![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 3 years ago
#6050 closed defect (can't reproduce)
ISOLDE vs. submodels
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.15.0-166-generic-x86_64-with-glibc2.27
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Simply put, I'm trying to start an ISOLDE simulation with a model that has multiple chains in it. I select the single model (select #2 in this case) but I always get the error complaining about the selection needing to be within a single model. This also happens when I select a single chain within that model. So far seems to only happen with this model, which contains only the atomic coordinate rows for each chain and no extra information. The source of those models is the EBI AlphaFold server.
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /data/data_epk/Commander_fits/flexible_fitting/Starting_point_for_ISOLDE.cxs
> format session
Opened cryosparc_P4_J86_006_volume_map_sharp.mrc as #1, grid size 568,568,568,
pixel 0.82, shown at level 0.19, step 2, values float32
Opened cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian as #11, grid size
568,568,568, pixel 0.82, shown at level 0.117, step 1, values float32
Log from Fri Jan 28 14:24:25 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /data/data_epk/Commander_fits/Rigid_body/Ccomplex_fits_COMMD_rigid_body_fitted_ring_combined_COMMD_MODELS.cxs
> format session
Opened cryosparc_P4_J86_006_volume_map_sharp.mrc as #1, grid size 568,568,568,
pixel 0.82, shown at level 0.19, step 2, values float32
Opened cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian as #11, grid size
568,568,568, pixel 0.82, shown at level 0.117, step 1, values float32
Log from Thu Jan 27 15:53:10 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /data/data_epk/Commander_fits/Rigid_body/Ccomplex_fits_COMMD_rigid_body_fitted_ring.cxs
> format session
Opened cryosparc_P4_J86_006_volume_map_sharp.mrc as #1, grid size 568,568,568,
pixel 0.82, shown at level 0.19, step 2, values float32
Opened cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian as #11, grid size
568,568,568, pixel 0.82, shown at level 0.117, step 1, values float32
Log from Wed Jan 26 19:10:28 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:/Work/CComplex Fits
> Umeå/Ccomplex_fits_COMMD_initial_positions_inner_ring_2done.cxs"
Opened cryosparc_P4_J86_006_volume_map_sharp.mrc as #1, grid size 568,568,568,
pixel 0.82, shown at level 0.19, step 2, values float32
Opened cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian as #11, grid size
568,568,568, pixel 0.82, shown at level 0.218, step 1, values float32
Log from Tue Jan 25 17:26:46 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:/Work/CComplex Fits Umeå/cryosparc_P4_J86_006_volume_map_sharp.mrc"
Opened cryosparc_P4_J86_006_volume_map_sharp.mrc as #1, grid size 568,568,568,
pixel 0.82, shown at level 0.0623, step 4, values float32
> select #1
2 models selected
> volume #1 step 2
> set bgColor white
> lighting soft
> graphics silhouettes true
> volume #1 level 0.1901
> open "D:/Work/CComplex Fits/site1/S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb
> 1.pdb" "D:/Work/CComplex Fits/site1/S1_hCOMMD2_AF-Q86X83-F1-model_v1.pdb
> 1.pdb" "D:/Work/CComplex Fits/site1/S1_hCOMMD3_AF-Q9UBI1-F1-model_v1.pdb
> 1.pdb" "D:/Work/CComplex Fits/site1/S1_hCOMMD4_AF-Q9H0A8-F1-model_v1.pdb
> 1.pdb" "D:/Work/CComplex Fits/site1/S1_hCOMMD5_AF-Q9GZQ3-F1-model_v1.pdb
> 1.pdb" "D:/Work/CComplex Fits/site1/S1_hCOMMD7_AF-F1QJA8-F1-model_v1.pdb
> 1.pdb" "D:/Work/CComplex Fits/site1/S1_hCOMMD8_AF-Q9NX08-F1-model_v1.pdb
> 1.pdb" "D:/Work/CComplex Fits/site1/S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb
> 1.pdb" "D:/Work/CComplex Fits/site1/S1_hCOMMD10_AF-Q9Y6G5-F1-model_v1.pdb
> 1.pdb"
Summary of feedback from opening D:/Work/CComplex
Fits/site1/S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 1.pdb
---
warning | Ignored bad PDB record found on line 915
END
Chain information for S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 1.pdb #2
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD2_AF-Q86X83-F1-model_v1.pdb 1.pdb #3
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD3_AF-Q9UBI1-F1-model_v1.pdb 1.pdb #4
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD4_AF-Q9H0A8-F1-model_v1.pdb 1.pdb #5
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD5_AF-Q9GZQ3-F1-model_v1.pdb 1.pdb #6
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD7_AF-F1QJA8-F1-model_v1.pdb 1.pdb #7
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD8_AF-Q9NX08-F1-model_v1.pdb 1.pdb #8
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb #9
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD10_AF-Q9Y6G5-F1-model_v1.pdb 1.pdb #10
---
Chain | Description
A | No description available
> select #1
2 models selected
> transparency sel 50
> select clear
> hide #3-10
> hide #3-10 target m
> select #2
887 atoms, 904 bonds, 114 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.14265,0.072776,-0.98709,491.31,-0.22906,0.96779,0.10445,-9.7555,0.9629,0.241,-0.12138,-69.298
> view matrix models
> #2,-0.14265,0.072776,-0.98709,489.44,-0.22906,0.96779,0.10445,-17.723,0.9629,0.241,-0.12138,-57.31
> view matrix models
> #2,-0.14265,0.072776,-0.98709,490.33,-0.22906,0.96779,0.10445,31.461,0.9629,0.241,-0.12138,-37.488
> view matrix models
> #2,-0.14265,0.072776,-0.98709,502.18,-0.22906,0.96779,0.10445,40.331,0.9629,0.241,-0.12138,-39.629
> show #3 models
> hide #2 models
> ~select #2
Nothing selected
> select #3
952 atoms, 966 bonds, 120 residues, 1 model selected
> view matrix models #3,1,0,0,1.0051,0,1,0,-64.495,0,0,1,-9.899
> view matrix models #3,1,0,0,13.098,0,1,0,-69.01,0,0,1,-11.776
> view matrix models #3,1,0,0,13.581,0,1,0,-64.725,0,0,1,-10.17
> hide #3 models
> show #4 models
> ~select #3
Nothing selected
> select #4
937 atoms, 953 bonds, 119 residues, 1 model selected
> view matrix models #4,1,0,0,15.968,0,1,0,0.55261,0,0,1,0.49353
> view matrix models #4,1,0,0,13.379,0,1,0,-5.0998,0,0,1,-38.219
> lighting shadows true intensity 0.5
> view matrix models #4,1,0,0,13.365,0,1,0,-5.5358,0,0,1,-36.66
> lighting shadows false
> lighting shadows true
> lighting shadows false
> select #2-10 target m
Expected a keyword
> select #2-10
8783 atoms, 8933 bonds, 1116 residues, 9 models selected
> lighting shadows true
> lighting shadows false
> select clear
> select #1
2 models selected
> lighting shadows true
> lighting shadows false
> lighting shadows true
> select #4
937 atoms, 953 bonds, 119 residues, 1 model selected
> hide #4 models
> ~select #4
Nothing selected
> select #5
971 atoms, 984 bonds, 126 residues, 1 model selected
> show #5 models
> view matrix models #5,1,0,0,4.0234,0,1,0,-40.553,0,0,1,27.705
> view matrix models #5,1,0,0,14.297,0,1,0,-42.244,0,0,1,27.94
> hide #5 models
> ~select #5
Nothing selected
> select #6
1119 atoms, 1140 bonds, 148 residues, 1 model selected
> show #6 models
> view matrix models #6,1,0,0,0.81323,0,1,0,-46.934,0,0,1,33.83
> view matrix models #6,1,0,0,-28.192,0,1,0,-56.265,0,0,1,21.823
> view matrix models #6,1,0,0,-29.479,0,1,0,-55.445,0,0,1,26.589
> hide #6 models
> show #7 models
> ~select #6
Nothing selected
> select #7
1041 atoms, 1062 bonds, 130 residues, 1 model selected
> view matrix models #7,1,0,0,1.1868,0,1,0,-3.4155,0,0,1,26.461
> view matrix models #7,1,0,0,-38.78,0,1,0,-6.6906,0,0,1,26.621
> view matrix models #7,1,0,0,-39.084,0,1,0,-5.9682,0,0,1,27.541
> hide #7 models
> ~select #7
Nothing selected
> select #8
926 atoms, 947 bonds, 113 residues, 1 model selected
> show #8 models
> view matrix models #8,1,0,0,-39.171,0,1,0,1.2347,0,0,1,-2.3857
> view matrix models #8,1,0,0,-39.069,0,1,0,-0.51771,0,0,1,-5.4326
> view matrix models #8,1,0,0,-40.524,0,1,0,-1.2663,0,0,1,-6.2369
> hide #8 models
> show #9 models
> select #9
919 atoms, 930 bonds, 118 residues, 1 model selected
> select #8
926 atoms, 947 bonds, 113 residues, 1 model selected
> view matrix models #8,1,0,0,-43.556,0,1,0,-50.934,0,0,1,-9.3943
> show #8 models
> hide #9 models
> view matrix models #8,1,0,0,-40.318,0,1,0,1.0271,0,0,1,-7.0222
> hide #8 models
> show #9 models
> select #9
919 atoms, 930 bonds, 118 residues, 1 model selected
> select #8
926 atoms, 947 bonds, 113 residues, 1 model selected
> select #9
919 atoms, 930 bonds, 118 residues, 1 model selected
> view matrix models #9,1,0,0,2.884,0,1,0,-67.421,0,0,1,-8.0057
> view matrix models #9,1,0,0,-38.672,0,1,0,-71.189,0,0,1,-24.381
> view matrix models #9,1,0,0,-41.547,0,1,0,-64.778,0,0,1,-14.545
> hide #9 models
> ~select #9
Nothing selected
> show #10 models
> select #10
1031 atoms, 1047 bonds, 128 residues, 1 model selected
> view matrix models #10,1,0,0,1.1271,0,1,0,-42.456,0,0,1,-38.366
> view matrix models #10,1,0,0,6.8588,0,1,0,-43.567,0,0,1,-39.689
> view matrix models #10,1,0,0,11.566,0,1,0,-41.941,0,0,1,-39.908
> hide #10 models
> ~select #10
Nothing selected
> show #2 models
> select #2
887 atoms, 904 bonds, 114 residues, 1 model selected
> fitmap sel inMap #1 search 100 radius 5
Found 82 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
0.2294 (7), 0.1923 (1), 0.1917 (1), 0.1906 (1), 0.1877 (2), 0.1813 (1), 0.1812
(1), 0.1811 (1), 0.1797 (1), 0.1774 (1), 0.1752 (1), 0.174 (1), 0.1734 (1),
0.172 (3), 0.1705 (2), 0.1688 (1), 0.1685 (2), 0.168 (1), 0.1678 (1), 0.1667
(3), 0.1663 (1), 0.1657 (1), 0.1634 (2), 0.1628 (1), 0.1625 (1), 0.1623 (1),
0.1622 (1), 0.1622 (1), 0.1621 (1), 0.162 (1), 0.1616 (1), 0.161 (1), 0.1595
(1), 0.1593 (2), 0.1581 (1), 0.158 (1), 0.1578 (1), 0.1574 (1), 0.1566 (1),
0.156 (1), 0.1551 (1), 0.1536 (2), 0.1521 (1), 0.152 (1), 0.152 (1), 0.151
(1), 0.1509 (1), 0.1508 (1), 0.1506 (1), 0.1494 (1), 0.1486 (1), 0.1485 (1),
0.1483 (1), 0.1483 (2), 0.1472 (1), 0.1471 (1), 0.1467 (1), 0.1466 (1), 0.1464
(1), 0.1462 (1), 0.1458 (1), 0.1452 (1), 0.1449 (1), 0.1443 (1), 0.1433 (1),
0.1418 (2), 0.1417 (1), 0.1398 (1), 0.1395 (1), 0.1389 (1), 0.1385 (1), 0.1376
(1), 0.136 (1), 0.1348 (1), 0.1328 (1), 0.1316 (1), 0.1282 (1), 0.1281 (1),
0.1265 (1), 0.1221 (1), 0.1185 (1), 0.111 (1)
Best fit found:
Fit molecule S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 1.pdb (#2) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 887 atoms
average map value = 0.2294, steps = 132
shifted from previous position = 4.85
rotated from previous position = 27.9 degrees
atoms outside contour = 360, contour level = 0.19008
Position of S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 1.pdb (#2) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.83451368 0.48502797 -0.26140936 -10.60302581
-0.50013678 0.46774269 -0.72875238 422.29276681
-0.23119295 0.73889422 0.63291798 -49.43885981
Axis 0.83016663 -0.01709175 -0.55725329
Axis point 0.00000000 254.04924130 394.19463869
Rotation angle (degrees) 62.12221241
Shift along axis 11.52996623
Found 82 fits. List window not yet implemented.
