1),
1.03 (1), 1.026 (1), 1.021 (1), 1.016 (1), 1.015 (1), 1 (1), 0.9962 (1),
0.9956 (1), 0.9899 (1), 0.9896 (1), 0.986 (1), 0.9827 (1), 0.9824 (1), 0.9823
(1), 0.982 (1), 0.976 (1), 0.9684 (1), 0.9531 (1), 0.9499 (1), 0.9492 (1),
0.9431 (1), 0.94 (1), 0.94 (1), 0.9267 (1), 0.9132 (1), 0.9059 (1), 0.9002
(1), 0.8999 (1), 0.8917 (1), 0.8807 (1), 0.8711 (1), 0.8571 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.444, steps = 240
shifted from previous position = 25.2
rotated from previous position = 74.2 degrees
atoms outside contour = 2738, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
0.06522810 -0.15990584 -0.98497486 174.09313224
-0.45566046 0.87338513 -0.17196479 117.06815579
0.88776039 0.46003078 -0.01589354 168.08153692
Axis 0.31623400 -0.93706758 -0.14798785
Axis point 26.55741161 0.00000000 177.07571838
Rotation angle (degrees) 92.21446942
Shift along axis -79.52063177
Found 95 fits.
command time 3.836 seconds
draw time 0.01538 seconds
> time fitmap #3 in #1 search 100 radius 30
> fitmap #3 inMap #1 search 100 radius 30
Found 91 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
1.238 (1), 1.207 (1), 1.2 (1), 1.2 (2), 1.179 (1), 1.165 (1), 1.155 (2), 1.145
(1), 1.134 (1), 1.132 (1), 1.127 (1), 1.124 (1), 1.119 (1), 1.119 (2), 1.118
(1), 1.117 (1), 1.113 (2), 1.111 (1), 1.109 (2), 1.109 (1), 1.108 (1), 1.105
(1), 1.105 (2), 1.103 (1), 1.101 (1), 1.096 (1), 1.093 (1), 1.093 (1), 1.093
(1), 1.088 (1), 1.082 (1), 1.082 (1), 1.081 (1), 1.081 (1), 1.081 (1), 1.08
(1), 1.079 (1), 1.073 (1), 1.065 (1), 1.065 (1), 1.063 (1), 1.06 (1), 1.059
(1), 1.059 (2), 1.055 (1), 1.052 (1), 1.052 (1), 1.051 (1), 1.05 (1), 1.045
(1), 1.031 (1), 1.023 (1), 1.02 (1), 1.017 (1), 1.017 (1), 1.011 (1), 1.011
(1), 1.008 (1), 1.008 (1), 1.001 (1), 1 (1), 0.997 (1), 0.9959 (1), 0.9953
(1), 0.9937 (1), 0.9936 (1), 0.9903 (1), 0.9835 (1), 0.9801 (1), 0.9789 (1),
0.9778 (1), 0.9743 (1), 0.9735 (1), 0.9628 (1), 0.9569 (1), 0.9545 (1), 0.9544
(2), 0.9525 (1), 0.9514 (1), 0.9419 (1), 0.9416 (1), 0.9341 (1), 0.93 (1),
0.9274 (1), 0.9196 (1), 0.9187 (1), 0.8853 (1), 0.8505 (1), 0.8101 (1), 0.8033
(2), 0.7136 (1)
Best fit found:
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms
average map value = 1.238, steps = 164
shifted from previous position = 8.85
rotated from previous position = 36.5 degrees
atoms outside contour = 2843, contour level = 2
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:
Matrix rotation and translation
-0.19378643 0.75498811 -0.62644974 116.86207503
0.97869599 0.10462559 -0.17665753 157.43014143
-0.06783154 -0.64733775 -0.75917886 234.15710389
Axis -0.61610347 -0.73121112 0.29282557
Axis point -44.39069415 0.00000000 154.55037084
Rotation angle (degrees) 157.54352347
Shift along axis -118.54661306
Found 91 fits.
command time 3.854 seconds
draw time 0.01457 seconds
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac18,3
Processor Name: Quad-Core Intel Core i7
Processor Speed: 4.2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 522.0.0.0.0
OS Loader Version: 577.140.2~15
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 13.6.1 (22G313)
Kernel Version: Darwin 22.6.0
Time since boot: 11 days, 21 hours, 52 minutes
Graphics/Displays:
Radeon Pro 580:
Chipset Model: Radeon Pro 580
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1X-025
EFI Driver Version: 01.00.931
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.13.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.12
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.51
ChimeraX-AtomicLibrary: 12.1.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202311100228
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.1
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.12
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.14.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.44.0
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.0
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.7
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.0.0
prompt-toolkit: 3.0.40
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.9
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (6)
comment:1 by , 2 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Fit search results list may show wrong results for subsequent searches. |
comment:2 by , 2 years ago
comment:3 by , 2 years ago
Running 10000 placements, 142 getting got the correct fit, so 1 in 70. With Poisson distribution that gives about 95% chance of getting the correct fit with 3x 70 = 210 placements and about a 75% with 100 placements.
comment:4 by , 2 years ago
A separate bug is that clicking on fit list lines causes the structure to sometime fly off screen then back even when only a small motion is required. Somehow the interpolation is not taking a nice path. Should be able to fix that.
comment:6 by , 2 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
This bug is not actually a bug. It was real variability in the fitting procedure as far as I can tell.
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I think the fit list Clear List button is working correctly and it was just coincidence that subsequent fit searches did not find the correct fit. When searching with 100 placements often only 1 or 2 get the correct fit, so I suspect some of the time 0 will find the correct fit. Probably 300 placements would be much more reliable.