> hide #2 models
> show #3 models
> select #3
952 atoms, 966 bonds, 120 residues, 1 model selected
> select #2
887 atoms, 904 bonds, 114 residues, 1 model selected
> select #3
952 atoms, 966 bonds, 120 residues, 1 model selected
> fitmap sel inMap #1 search 100 radius 5
Found 94 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
0.318 (2), 0.2201 (1), 0.2157 (1), 0.2137 (1), 0.2131 (1), 0.2124 (1), 0.2119
(1), 0.2118 (1), 0.2118 (1), 0.2115 (1), 0.2107 (1), 0.2106 (1), 0.2099 (1),
0.2098 (1), 0.2089 (1), 0.2085 (1), 0.2082 (1), 0.2074 (1), 0.2073 (1), 0.2066
(2), 0.2064 (1), 0.2064 (1), 0.206 (1), 0.2055 (1), 0.2055 (1), 0.2051 (1),
0.205 (1), 0.205 (2), 0.205 (1), 0.2045 (1), 0.2025 (1), 0.2025 (1), 0.2019
(1), 0.2017 (1), 0.2014 (1), 0.201 (1), 0.2007 (2), 0.2003 (1), 0.2 (1),
0.1997 (1), 0.1995 (1), 0.1994 (1), 0.1993 (1), 0.198 (1), 0.1978 (1), 0.1973
(2), 0.1972 (1), 0.1968 (1), 0.1965 (1), 0.1964 (1), 0.1962 (1), 0.1937 (1),
0.1935 (1), 0.1935 (1), 0.1929 (1), 0.1927 (1), 0.1924 (1), 0.1923 (1), 0.1922
(1), 0.1916 (1), 0.1914 (1), 0.1912 (1), 0.191 (1), 0.1896 (1), 0.1896 (1),
0.1885 (1), 0.1882 (1), 0.187 (1), 0.1867 (1), 0.1855 (1), 0.1846 (1), 0.1846
(1), 0.1838 (1), 0.1834 (2), 0.1822 (1), 0.1819 (1), 0.1811 (1), 0.1811 (1),
0.1808 (1), 0.1802 (1), 0.1796 (1), 0.1793 (1), 0.1758 (1), 0.1754 (1), 0.1742
(1), 0.1735 (1), 0.1735 (1), 0.1727 (1), 0.1704 (1), 0.168 (1), 0.1671 (1),
0.1659 (1), 0.1614 (1), 0.1605 (1)
Best fit found:
Fit molecule S1_hCOMMD2_AF-Q86X83-F1-model_v1.pdb 1.pdb (#3) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 952 atoms
average map value = 0.318, steps = 156
shifted from previous position = 3.55
rotated from previous position = 34.3 degrees
atoms outside contour = 251, contour level = 0.19008
Position of S1_hCOMMD2_AF-Q86X83-F1-model_v1.pdb 1.pdb (#3) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.89051260 0.12703104 -0.43686428 109.07075884
0.36975008 -0.76156873 0.53225738 184.70241215
-0.26508897 -0.63551250 -0.72515631 610.36835839
Axis -0.96907668 -0.14254816 0.20142098
Axis point 0.00000000 190.17118413 284.81029950
Rotation angle (degrees) 142.94963874
Shift along axis -9.08592235
Found 94 fits. List window not yet implemented.
> hide #3 models
> ~select #3
Nothing selected
> select #4
937 atoms, 953 bonds, 119 residues, 1 model selected
> show #4 models
> fitmap sel inMap #1 search 100 radius 5
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:
0.2055 (2), 0.2022 (1), 0.192 (1), 0.1893 (1), 0.1872 (1), 0.1859 (1), 0.1858
(1), 0.1848 (1), 0.1836 (1), 0.1834 (1), 0.183 (1), 0.1829 (1), 0.1827 (1),
0.182 (1), 0.1816 (1), 0.1816 (2), 0.181 (2), 0.1808 (2), 0.1804 (1), 0.18
(2), 0.1795 (1), 0.1794 (1), 0.1788 (1), 0.1787 (1), 0.1783 (1), 0.1778 (1),
0.1776 (1), 0.1775 (1), 0.1772 (1), 0.177 (1), 0.1764 (1), 0.1759 (1), 0.1759
(1), 0.1759 (1), 0.1758 (1), 0.1755 (1), 0.1753 (2), 0.1752 (1), 0.1751 (1),
0.1751 (1), 0.175 (1), 0.1748 (1), 0.1747 (1), 0.1747 (1), 0.1744 (1), 0.1742
(1), 0.1742 (1), 0.1742 (1), 0.1739 (1), 0.1733 (1), 0.1732 (1), 0.1731 (1),
0.1728 (1), 0.1727 (1), 0.1725 (1), 0.1723 (1), 0.1719 (1), 0.1716 (1), 0.1716
(1), 0.1716 (1), 0.1711 (1), 0.1708 (1), 0.1703 (1), 0.17 (1), 0.17 (1), 0.169
(2), 0.169 (1), 0.1688 (1), 0.1686 (1), 0.1678 (1), 0.1669 (1), 0.1667 (1),
0.1667 (1), 0.1665 (1), 0.1655 (1), 0.1654 (1), 0.1653 (1), 0.1648 (1), 0.1641
(1), 0.164 (2), 0.164 (1), 0.1638 (1), 0.1637 (1), 0.1632 (1), 0.1629 (1),
0.1628 (1), 0.1627 (1), 0.1617 (1), 0.1602 (1), 0.159 (1), 0.1577 (1), 0.1551
(1)
Best fit found:
Fit molecule S1_hCOMMD3_AF-Q9UBI1-F1-model_v1.pdb 1.pdb (#4) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 937 atoms
average map value = 0.2055, steps = 212
shifted from previous position = 5.36
rotated from previous position = 47.6 degrees
atoms outside contour = 420, contour level = 0.19008
Position of S1_hCOMMD3_AF-Q9UBI1-F1-model_v1.pdb 1.pdb (#4) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.95222074 0.29609114 -0.07487147 -35.01889751
-0.30244518 0.94827986 -0.09639603 103.64968760
0.04245708 0.11443481 0.99252307 -74.46126794
Axis 0.32669823 -0.18180941 -0.92747701
Axis point 329.38442560 214.20669214 0.00000000
Rotation angle (degrees) 18.82441698
Shift along axis 38.77601432
Found 92 fits. List window not yet implemented.
> hide #4 models
> show #5 models
> select #5
971 atoms, 984 bonds, 126 residues, 1 model selected
> select #4
937 atoms, 953 bonds, 119 residues, 1 model selected
> select #5
971 atoms, 984 bonds, 126 residues, 1 model selected
> fitmap sel inMap #1 search 100 radius 5
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:
0.3743 (2), 0.2298 (1), 0.2261 (1), 0.2243 (1), 0.2207 (1), 0.2206 (1), 0.2203
(1), 0.2203 (1), 0.2174 (1), 0.2174 (1), 0.2173 (1), 0.2172 (1), 0.2171 (1),
0.217 (1), 0.2166 (1), 0.2164 (1), 0.2163 (1), 0.2154 (1), 0.2147 (1), 0.2138
(1), 0.2132 (1), 0.2122 (1), 0.2121 (1), 0.2115 (1), 0.2114 (1), 0.2112 (1),
0.2109 (1), 0.2108 (1), 0.2107 (1), 0.2103 (1), 0.2093 (1), 0.2092 (1), 0.209
(1), 0.2086 (1), 0.2084 (1), 0.2084 (1), 0.2083 (1), 0.2083 (1), 0.208 (1),
0.2078 (1), 0.2074 (1), 0.2072 (1), 0.207 (1), 0.2067 (1), 0.2066 (1), 0.2066
(1), 0.2055 (1), 0.2053 (1), 0.2053 (1), 0.2051 (1), 0.2051 (1), 0.2046 (1),
0.2045 (1), 0.2042 (1), 0.204 (1), 0.2039 (1), 0.2035 (1), 0.2034 (1), 0.2032
(1), 0.2031 (1), 0.2029 (1), 0.2029 (1), 0.2028 (1), 0.2028 (1), 0.2023 (1),
0.201 (1), 0.2006 (1), 0.2003 (1), 0.2 (1), 0.1989 (1), 0.1988 (1), 0.1987
(2), 0.1987 (1), 0.198 (2), 0.198 (1), 0.1975 (1), 0.1971 (1), 0.1967 (1),
0.1967 (1), 0.1957 (1), 0.1957 (1), 0.1946 (1), 0.1943 (1), 0.1943 (1), 0.1943
(1), 0.1935 (1), 0.193 (1), 0.1927 (1), 0.1925 (1), 0.1917 (1), 0.1901 (1),
0.1899 (1), 0.1899 (1), 0.1886 (1), 0.1856 (1), 0.1829 (1), 0.181 (1)
Best fit found:
Fit molecule S1_hCOMMD4_AF-Q9H0A8-F1-model_v1.pdb 1.pdb (#5) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 971 atoms
average map value = 0.3743, steps = 200
shifted from previous position = 6.78
rotated from previous position = 48.9 degrees
atoms outside contour = 203, contour level = 0.19008
Position of S1_hCOMMD4_AF-Q9H0A8-F1-model_v1.pdb 1.pdb (#5) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.91461584 0.02791882 -0.40335890 119.27393508
-0.09007752 -0.95847067 -0.27059198 552.41005240
-0.39416227 0.28382128 -0.87411761 471.35864186
Axis 0.97796426 -0.01622251 -0.20814114
Axis point 0.00000000 242.17719149 289.24900498
Rotation angle (degrees) 163.53361774
Shift along axis 9.57504339
Found 97 fits. List window not yet implemented.
> hide #5 models
> show #6 models
> select #6
1119 atoms, 1140 bonds, 148 residues, 1 model selected
> select #5
971 atoms, 984 bonds, 126 residues, 1 model selected
> select #6
1119 atoms, 1140 bonds, 148 residues, 1 model selected
> hide #!1 models
Drag select of 14 residues
Drag select of 9 residues
Drag select of 1 residues
> show #!1 models
> fitmap sel inMap #1 search 100 radius 5
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:
0.3493 (4), 0.2337 (1), 0.2297 (1), 0.2238 (1), 0.2219 (1), 0.2217 (1), 0.2199
(1), 0.2196 (1), 0.2189 (1), 0.2177 (1), 0.2173 (1), 0.2172 (1), 0.2166 (1),
0.2161 (1), 0.2157 (1), 0.2157 (1), 0.2152 (1), 0.2143 (1), 0.2143 (1), 0.2142
(1), 0.214 (1), 0.2137 (1), 0.2136 (1), 0.2135 (1), 0.2126 (1), 0.2116 (1),
0.2115 (1), 0.2112 (1), 0.2094 (1), 0.2089 (1), 0.2084 (1), 0.2072 (1), 0.2063
(1), 0.206 (1), 0.2058 (1), 0.2058 (1), 0.2058 (1), 0.2055 (1), 0.2054 (1),
0.2054 (1), 0.2051 (1), 0.2046 (1), 0.2042 (1), 0.2029 (1), 0.2028 (1), 0.2027
(1), 0.2018 (1), 0.201 (1), 0.2003 (1), 0.1999 (1), 0.1997 (1), 0.1995 (1),
0.1992 (1), 0.1991 (1), 0.1988 (1), 0.1987 (1), 0.1987 (1), 0.1985 (1), 0.1981
(1), 0.1979 (1), 0.1977 (1), 0.1974 (1), 0.1972 (1), 0.1966 (1), 0.1964 (1),
0.1963 (1), 0.196 (1), 0.1958 (1), 0.1958 (1), 0.1957 (1), 0.1955 (1), 0.1952
(1), 0.1951 (1), 0.195 (1), 0.1947 (1), 0.1945 (1), 0.1937 (1), 0.1932 (1),
0.1929 (1), 0.1929 (1), 0.1923 (1), 0.1916 (1), 0.1911 (1), 0.1911 (1), 0.1907
(1), 0.19 (1), 0.1889 (1), 0.1889 (1), 0.1882 (1), 0.188 (1), 0.1879 (1),
0.186 (1), 0.1843 (1), 0.1836 (1), 0.1825 (1), 0.1822 (1), 0.178 (1)
Best fit found:
Fit molecule S1_hCOMMD5_AF-Q9GZQ3-F1-model_v1.pdb 1.pdb (#6) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 962 atoms
average map value = 0.3493, steps = 92
shifted from previous position = 3.75
rotated from previous position = 21.1 degrees
atoms outside contour = 228, contour level = 0.19008
Position of S1_hCOMMD5_AF-Q9GZQ3-F1-model_v1.pdb 1.pdb (#6) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.83100439 0.29778181 0.46984858 226.57775955
0.51525643 0.09376047 0.85189186 -133.56470226
0.20962468 0.95001836 -0.23134936 5.16464114
Axis 0.27794361 0.73708503 0.61599757
Axis point 139.98351236 0.00000000 44.17917018
Rotation angle (degrees) 169.83274093
Shift along axis -32.29129596
Found 97 fits. List window not yet implemented.
> hide #6 models
> show #7 models
> select #7
1041 atoms, 1062 bonds, 130 residues, 1 model selected
> fitmap sel inMap #1 search 100 radius 5
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:
0.2236 (1), 0.2205 (1), 0.2179 (1), 0.2173 (1), 0.2163 (1), 0.2163 (1), 0.2159
(1), 0.2154 (1), 0.2147 (3), 0.2145 (1), 0.2139 (1), 0.2138 (1), 0.2129 (1),
0.2127 (1), 0.2124 (1), 0.2124 (1), 0.2123 (1), 0.2121 (1), 0.2121 (1), 0.212
(1), 0.2119 (1), 0.2117 (1), 0.2112 (1), 0.2111 (1), 0.21 (1), 0.2099 (1),
0.2093 (1), 0.2092 (1), 0.2089 (1), 0.2087 (1), 0.208 (2), 0.2075 (1), 0.2065
(1), 0.2063 (1), 0.2061 (1), 0.2061 (1), 0.2052 (1), 0.2049 (1), 0.2047 (1),
0.2039 (1), 0.2039 (1), 0.2037 (1), 0.2034 (1), 0.2031 (1), 0.2027 (1), 0.2027
(1), 0.2024 (1), 0.2023 (1), 0.2018 (1), 0.2016 (1), 0.2013 (1), 0.2013 (1),
0.2008 (1), 0.2007 (1), 0.2007 (1), 0.2004 (1), 0.1993 (1), 0.1989 (1), 0.1983
(1), 0.198 (1), 0.1971 (2), 0.1967 (1), 0.1964 (1), 0.1955 (1), 0.195 (1),
0.1934 (1), 0.1933 (1), 0.1932 (1), 0.1932 (1), 0.1929 (1), 0.1927 (1), 0.1922
(1), 0.1919 (1), 0.1917 (1), 0.1915 (1), 0.1913 (1), 0.1904 (1), 0.19 (2),
0.1899 (1), 0.1888 (1), 0.1874 (1), 0.1866 (1), 0.1858 (1), 0.185 (1), 0.1833
(1), 0.1824 (1), 0.1822 (1), 0.1814 (1), 0.1806 (1), 0.1806 (1), 0.1778 (1),
0.1774 (1), 0.1756 (1), 0.1737 (1), 0.1627 (1)
Best fit found:
Fit molecule S1_hCOMMD7_AF-F1QJA8-F1-model_v1.pdb 1.pdb (#7) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 1041 atoms
average map value = 0.2236, steps = 120
shifted from previous position = 3.52
rotated from previous position = 21.3 degrees
atoms outside contour = 502, contour level = 0.19008
Position of S1_hCOMMD7_AF-F1QJA8-F1-model_v1.pdb 1.pdb (#7) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.69428321 0.71804219 0.04884902 173.18534846
-0.23830015 -0.29339897 0.92581316 182.76963378
0.67910514 0.63113586 0.37481158 -163.69587404
Axis -0.24916810 -0.53292100 -0.80864730
Axis point 147.92267918 110.68461005 0.00000000
Rotation angle (degrees) 143.74910105
Shift along axis -8.18181384
Found 95 fits. List window not yet implemented.
> volume gaussian #1 sDev 2
Opened cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian as #11, grid size
568,568,568, pixel 0.82, shown at step 1, values float32
> select #11
2 models selected
> transparency sel 50
> select clear
> volume #11 level 0.2405
> select #11
2 models selected
> select #7
1041 atoms, 1062 bonds, 130 residues, 1 model selected
> fitmap sel inMap #11 search 100 radius 5
Found 50 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
0.2052 (1), 0.1985 (8), 0.1969 (4), 0.1942 (4), 0.1941 (2), 0.1938 (4), 0.1918
(3), 0.1915 (2), 0.1905 (1), 0.1904 (3), 0.1894 (1), 0.1891 (1), 0.189 (3),
0.1885 (3), 0.1885 (3), 0.1884 (5), 0.1884 (1), 0.1882 (3), 0.1882 (2), 0.1881
(1), 0.187 (2), 0.187 (4), 0.1869 (4), 0.1863 (2), 0.1863 (3), 0.186 (1),
0.1856 (1), 0.1854 (2), 0.1848 (2), 0.1844 (1), 0.1843 (1), 0.1835 (2), 0.1832
(1), 0.183 (1), 0.1825 (1), 0.1822 (1), 0.1821 (1), 0.1813 (2), 0.1808 (1),
0.1804 (1), 0.1803 (1), 0.1798 (1), 0.1786 (1), 0.1783 (1), 0.177 (1), 0.1766
(1), 0.1758 (1), 0.1753 (2), 0.1733 (1), 0.1698 (1)
Best fit found:
Fit molecule S1_hCOMMD7_AF-F1QJA8-F1-model_v1.pdb 1.pdb (#7) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 1041 atoms
average map value = 0.2052, steps = 240
shifted from previous position = 6.46
rotated from previous position = 67.1 degrees
atoms outside contour = 667, contour level = 0.24054
Position of S1_hCOMMD7_AF-F1QJA8-F1-model_v1.pdb 1.pdb (#7) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.99129687 -0.01984535 0.13014085 419.61004109
0.02252460 0.94842546 0.31619899 -70.47042061
-0.12970395 0.31637841 -0.93972414 411.77977472
Axis 0.00068146 0.98696507 0.16093320
Axis point 223.63597826 0.00000000 197.58251287
Rotation angle (degrees) 172.43572612
Shift along axis -2.99685800
Found 50 fits. List window not yet implemented.
> hide #7 models
> ~select #7
Nothing selected
> select #8
926 atoms, 947 bonds, 113 residues, 1 model selected
> show #8 models
Drag select of 6 residues
> fitmap sel inMap #11 search 100 radius 5
Found 32 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
0.2258 (10), 0.2008 (6), 0.1999 (14), 0.195 (1), 0.1935 (2), 0.1928 (4),
0.1928 (6), 0.1922 (2), 0.1892 (1), 0.1892 (1), 0.1892 (3), 0.1885 (1), 0.1879
(6), 0.1868 (1), 0.1863 (3), 0.1861 (1), 0.186 (5), 0.1857 (1), 0.1854 (4),
0.1845 (1), 0.1843 (11), 0.1838 (1), 0.1835 (3), 0.1825 (1), 0.1825 (1),
0.1813 (1), 0.1805 (2), 0.1787 (1), 0.1776 (1), 0.1775 (3), 0.1764 (1), 0.1763
(1)
Best fit found:
Fit molecule S1_hCOMMD8_AF-Q9NX08-F1-model_v1.pdb 1.pdb (#8) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 880 atoms
average map value = 0.2258, steps = 72
shifted from previous position = 3.97
rotated from previous position = 10.7 degrees
atoms outside contour = 467, contour level = 0.24054
Position of S1_hCOMMD8_AF-Q9NX08-F1-model_v1.pdb 1.pdb (#8) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.72899264 -0.55716830 0.39765967 433.97317943
-0.53851917 0.10818342 -0.83563951 549.20409048
0.42257168 -0.82332244 -0.37891073 416.49140000
Axis 0.36802487 -0.74435272 0.55722233
Axis point 350.36181547 0.00000000 416.28717537
Rotation angle (degrees) 179.04116715
Shift along axis -17.01032533
Found 32 fits. List window not yet implemented.
> hide #8 models
> show #9 models
> select #9
919 atoms, 930 bonds, 118 residues, 1 model selected
> volume #11 level 0.1007
> fitmap sel inMap #11 search 100 radius 5
Found 46 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
0.2031 (3), 0.2005 (1), 0.2 (1), 0.1997 (5), 0.1991 (1), 0.199 (1), 0.1986
(1), 0.1986 (5), 0.1984 (1), 0.1981 (8), 0.198 (6), 0.1978 (3), 0.1978 (4),
0.1975 (1), 0.1962 (3), 0.1949 (1), 0.1945 (4), 0.1944 (4), 0.1944 (3), 0.1943
(1), 0.1942 (2), 0.1942 (9), 0.194 (1), 0.1935 (1), 0.1934 (2), 0.1927 (1),
0.1927 (1), 0.1925 (2), 0.1922 (1), 0.192 (2), 0.1918 (1), 0.1915 (1), 0.1911
(1), 0.1908 (1), 0.1904 (1), 0.19 (1), 0.1899 (2), 0.1897 (1), 0.1893 (2),
0.1892 (1), 0.1884 (3), 0.1878 (1), 0.1867 (1), 0.1843 (1), 0.1843 (2), 0.1831
(1)
Best fit found:
Fit molecule S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 919 atoms
average map value = 0.2031, steps = 264
shifted from previous position = 32.2
rotated from previous position = 30.2 degrees
atoms outside contour = 67, contour level = 0.10067
Position of S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
0.19029689 -0.16750513 0.96733093 7.38897980
-0.09765093 0.97722019 0.18842783 -63.86837171
-0.97685791 -0.13031796 0.16960492 426.84939085
Axis -0.16168643 0.98620582 0.03543412
Axis point 256.06296028 0.00000000 214.89837947
Rotation angle (degrees) 80.29583683
Shift along axis -49.05702516
Found 46 fits. List window not yet implemented.
> view matrix models
> #9,0.1903,-0.16751,0.96733,-17.285,-0.097651,0.97722,0.18843,-73.136,-0.97686,-0.13032,0.1696,444.41
> hide #9 models
> show #10 models
> select #10
1031 atoms, 1047 bonds, 128 residues, 1 model selected
> fitmap sel inMap #11 search 100 radius 5
Found 34 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
0.2007 (8), 0.1964 (1), 0.1867 (4), 0.1851 (10), 0.1833 (9), 0.1818 (1),
0.1817 (1), 0.1808 (2), 0.1805 (9), 0.1804 (2), 0.1781 (7), 0.1777 (11),
0.1755 (1), 0.1755 (2), 0.1734 (5), 0.1716 (2), 0.1713 (2), 0.171 (1), 0.1708
(1), 0.1702 (2), 0.17 (2), 0.1699 (2), 0.1692 (1), 0.1687 (1), 0.1672 (2),
0.167 (2), 0.1668 (1), 0.1667 (2), 0.1664 (1), 0.166 (1), 0.1613 (1), 0.1597
(1), 0.1594 (1), 0.1541 (1)
Best fit found:
Fit molecule S1_hCOMMD10_AF-Q9Y6G5-F1-model_v1.pdb 1.pdb (#10) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 1031 atoms
average map value = 0.2007, steps = 256
shifted from previous position = 2.61
rotated from previous position = 64.9 degrees
atoms outside contour = 106, contour level = 0.10067
Position of S1_hCOMMD10_AF-Q9Y6G5-F1-model_v1.pdb 1.pdb (#10) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
0.86933496 0.31955781 -0.37701391 44.77662709
0.16166761 0.53700230 0.82794449 -147.09615058
0.46703347 -0.78071207 0.41517277 184.18195339
Axis -0.88218485 -0.46287432 -0.08658675
Axis point 0.00000000 77.18800741 213.76334895
Rotation angle (degrees) 65.74772727
Shift along axis 12.63805176
Found 34 fits. List window not yet implemented.
> save "D:/Work/CComplex Fits Umeå/Ccomplex_fits_COMMD_initial_positions.cxs"
> save "D:/Work/CComplex Fits Umeå/Ccomplex_fits_COMMD_initial_positions.cxs"
> includeMaps true
> open "D:/Work/CComplex Fits/site1/S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb
> 2.pdb" "D:/Work/CComplex Fits/site1/S1_hCOMMD2_AF-Q86X83-F1-model_v1.pdb
> 2.pdb" "D:/Work/CComplex Fits/site1/S1_hCOMMD3_AF-Q9UBI1-F1-model_v1.pdb
> 2.pdb" "D:/Work/CComplex Fits/site1/S1_hCOMMD4_AF-Q9H0A8-F1-model_v1.pdb
> 2.pdb" "D:/Work/CComplex Fits/site1/S1_hCOMMD5_AF-Q9GZQ3-F1-model_v1.pdb
> 2.pdb" "D:/Work/CComplex
> Fits/site1/S1_hCOMMD6_AF-Q7Z4G1-F1-model_v1.pdb.pdb" "D:/Work/CComplex
> Fits/site1/S1_hCOMMD7_AF-F1QJA8-F1-model_v1.pdb 2.pdb" "D:/Work/CComplex
> Fits/site1/S1_hCOMMD8_AF-Q9NX08-F1-model_v1.pdb 2.pdb" "D:/Work/CComplex
> Fits/site1/S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 2.pdb" "D:/Work/CComplex
> Fits/site1/S1_hCOMMD10_AF-Q9Y6G5-F1-model_v1.pdb 2.pdb"
Chain information for S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb #12
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD2_AF-Q86X83-F1-model_v1.pdb 2.pdb #13
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD3_AF-Q9UBI1-F1-model_v1.pdb 2.pdb #14
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD4_AF-Q9H0A8-F1-model_v1.pdb 2.pdb #15
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD5_AF-Q9GZQ3-F1-model_v1.pdb 2.pdb #16
---
Chain | Description
A | No description available
S1_hCOMMD6_AF-Q7Z4G1-F1-model_v1.pdb.pdb title:
Alphafold V2.0 prediction for comm domain-containing protein 6 (Q7Z4G1) [more
info...]
Chain information for S1_hCOMMD6_AF-Q7Z4G1-F1-model_v1.pdb.pdb #17
---
Chain | Description
A | comm domain-containing protein 6
Chain information for S1_hCOMMD7_AF-F1QJA8-F1-model_v1.pdb 2.pdb #18
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD8_AF-Q9NX08-F1-model_v1.pdb 2.pdb #19
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 2.pdb #20
---
Chain | Description
A | No description available
Chain information for S1_hCOMMD10_AF-Q9Y6G5-F1-model_v1.pdb 2.pdb #21
---
Chain | Description
A | No description available
> volume #11 level 0.1946
> cofr centerOfView
> select clear
> show #2 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #19 models
> hide #20 models
> hide #21 models
> show #12 models
> hide #2 models
> select #12
604 atoms, 614 bonds, 76 residues, 1 model selected
> view matrix models #12,1,0,0,70.96,0,1,0,-6.0479,0,0,1,7.013
> select #11
2 models selected
> select clear
> select #12/A:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
91 atoms, 92 bonds, 12 residues, 1 model selected
> select up
604 atoms, 614 bonds, 76 residues, 1 model selected
> view matrix models
> #12,0.72782,-0.44702,-0.52006,303.76,0.60657,0.77342,0.18409,-70.991,0.31993,-0.44944,0.83406,86.825
> view matrix models
> #12,-0.16227,-0.058229,-0.98503,426.98,0.9841,-0.08262,-0.15723,111.3,-0.072228,-0.99488,0.070709,394.24
> view matrix models
> #12,-0.29137,0.24286,-0.92527,371.33,0.81362,-0.44579,-0.37322,246.9,-0.50312,-0.86156,-0.067705,448.72
> view matrix models
> #12,-0.29137,0.24286,-0.92527,382.71,0.81362,-0.44579,-0.37322,245.95,-0.50312,-0.86156,-0.067705,451.19
> view matrix models
> #12,-0.32533,-0.24247,-0.91399,484.96,0.4726,-0.87888,0.064941,301.3,-0.81903,-0.41082,0.40052,316.08
> view matrix models
> #12,-0.32533,-0.24247,-0.91399,484.54,0.4726,-0.87888,0.064941,296.71,-0.81903,-0.41082,0.40052,321.57
> view matrix models
> #12,-0.54771,-0.17116,-0.81897,482.11,0.387,-0.91967,-0.066615,339.97,-0.74179,-0.35343,0.56995,269.2
> view matrix models
> #12,-0.61671,-0.24496,-0.7481,491.35,0.39071,-0.92028,-0.020752,336.51,-0.68338,-0.30509,0.66326,252.24
> view matrix models
> #12,-0.60179,0.66244,-0.44613,248.61,-0.59935,-0.74378,-0.29594,479.94,-0.52786,0.089294,0.84463,118.12
> view matrix models
> #12,-0.69767,0.40822,-0.58874,339.1,-0.39108,-0.90555,-0.16446,462.2,-0.60027,0.1155,0.79142,131.81
> view matrix models
> #12,-0.69767,0.40822,-0.58874,335.05,-0.39108,-0.90555,-0.16446,462,-0.60027,0.1155,0.79142,133.97
> view matrix models
> #12,-0.5697,0.53147,-0.62688,299.71,-0.51253,-0.82602,-0.23452,474.21,-0.64246,0.18769,0.74298,133.37
> fitmap sel inMap #11 search 50 radius 5
Found 38 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.2132 (3), 0.2114 (1), 0.2093 (2), 0.2085 (1), 0.2084 (1), 0.2057 (2), 0.2054
(1), 0.2052 (1), 0.2051 (1), 0.2043 (1), 0.2028 (1), 0.2021 (1), 0.2018 (2),
0.2013 (1), 0.2012 (1), 0.2006 (1), 0.2005 (1), 0.2 (1), 0.1994 (2), 0.1991
(1), 0.1982 (3), 0.1977 (1), 0.1973 (1), 0.1957 (1), 0.1948 (1), 0.1931 (2),
0.1928 (1), 0.1925 (2), 0.1923 (1), 0.1909 (1), 0.1908 (1), 0.1905 (2), 0.188
(1), 0.1871 (2), 0.1861 (1), 0.1809 (1), 0.1794 (1), 0.1603 (1)
Best fit found:
Fit molecule S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 604 atoms
average map value = 0.2132, steps = 172
shifted from previous position = 20.3
rotated from previous position = 31.7 degrees
atoms outside contour = 242, contour level = 0.19463
Position of S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
0.18091677 0.10954297 -0.97737890 369.29830551
0.51946490 0.83320538 0.18953928 -75.94208630
0.83512002 -0.54200481 0.09383712 199.24328613
Axis -0.36630610 -0.90757263 0.20526022
Axis point 81.07493884 0.00000000 300.36079853
Rotation angle (degrees) 86.90569100
Shift along axis -25.45654056
Found 38 fits. List window not yet implemented.
> view matrix models
> #12,0.18092,0.10954,-0.97738,359.07,0.51946,0.83321,0.18954,-76.308,0.83512,-0.542,0.093837,209.65
> view matrix models
> #12,-0.42358,-0.58411,-0.69238,530.18,0.021246,0.75772,-0.65223,155.84,0.90561,-0.29098,-0.30854,220.94
> view matrix models
> #12,-0.95865,0.26155,-0.11218,322.62,0.27987,0.93789,-0.205,4.4932,0.051594,-0.22792,-0.97231,439.5
> view matrix models
> #12,-0.95865,0.26155,-0.11218,317.02,0.27987,0.93789,-0.205,6.7238,0.051594,-0.22792,-0.97231,431.6
> view matrix models
> #12,-0.95865,0.26155,-0.11218,318.88,0.27987,0.93789,-0.205,-1.0151,0.051594,-0.22792,-0.97231,428.5
> view matrix models
> #12,-0.95865,0.26155,-0.11218,319.15,0.27987,0.93789,-0.205,-0.96763,0.051594,-0.22792,-0.97231,428.59
> view matrix models
> #12,-0.95856,0.26183,-0.11233,319.11,0.28018,0.93783,-0.20488,-1.0154,0.051701,-0.22786,-0.97232,428.56
> view matrix models
> #12,0.29131,0.78062,-0.55297,126.92,-0.77354,-0.14787,-0.61626,434.79,-0.56283,0.60727,0.56076,62.675
> view matrix models
> #12,0.29131,0.78062,-0.55297,131.81,-0.77354,-0.14787,-0.61626,421.44,-0.56283,0.60727,0.56076,75.798
> view matrix models
> #12,-0.9346,-0.19849,-0.29517,448.31,0.13818,-0.96725,0.21291,321.14,-0.32777,0.15819,0.93142,70.699
> view matrix models
> #12,-0.9346,-0.19849,-0.29517,448.61,0.13818,-0.96725,0.21291,329.81,-0.32777,0.15819,0.93142,75.15
> view matrix models
> #12,-0.9346,-0.19849,-0.29517,441.74,0.13818,-0.96725,0.21291,332.6,-0.32777,0.15819,0.93142,76.095
> view matrix models
> #12,-0.93456,-0.196,-0.29694,441.54,0.14409,-0.97158,0.18781,337.21,-0.32531,0.13273,0.93624,80.143
> view matrix models
> #12,-0.74738,-0.66188,0.057691,449.08,0.65836,-0.72612,0.19827,217.15,-0.089341,0.18616,0.97845,30.515
> view matrix models
> #12,-0.74738,-0.66188,0.057691,449.39,0.65836,-0.72612,0.19827,222.68,-0.089341,0.18616,0.97845,32.872
> view matrix models
> #12,-0.38275,-0.87123,0.30735,399.64,0.92189,-0.38187,0.065585,141,0.060228,0.30845,0.94933,-6.7432
> view matrix models
> #12,-0.38275,-0.87123,0.30735,402.21,0.92189,-0.38187,0.065585,141.02,0.060228,0.30845,0.94933,-6.4598
> fitmap sel inMap #11 search 50 radius 1
Found 43 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.2181 (1), 0.2148 (1), 0.212 (1), 0.2114 (1), 0.2093 (1), 0.2085 (1), 0.2081
(1), 0.2069 (1), 0.2063 (2), 0.2058 (1), 0.2057 (2), 0.2051 (1), 0.2043 (2),
0.2041 (1), 0.2036 (1), 0.2017 (1), 0.2003 (1), 0.2 (1), 0.1994 (1), 0.199
(3), 0.1983 (1), 0.1977 (1), 0.1975 (1), 0.1975 (1), 0.1962 (1), 0.195 (1),
0.195 (1), 0.1944 (2), 0.1937 (1), 0.1915 (1), 0.1902 (1), 0.1897 (1), 0.1889
(2), 0.188 (1), 0.1878 (1), 0.1849 (1), 0.1849 (1), 0.1843 (1), 0.1836 (1),
0.1779 (1), 0.177 (1), 0.1699 (1), 0.1671 (1)
Best fit found:
Fit molecule S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 604 atoms
average map value = 0.2181, steps = 348
shifted from previous position = 17.5
rotated from previous position = 79.5 degrees
atoms outside contour = 225, contour level = 0.19463
Position of S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.35262681 0.12823552 -0.92693583 427.42872905
-0.72778313 -0.66023648 0.18552531 388.50485870
-0.58820588 0.74002940 0.32614470 87.56197925
Axis 0.51596161 -0.31518550 -0.79651850
Axis point 314.80053456 101.38979057 0.00000000
Rotation angle (degrees) 147.49656820
Shift along axis 28.34098007
Found 43 fits. List window not yet implemented.
> undo
> ui tool show "Fit in Map"
Fit molecule S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 604 atoms
average map value = 0.1947, steps = 104
shifted from previous position = 1.06e-13
rotated from previous position = 42.5 degrees
atoms outside contour = 285, contour level = 0.19463
Position of S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.88196910 -0.35211639 0.31328049 357.63014282
0.42672187 -0.87879655 0.21360043 279.10321238
0.20009764 0.32207260 0.92532710 -23.23570811
Axis 0.13653584 0.14246526 0.98033750
Axis point 151.93768059 178.07264663 0.00000000
Rotation angle (degrees) 156.59489618
Shift along axis 65.81300855
> view matrix models
> #12,-0.88197,-0.35212,0.31328,360.98,0.42672,-0.8788,0.2136,277.7,0.2001,0.32207,0.92533,-23.772
Fit molecule S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 604 atoms
average map value = 0.1975, steps = 84
shifted from previous position = 8.53e-14
rotated from previous position = 29.1 degrees
atoms outside contour = 286, contour level = 0.19463
Position of S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.65001089 -0.68247973 0.33422655 394.31035517
0.75719851 -0.54444990 0.36086674 140.22711756
-0.06431458 0.48764312 0.87067093 -13.28315892
Axis 0.08456307 0.26583704 0.96030191
Axis point 168.42064578 163.40581697 0.00000000
Rotation angle (degrees) 131.44454979
Shift along axis 57.86581159
> view matrix models
> #12,-0.65001,-0.68248,0.33423,396.22,0.7572,-0.54445,0.36087,142.91,-0.064315,0.48764,0.87067,-16.518
Fit molecule S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 604 atoms
average map value = 0.1847, steps = 76
shifted from previous position = 2.86e-13
rotated from previous position = 16.6 degrees
atoms outside contour = 300, contour level = 0.19463
Position of S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.62985488 -0.69036336 0.35592329 391.26848662
0.75861159 -0.64513871 0.09112940 212.24765440
0.16670754 0.32740581 0.93006134 -24.63324452
Axis 0.15961863 0.12782638 0.97886787
Axis point 151.55685311 193.81429603 0.00000000
Rotation angle (degrees) 132.25768624
Shift along axis 65.47189621
> select #12/A:169
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
178 atoms, 177 bonds, 23 residues, 1 model selected
Fit molecule S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 178 atoms
average map value = 0.2317, steps = 144
shifted from previous position = 3.47e-13
rotated from previous position = 60.3 degrees
atoms outside contour = 52, contour level = 0.19463
Position of S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.94135383 -0.03339647 -0.33576446 415.18418321
-0.01164396 -0.99128203 0.13124194 371.82245798
-0.33722026 0.12745470 0.93275818 78.41509065
Axis -0.17115385 0.06579075 0.98304524
Axis point 213.37778001 184.47015325 0.00000000
Rotation angle (degrees) 179.36607593
Shift along axis 30.48768598
> select #12/A:158
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
62 atoms, 63 bonds, 7 residues, 1 model selected
> select up
604 atoms, 614 bonds, 76 residues, 1 model selected
> select down
62 atoms, 63 bonds, 7 residues, 1 model selected
> select #12/A:158
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #12/A:150
15 atoms, 14 bonds, 2 residues, 1 model selected
> select add #12/A:118
19 atoms, 17 bonds, 3 residues, 1 model selected
> select up
235 atoms, 237 bonds, 30 residues, 1 model selected
Fit molecule S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 235 atoms
average map value = 0.1635, steps = 116
shifted from previous position = 3.57e-13
rotated from previous position = 78.2 degrees
atoms outside contour = 142, contour level = 0.19463
Position of S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.26819421 -0.94994524 -0.16023735 477.83723049
0.36086905 -0.25328430 0.89756374 31.08963181
-0.89322198 0.18289665 0.41073516 238.18228594
Axis -0.42969282 0.44070623 0.78812569
Axis point 292.71887348 110.46451065 0.00000000
Rotation angle (degrees) 123.73631665
Shift along axis -3.90425662
> select #12
604 atoms, 614 bonds, 76 residues, 1 model selected
> ~select #12
Nothing selected
> select #12
604 atoms, 614 bonds, 76 residues, 1 model selected
> view matrix models
> #12,-0.94135,-0.033396,-0.33576,415.19,-0.011644,-0.99128,0.13124,372.14,-0.33722,0.12745,0.93276,77.914
> view matrix models
> #12,-0.73745,0.47982,-0.47533,307.84,0.51886,0.85302,0.056094,-63.496,0.43238,-0.20526,-0.87802,369.89
> view matrix models
> #12,-0.73745,0.47982,-0.47533,308.83,0.51886,0.85302,0.056094,-57.348,0.43238,-0.20526,-0.87802,359.66
> view matrix models
> #12,-0.77612,0.4859,-0.40193,299.5,0.43025,0.87401,0.22581,-80.447,0.46101,0.0023242,-0.88739,314.89
> select #12/A:183
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
178 atoms, 177 bonds, 23 residues, 1 model selected
Fit molecule S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 178 atoms
average map value = 0.2344, steps = 72
shifted from previous position = 2.29e-13
rotated from previous position = 33 degrees
atoms outside contour = 43, contour level = 0.19463
Position of S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.96178530 0.15446044 -0.22607768 359.86368399
0.21307233 0.94077737 -0.26370102 16.88291812
0.17195734 -0.30179464 -0.93773701 421.32100532
Axis -0.09426157 -0.98492642 0.14503346
Axis point 157.36899718 0.00000000 230.60447075
Rotation angle (degrees) 168.34235733
Shift along axis 10.55589660
> view matrix models
> #12,-0.96179,0.15446,-0.22608,359.58,0.21307,0.94078,-0.2637,17.574,0.17196,-0.30179,-0.93774,421.6
> view matrix models
> #12,-0.49445,0.68097,-0.54018,246.13,0.79813,0.60183,0.02812,-42.107,0.34425,-0.41723,-0.84108,405.32
> view matrix models
> #12,-0.49445,0.68097,-0.54018,245.15,0.79813,0.60183,0.02812,-39.632,0.34425,-0.41723,-0.84108,406.1
Fit molecule S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 178 atoms
average map value = 0.2167, steps = 88
shifted from previous position = 2.15e-13
rotated from previous position = 56.8 degrees
atoms outside contour = 70, contour level = 0.19463
Position of S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.95908631 -0.09979010 -0.26494434 414.53432979
0.03897852 0.88036795 -0.47268703 84.32791043
0.28041795 -0.46367477 -0.84045911 423.39002281
Axis 0.01601291 -0.96899452 0.24656278
Axis point 177.12641157 0.00000000 253.10588158
Rotation angle (degrees) 163.65584667
Shift along axis 29.31683773
> view matrix models
> #12,-0.95909,-0.09979,-0.26494,414.25,0.038979,0.88037,-0.47269,86.829,0.28042,-0.46367,-0.84046,425.77
Fit molecule S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 178 atoms
average map value = 0.2207, steps = 88
shifted from previous position = 2.98e-13
rotated from previous position = 38.9 degrees
atoms outside contour = 70, contour level = 0.19463
Position of S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.65304330 0.24502249 -0.71658811 383.32773482
0.40986650 0.91001135 -0.06236121 -35.71440271
0.63682337 -0.33442999 -0.69470325 330.09460933
Axis -0.19569153 -0.97347137 0.11856773
Axis point 126.65861445 0.00000000 242.45259958
Rotation angle (degrees) 135.96106586
Shift along axis -1.10847432
> view matrix models
> #12,-0.59496,0.37541,-0.71069,349.72,0.59987,0.79591,-0.081761,-33.73,0.53495,-0.47497,-0.69873,372.3
> view matrix models
> #12,-0.69331,0.13836,-0.70723,410.8,0.50421,0.79431,-0.33889,25.326,0.51488,-0.59155,-0.62046,384.88
> view matrix models
> #12,-0.90103,0.36019,-0.24166,308.99,0.42607,0.83939,-0.33749,26.093,0.081289,-0.40705,-0.90978,455.93
> view matrix models
> #12,-0.90103,0.36019,-0.24166,312.93,0.42607,0.83939,-0.33749,25.796,0.081289,-0.40705,-0.90978,451.24
Fit molecule S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 178 atoms
average map value = 0.2308, steps = 56
shifted from previous position = 3.18e-13
rotated from previous position = 20 degrees
atoms outside contour = 54, contour level = 0.19463
Position of S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.92063773 0.27252625 -0.27956343 339.65916266
0.29547841 0.95439582 -0.04267588 -31.68573459
0.25518383 -0.12189396 -0.95917835 380.10595121
Axis -0.14640998 -0.98831405 0.04241992
Axis point 145.66360835 0.00000000 213.03527306
Rotation angle (degrees) 164.30389002
Shift along axis -2.28997133
> view matrix models
> #12,0.32264,0.80942,-0.49066,103.43,0.78841,0.057028,0.61251,-29.592,0.52376,-0.58446,-0.61975,378.97
> view matrix models
> #12,0.32264,0.80942,-0.49066,112.81,0.78841,0.057028,0.61251,-26.223,0.52376,-0.58446,-0.61975,380.82
> view matrix models
> #12,0.68738,0.64328,-0.33719,71.416,0.58988,-0.2236,0.77592,28.307,0.42374,-0.73225,-0.53315,408.84
> select up
604 atoms, 614 bonds, 76 residues, 1 model selected
Fit molecule S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) using 604 atoms
average map value = 0.1819, steps = 60
shifted from previous position = 1.21e-13
rotated from previous position = 15.2 degrees
atoms outside contour = 324, contour level = 0.19463
Position of S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb (#12) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
0.85175270 0.44399906 -0.27817672 79.92396634
0.44386339 -0.32936552 0.83336890 58.23761246
0.27839314 -0.83329663 -0.47761285 438.07315735
Axis -0.94850991 -0.31674743 -0.00007721
Axis point 0.00000000 153.07790829 210.14068780
Rotation angle (degrees) 118.52960762
Shift along axis -94.28911386
> open 6bp6
Summary of feedback from opening 6bp6 fetched from pdb
---
note | Fetching compressed mmCIF 6bp6 from
http://files.rcsb.org/download/6bp6.cif
6bp6 title:
Crystal structure of Commd9 COMM domain [more info...]
Chain information for 6bp6 #22
---
Chain | Description
A B | COMM domain-containing protein 9
6bp6 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> sym #22 assembly 1
> view
> sequence chain #22/A#22/B
Alignment identifier is 1
> sym #22 assembly 1
> view
> select #23.2/A:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> close #24
> close #23.2-4
> mmaker #22 to #12
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 S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb, chain A (#12) with
6bp6, chain A (#22), sequence alignment score = 125.5
RMSD between 61 pruned atom pairs is 0.896 angstroms; (across all 75 pairs:
3.293)
> mmaker #22 to #12
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 S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb, chain A (#12) with
6bp6, chain A (#22), sequence alignment score = 125.5
RMSD between 61 pruned atom pairs is 0.896 angstroms; (across all 75 pairs:
3.293)
> mmaker #23 to #12
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 S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb 2.pdb, chain A (#12) with
6bp6, chain A (#23.1), sequence alignment score = 125.5
RMSD between 61 pruned atom pairs is 0.896 angstroms; (across all 75 pairs:
3.293)
> hide #12 models
> select #23.1/B:84
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
214 atoms, 214 bonds, 28 residues, 1 model selected
> select up
635 atoms, 639 bonds, 83 residues, 1 model selected
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 635 atoms
average map value = 0.1975, steps = 120
shifted from previous position = 4.19e-13
rotated from previous position = 58.6 degrees
atoms outside contour = 301, contour level = 0.19463
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
0.83277688 0.29140852 -0.47070558 214.32983305
-0.08151924 -0.77643277 -0.62490541 233.71697244
-0.54757400 0.55877834 -0.62283985 220.94914270
Axis 0.95195879 0.06182020 -0.29992121
Axis point 0.00000000 61.08005345 185.31196326
Rotation angle (degrees) 141.55891697
Shift along axis 152.21426315
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 635 atoms
average map value = 0.2032, steps = 152
shifted from previous position = 4.32
rotated from previous position = 9.21 degrees
atoms outside contour = 287, contour level = 0.19463
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
0.86048126 0.37752636 -0.34211963 206.41826007
0.02922944 -0.70697936 -0.70662990 227.96373452
-0.50864293 0.59804183 -0.61937738 216.97034992
Axis 0.95890044 0.12239038 -0.25598935
Axis point 0.00000000 47.47209744 178.43515358
Rotation angle (degrees) 137.13324383
Shift along axis 170.29302899
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 635 atoms
average map value = 0.2032, steps = 44
shifted from previous position = 0.00587
rotated from previous position = 0.0195 degrees
atoms outside contour = 288, contour level = 0.19463
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
0.86059067 0.37748215 -0.34189315 206.41922207
0.02945124 -0.70706573 -0.70653428 227.96261044
-0.50844500 0.59796763 -0.61961149 216.96964885
Axis 0.95893591 0.12243183 -0.25583660
Axis point 0.00000000 47.48443846 178.40328667
Rotation angle (degrees) 137.14213257
Shift along axis 170.34390626
> fitmap sel inMap #11 search 50 radius 1
Found 39 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.2154 (1), 0.2137 (1), 0.2133 (4), 0.213 (1), 0.2125 (1), 0.2078 (1), 0.2067
(1), 0.2066 (1), 0.2062 (2), 0.2051 (3), 0.2048 (1), 0.2046 (1), 0.2042 (1),
0.201 (1), 0.1985 (2), 0.1984 (1), 0.198 (3), 0.1977 (1), 0.1964 (1), 0.1961
(2), 0.1958 (1), 0.1954 (1), 0.1951 (1), 0.1945 (1), 0.1945 (1), 0.1944 (2),
0.1937 (1), 0.1918 (1), 0.1905 (1), 0.1896 (1), 0.1892 (1), 0.188 (1), 0.1835
(1), 0.183 (1), 0.1795 (1), 0.1787 (1), 0.1703 (1), 0.168 (1), 0.1649 (1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 635 atoms
average map value = 0.2154, steps = 248
shifted from previous position = 8.94
rotated from previous position = 46.2 degrees
atoms outside contour = 241, contour level = 0.19463
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
-0.44385430 -0.87446109 -0.19573234 271.94328175
-0.72583860 0.22274722 0.65080107 192.86263687
-0.52550134 0.43093098 -0.73358493 231.90331741
Axis -0.51942457 0.77905148 0.35110810
Axis point 214.01628706 0.00000000 50.58339655
Rotation angle (degrees) 167.78106736
Shift along axis 90.41903545
Found 39 fits. List window not yet implemented.
> select clear
> hide #!11 models
> select #23.1/B:82
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #23.1/A:76
18 atoms, 16 bonds, 2 residues, 1 model selected
> select up
428 atoms, 428 bonds, 56 residues, 1 model selected
> show #!11 models
> fitmap sel inMap #11 search 50 radius 1
Found 38 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.2292 (2), 0.2279 (1), 0.2251 (1), 0.2226 (1), 0.2223 (2), 0.222 (4), 0.2217
(1), 0.2212 (1), 0.2201 (1), 0.22 (1), 0.2197 (1), 0.2194 (1), 0.2156 (3),
0.2148 (1), 0.2146 (1), 0.2139 (1), 0.2124 (1), 0.2123 (1), 0.2121 (1), 0.2119
(1), 0.2107 (1), 0.2107 (1), 0.21 (1), 0.2092 (1), 0.209 (4), 0.2083 (1),
0.2047 (2), 0.2035 (1), 0.2027 (1), 0.2024 (1), 0.2009 (1), 0.2006 (1), 0.1951
(2), 0.1942 (1), 0.1939 (1), 0.1938 (1), 0.1938 (1), 0.1833 (1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 428 atoms
average map value = 0.2292, steps = 160
shifted from previous position = 11
rotated from previous position = 33.8 degrees
atoms outside contour = 140, contour level = 0.19463
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
0.01897455 0.47042206 0.88223745 205.76106428
0.99602730 0.06789128 -0.05762253 182.30256986
-0.08700318 0.87982601 -0.46726503 215.36587451
Axis 0.64775006 0.66971748 0.36317814
Axis point 44.83278952 0.00000000 61.55193262
Rotation angle (degrees) 133.64591110
Shift along axis 333.58913662
Found 38 fits. List window not yet implemented.
> fitmap sel inMap #11 search 50 radius 5
Found 42 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.23 (2), 0.2292 (3), 0.2289 (1), 0.2287 (1), 0.2284 (1), 0.2279 (1), 0.2251
(1), 0.2234 (1), 0.2232 (2), 0.2231 (1), 0.2229 (1), 0.2226 (1), 0.2217 (2),
0.2215 (1), 0.2198 (2), 0.2194 (1), 0.2192 (1), 0.2188 (1), 0.2151 (2), 0.2149
(1), 0.2148 (1), 0.2146 (1), 0.2146 (2), 0.2142 (1), 0.2131 (1), 0.2123 (1),
0.212 (1), 0.2116 (1), 0.2108 (1), 0.2101 (1), 0.209 (1), 0.2086 (1), 0.2071
(1), 0.2068 (1), 0.2068 (1), 0.2059 (1), 0.2016 (1), 0.1999 (1), 0.1937 (1),
0.1893 (1), 0.1828 (1), 0.1811 (1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 428 atoms
average map value = 0.23, steps = 240
shifted from previous position = 10.8
rotated from previous position = 68 degrees
atoms outside contour = 138, contour level = 0.19463
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
0.85541596 0.19873172 0.47829817 211.10566850
-0.49901982 0.06890228 0.86384696 183.41959426
0.13871802 -0.97762882 0.15811121 247.52475552
Axis -0.92152095 0.16993448 -0.34917248
Axis point 0.00000000 201.81316456 -43.94420857
Rotation angle (degrees) 87.63790108
Shift along axis -249.79781486
Found 42 fits. List window not yet implemented.
> hide #!11 models
> show #!11 models
> hide #!23 models
> show #!23 models
> select up
1247 atoms, 1248 bonds, 169 residues, 1 model selected
> fitmap sel inMap #11 search 50 radius 5
Found 41 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.1965 (1), 0.1943 (4), 0.1936 (1), 0.1926 (1), 0.1913 (1), 0.1912 (2), 0.1904
(1), 0.1902 (1), 0.1897 (3), 0.1897 (1), 0.1894 (1), 0.1889 (1), 0.1863 (1),
0.1861 (2), 0.1845 (1), 0.1842 (2), 0.1841 (1), 0.1825 (1), 0.1818 (2), 0.1815
(1), 0.1813 (1), 0.1804 (1), 0.18 (1), 0.1798 (1), 0.1796 (1), 0.1793 (1),
0.1792 (1), 0.1783 (1), 0.1775 (1), 0.1769 (1), 0.1764 (1), 0.1763 (1), 0.1762
(1), 0.1753 (1), 0.1749 (1), 0.1729 (1), 0.1721 (1), 0.1683 (1), 0.1646 (1),
0.1627 (1), 0.146 (1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 1247 atoms
average map value = 0.1965, steps = 176
shifted from previous position = 16.6
rotated from previous position = 4.65 degrees
atoms outside contour = 593, contour level = 0.19463
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
0.93866355 0.18113011 0.29343233 205.13961821
0.26424135 0.16891148 -0.94955005 205.55702951
-0.22155626 0.96884504 0.11068895 200.32951915
Axis 0.96496105 0.25904149 0.04180531
Axis point 0.00000000 -34.30393874 175.68962879
Rotation angle (degrees) 83.73471884
Shift along axis 259.57437872
Found 41 fits. List window not yet implemented.
> view matrix models
> #23.1,-0.88049,-0.066099,-0.46944,252.1,0.46864,0.028086,-0.88294,205.56,0.071547,-0.99742,0.006248,255.61
> view matrix models
> #23.1,-0.85603,-0.20359,-0.47515,255.88,0.47696,0.043296,-0.87786,204.91,0.1993,-0.9781,0.060042,252.25
> view matrix models
> #23.1,-0.85603,-0.20359,-0.47515,251.69,0.47696,0.043296,-0.87786,205.32,0.1993,-0.9781,0.060042,252.25
> view matrix models
> #23.1,0.73643,0.65805,0.15699,191.94,-0.31954,0.13381,0.93808,188.82,0.59629,-0.74099,0.30882,235.37
> view matrix models
> #23.1,0.73643,0.65805,0.15699,202.53,-0.31954,0.13381,0.93808,187.67,0.59629,-0.74099,0.30882,234.17
> fitmap sel inMap #11 search 50 radius 5
Found 46 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.1968 (3), 0.1967 (2), 0.1958 (1), 0.1912 (2), 0.1905 (1), 0.1903 (1), 0.1902
(1), 0.189 (1), 0.1874 (1), 0.1866 (1), 0.1866 (1), 0.1863 (1), 0.1862 (1),
0.1861 (1), 0.1859 (1), 0.1859 (1), 0.1856 (1), 0.1851 (1), 0.185 (1), 0.1847
(1), 0.184 (1), 0.1834 (1), 0.183 (1), 0.1825 (1), 0.1823 (1), 0.1821 (1),
0.1819 (1), 0.1814 (1), 0.1813 (1), 0.1811 (1), 0.1804 (1), 0.1803 (1), 0.1787
(1), 0.1776 (1), 0.1776 (1), 0.1768 (1), 0.1765 (1), 0.1764 (1), 0.176 (1),
0.1755 (1), 0.1745 (1), 0.1675 (1), 0.1672 (1), 0.1633 (1), 0.1627 (1), 0.1595
(1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 1247 atoms
average map value = 0.1968, steps = 152
shifted from previous position = 8.28
rotated from previous position = 27.2 degrees
atoms outside contour = 584, contour level = 0.19463
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
0.86198410 0.46192361 -0.20882975 204.42736392
0.24354620 -0.01606124 0.96975625 184.64520973
0.44459931 -0.88677425 -0.12634425 252.47265615
Axis -0.93752644 -0.32997412 -0.11027807
Axis point 0.00000000 158.94958139 71.55483475
Rotation angle (degrees) 98.06003874
Shift along axis -280.42639597
Found 46 fits. List window not yet implemented.
> color sel bychain
> hide #!23 models
> show #!23 models
> view matrix models
> #23.1,0.86198,0.46192,-0.20883,201.59,0.24355,-0.016061,0.96976,210.48,0.4446,-0.88677,-0.12634,272.54
> view matrix models
> #23.1,0.84599,0.52895,-0.067196,197.8,0.51799,-0.78542,0.33883,238.15,0.12645,-0.32145,-0.93844,272.52
> view matrix models
> #23.1,0.84599,0.52895,-0.067196,199.37,0.51799,-0.78542,0.33883,253.16,0.12645,-0.32145,-0.93844,270.38
> view matrix models
> #23.1,0.74076,-0.18471,-0.64588,230.6,-0.22383,-0.97438,0.021948,275.01,-0.63339,0.12831,-0.76312,266.42
> view matrix models
> #23.1,0.23614,-0.44664,-0.86299,249.45,-0.469,-0.8302,0.30134,270.53,-0.85105,0.33358,-0.40552,258.56
> view matrix models
> #23.1,0.23614,-0.44664,-0.86299,254.16,-0.469,-0.8302,0.30134,270.09,-0.85105,0.33358,-0.40552,257.69
> view matrix models
> #23.1,0.099062,-0.4868,-0.86788,257.58,-0.44979,-0.79989,0.39733,267.49,-0.88762,0.35101,-0.2982,256.19
> view matrix models
> #23.1,0.0017153,-0.12241,-0.99248,250.1,-0.35845,-0.9266,0.11367,273.93,-0.93355,0.35556,-0.045468,253.11
> fitmap sel inMap #11 search 50 radius 5
Found 46 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.1931 (1), 0.1891 (1), 0.1886 (1), 0.1882 (1), 0.1864 (1), 0.1859 (1), 0.1857
(1), 0.1856 (1), 0.1853 (1), 0.1852 (1), 0.185 (1), 0.185 (1), 0.1845 (1),
0.1843 (2), 0.1824 (1), 0.182 (2), 0.1813 (1), 0.1808 (1), 0.1808 (1), 0.1807
(1), 0.1804 (1), 0.1802 (1), 0.1799 (1), 0.1792 (1), 0.1791 (1), 0.1783 (2),
0.1782 (1), 0.1781 (1), 0.178 (1), 0.1777 (1), 0.1776 (1), 0.1769 (2), 0.1769
(1), 0.176 (1), 0.1759 (1), 0.1756 (1), 0.175 (1), 0.1747 (1), 0.1734 (1),
0.1717 (1), 0.1708 (1), 0.1704 (1), 0.1691 (1), 0.1679 (1), 0.1636 (1), 0.1354
(1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 1247 atoms
average map value = 0.1931, steps = 184
shifted from previous position = 21.5
rotated from previous position = 23.6 degrees
atoms outside contour = 592, contour level = 0.19463
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
0.91811104 0.29036818 -0.26973741 209.66450220
0.38047243 -0.83631097 0.39474634 231.98865898
-0.11096252 -0.46504861 -0.87830345 274.39089909
Axis -0.97819265 -0.18063892 0.10251202
Axis point 0.00000000 131.76202999 125.40676127
Rotation angle (degrees) 153.92920298
Shift along axis -218.87008999
Found 46 fits. List window not yet implemented.
> fitmap sel inMap #1 search 50 radius 5
Found 49 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.2147 (1), 0.2115 (1), 0.2094 (1), 0.2083 (1), 0.2071 (1), 0.2062 (1), 0.2046
(1), 0.2041 (1), 0.2036 (1), 0.2035 (1), 0.2028 (1), 0.1995 (1), 0.1992 (1),
0.1963 (1), 0.1946 (1), 0.1931 (1), 0.1919 (2), 0.191 (1), 0.1905 (1), 0.1903
(1), 0.1896 (1), 0.1858 (1), 0.1846 (1), 0.1841 (1), 0.1821 (1), 0.1807 (1),
0.1803 (1), 0.1798 (1), 0.1793 (1), 0.1783 (1), 0.1757 (1), 0.1753 (1), 0.1752
(1), 0.1746 (1), 0.1738 (1), 0.1736 (1), 0.1735 (1), 0.1725 (1), 0.1716 (1),
0.171 (1), 0.1705 (1), 0.1616 (1), 0.1611 (1), 0.1569 (1), 0.1553 (1), 0.1449
(1), 0.1435 (1), 0.1377 (1), 0.1357 (1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 1247 atoms
average map value = 0.2147, steps = 276
shifted from previous position = 5.31
rotated from previous position = 38.3 degrees
atoms outside contour = 689, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.85365122 0.36586047 -0.37070975 242.23399741
0.22527650 0.90108278 0.37054032 177.28202627
0.46960623 0.23280002 -0.85163026 241.20912401
Axis -0.15959585 -0.97365075 -0.16289073
Axis point 83.24047399 0.00000000 129.33754320
Rotation angle (degrees) 154.43540214
Shift along axis -250.56104853
Found 49 fits. List window not yet implemented.
> fitmap sel inMap #1 search 50 radius 5
Found 50 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.3073 (1), 0.2133 (1), 0.2075 (1), 0.2073 (1), 0.2069 (1), 0.2054 (1), 0.2038
(1), 0.2024 (1), 0.1997 (1), 0.1996 (1), 0.1991 (1), 0.1978 (1), 0.1935 (1),
0.1926 (1), 0.1922 (1), 0.1916 (1), 0.1913 (1), 0.1895 (1), 0.1893 (1), 0.1887
(1), 0.1882 (1), 0.1882 (1), 0.1873 (1), 0.1864 (1), 0.1864 (1), 0.1855 (1),
0.1854 (1), 0.1853 (1), 0.1847 (1), 0.1843 (1), 0.1837 (1), 0.1836 (1), 0.1835
(1), 0.1832 (1), 0.1831 (1), 0.1821 (1), 0.1806 (1), 0.18 (1), 0.1788 (1),
0.178 (1), 0.1778 (1), 0.1741 (1), 0.1735 (1), 0.1729 (1), 0.1723 (1), 0.163
(1), 0.1626 (1), 0.1454 (1), 0.1407 (1), 0.1361 (1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 1247 atoms
average map value = 0.3073, steps = 128
shifted from previous position = 2.91
rotated from previous position = 22.5 degrees
atoms outside contour = 486, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.09259268 0.01677457 -0.99556274 246.76901397
0.70784050 -0.70209002 -0.07766269 227.80513514
-0.70027735 -0.71189053 0.05313476 278.43418112
Axis -0.64495543 -0.30027996 0.70275489
Axis point 210.34356537 215.68725149 0.00000000
Rotation angle (degrees) 150.54870771
Shift along axis -31.88934906
Found 50 fits. List window not yet implemented.
> show #16 models
> hide #16 models
> show #6 models
> show #5 models
> show #3 models
> hide #!11 models
> select #23.1/A:55
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
49 atoms, 48 bonds, 7 residues, 1 model selected
> select up
612 atoms, 609 bonds, 86 residues, 1 model selected
> mmaker #13 to sel
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 6bp6, chain A (#23.1) with S1_hCOMMD2_AF-Q86X83-F1-model_v1.pdb
2.pdb, chain A (#13), sequence alignment score = 127.5
RMSD between 50 pruned atom pairs is 0.999 angstroms; (across all 76 pairs:
4.725)
> show #13 models
> hide #!23 models
> show #!23 models
> select #23.1/A:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
214 atoms, 214 bonds, 28 residues, 1 model selected
> select up
612 atoms, 609 bonds, 86 residues, 1 model selected
> select #23.1/B:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
214 atoms, 214 bonds, 28 residues, 1 model selected
> select up
635 atoms, 639 bonds, 83 residues, 1 model selected
> mmaker #15 to sel
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 6bp6, chain B (#23.1) with S1_hCOMMD4_AF-Q9H0A8-F1-model_v1.pdb
2.pdb, chain A (#15), sequence alignment score = 138.2
RMSD between 46 pruned atom pairs is 1.107 angstroms; (across all 71 pairs:
3.356)
> show #15 models
> hide #!23 models
Drag select of 1 residues
> show #!11 models
> save "D:/Work/CComplex Fits
> Umeå/Ccomplex_fits_COMMD_initial_positions_inner_ring_start.cxs" includeMaps
> true
> show #!23 models
> select #23
1247 atoms, 1248 bonds, 2 pseudobonds, 169 residues, 3 models selected
> view matrix models #23,1,0,0,-10.059,0,1,0,14.442,0,0,1,2.7844
> view matrix models
> #23,0.75777,0.59627,-0.26504,-17.889,-0.086077,0.49397,0.86521,-69.628,0.64682,-0.63282,0.42564,132.32
> view matrix models
> #23,0.75777,0.59627,-0.26504,-19.138,-0.086077,0.49397,0.86521,-56.539,0.64682,-0.63282,0.42564,117.57
> view matrix models
> #23,0.91806,0.36904,-0.14483,-36.629,0.010341,0.3429,0.93931,-64.384,0.3963,-0.86384,0.31099,253.99
> view matrix models
> #23,0.97962,0.18028,-0.088538,-23.829,0.047805,0.21886,0.97458,-54.857,0.19508,-0.95896,0.20579,347.18
> view matrix models
> #23,0.97962,0.18028,-0.088538,-14.606,0.047805,0.21886,0.97458,-47.237,0.19508,-0.95896,0.20579,351.32
> view matrix models
> #23,0.97962,0.18028,-0.088538,-11.26,0.047805,0.21886,0.97458,-46.661,0.19508,-0.95896,0.20579,349.6
> view matrix models
> #23,0.97524,0.065983,-0.21109,44.831,0.18281,0.29673,0.9373,-85.579,0.12448,-0.95268,0.27732,346.9
> fitmap sel inMap #11 search 50 radius 5
Found 40 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.2097 (1), 0.1957 (1), 0.1908 (1), 0.1886 (1), 0.1882 (3), 0.1872 (2), 0.1868
(1), 0.1868 (1), 0.1864 (2), 0.1857 (1), 0.1857 (1), 0.1854 (3), 0.1849 (1),
0.1845 (1), 0.1843 (1), 0.1831 (1), 0.183 (1), 0.1824 (1), 0.1823 (1), 0.1823
(1), 0.1814 (1), 0.1812 (1), 0.1808 (3), 0.1807 (1), 0.1792 (1), 0.1786 (1),
0.1774 (2), 0.1774 (1), 0.1772 (1), 0.1753 (1), 0.1746 (1), 0.174 (1), 0.1734
(1), 0.1717 (1), 0.1717 (2), 0.1699 (1), 0.1678 (1), 0.1645 (1), 0.1635 (1),
0.1633 (1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 1247 atoms
average map value = 0.2097, steps = 260
shifted from previous position = 35.1
rotated from previous position = 53.2 degrees
atoms outside contour = 525, contour level = 0.19463
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
-0.10061951 -0.08666392 -0.99114326 243.03178778
-0.40286572 -0.90732733 0.12023365 285.25187273
-0.90971140 0.41139564 0.05638091 240.30796251
Axis 0.66554131 -0.18613785 -0.72277760
Axis point 253.07441811 89.75432670 0.00000000
Rotation angle (degrees) 167.36491850
Shift along axis -65.03768755
Found 40 fits. List window not yet implemented.
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> show #!23 models
> select #23.1/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
214 atoms, 214 bonds, 28 residues, 1 model selected
> select up
612 atoms, 609 bonds, 86 residues, 1 model selected
> select up
1247 atoms, 1248 bonds, 169 residues, 1 model selected
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 1247 atoms
average map value = 0.1863, steps = 120
shifted from previous position = 7.54
rotated from previous position = 15.4 degrees
atoms outside contour = 661, contour level = 0.19463
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
0.14750985 -0.17932500 -0.97266812 248.52749278
-0.43275300 -0.89599794 0.09956074 283.78715288
-0.88936247 0.40623901 -0.20977197 243.14743173
Axis 0.75449342 -0.20494953 -0.62348646
Axis point 0.00000000 160.04585518 243.26268458
Rotation angle (degrees) 168.27382810
Shift along axis -22.24882032
> view matrix models
> #23.1,0.14751,-0.17933,-0.97267,248.89,-0.43275,-0.896,0.099561,283.37,-0.88936,0.40624,-0.20977,242.95
> view matrix models
> #23.1,0.12198,-0.079277,-0.98936,246.56,-0.3145,-0.94853,0.037231,283.98,-0.94139,0.30661,-0.14063,245.73
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 1247 atoms
average map value = 0.1863, steps = 76
shifted from previous position = 0.74
rotated from previous position = 8.97 degrees
atoms outside contour = 661, contour level = 0.19463
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
0.14744090 -0.17927833 -0.97268718 248.52791258
-0.43273386 -0.89600823 0.09955127 283.78826608
-0.88938321 0.40623690 -0.20968808 243.14824045
Axis 0.75446999 -0.20493410 -0.62351988
Axis point 0.00000000 160.04403266 243.27357254
Rotation angle (degrees) 168.27317350
Shift along axis -22.25880330
> fitmap sel inMap #1 search 50 radius 5
Found 50 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.2767 (1), 0.2133 (1), 0.208 (1), 0.207 (1), 0.2067 (1), 0.2067 (1), 0.205
(1), 0.2046 (1), 0.2045 (1), 0.2023 (1), 0.2023 (1), 0.1997 (1), 0.1996 (1),
0.1995 (1), 0.1969 (1), 0.1958 (1), 0.1928 (1), 0.1917 (1), 0.1871 (1), 0.1855
(1), 0.1834 (1), 0.1833 (1), 0.1828 (1), 0.1825 (1), 0.182 (1), 0.182 (1),
0.1782 (1), 0.1774 (1), 0.1756 (1), 0.1755 (1), 0.1732 (1), 0.1731 (1), 0.1711
(1), 0.1696 (1), 0.1696 (1), 0.1694 (1), 0.1692 (1), 0.1641 (1), 0.1614 (1),
0.1606 (1), 0.1601 (1), 0.1589 (1), 0.1568 (1), 0.153 (1), 0.1472 (1), 0.1458
(1), 0.1446 (1), 0.1423 (1), 0.142 (1), 0.1383 (1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 1247 atoms
average map value = 0.2767, steps = 180
shifted from previous position = 2.37
rotated from previous position = 44.1 degrees
atoms outside contour = 533, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
0.00802514 -0.02108225 -0.99974546 246.64822932
-0.47532559 -0.87968644 0.01473500 285.94239477
-0.87977332 0.47508650 -0.01708058 238.64413948
Axis 0.69987307 -0.18239382 -0.69058684
Axis point 0.00000000 149.97272867 274.58604263
Rotation angle (degrees) 160.79905998
Shift along axis -44.33617361
Found 50 fits. List window not yet implemented.
> volume #11 level 0.2181
> hide #!11 models
> select #15/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #13/A:121
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/A:120
14 atoms, 12 bonds, 2 residues, 2 models selected
> select up
33 atoms, 33 bonds, 5 residues, 2 models selected
> select up
1602 atoms, 1626 bonds, 199 residues, 2 models selected
> color sel tab02
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color name tab01 #1f77b4
Color 'tab01' is opaque, 12.16% red, 46.67% green, and 70.59% blue
> color name tab02 #aec7e8
Color 'tab02' is opaque, 68.24% red, 78.04% green, and 90.98% blue
> color name tab03 #ff7f0e
Color 'tab03' is opaque, 100% red, 49.8% green, and 5.49% blue
> color name tab04 #ffbb78
Color 'tab04' is opaque, 100% red, 73.33% green, and 47.06% blue
> color name tab05 #2ca02c
Color 'tab05' is opaque, 17.25% red, 62.75% green, and 17.25% blue
> color name tab06 #98df8a
Color 'tab06' is opaque, 59.61% red, 87.45% green, and 54.12% blue
> color name tab07 #d62728
Color 'tab07' is opaque, 83.92% red, 15.29% green, and 15.69% blue
> color name tab08 #ff9896
Color 'tab08' is opaque, 100% red, 59.61% green, and 58.82% blue
> color name tab09 #9467bd
Color 'tab09' is opaque, 58.04% red, 40.39% green, and 74.12% blue
> color name tab10 #c5b0d5
Color 'tab10' is opaque, 77.25% red, 69.02% green, and 83.53% blue
> color name tab11 #8c564b
Color 'tab11' is opaque, 54.9% red, 33.73% green, and 29.41% blue
> color name tab12 #c49c94
Color 'tab12' is opaque, 76.86% red, 61.18% green, and 58.04% blue
> color name tab13 #e377c2
Color 'tab13' is opaque, 89.02% red, 46.67% green, and 76.08% blue
> color name tab14 #f7b6d2
Color 'tab14' is opaque, 96.86% red, 71.37% green, and 82.35% blue
> color name tab15 #7f7f7f
Color 'tab15' is opaque, 49.8% red, 49.8% green, and 49.8% blue
> color name tab16 #c7c7c7
Color 'tab16' is opaque, 78.04% red, 78.04% green, and 78.04% blue
> color name tab17 #bcbd22
Color 'tab17' is opaque, 73.73% red, 74.12% green, and 13.33% blue
> color name tab18 #dbdb8d
Color 'tab18' is opaque, 85.88% red, 85.88% green, and 55.29% blue
> color name tab19 #17becf
Color 'tab19' is opaque, 9.02% red, 74.51% green, and 81.18% blue
> color name tab20 #9edae5
Color 'tab20' is opaque, 61.96% red, 85.49% green, and 89.8% blue
> color sel tab02
> select clear
> select #15/A:140
12 atoms, 12 bonds, 1 residue, 1 model selected
> show #!11 models
> hide #!11 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!11 models
> show #7 models
> hide #!11 models
> select #15/A:158
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
89 atoms, 90 bonds, 11 residues, 1 model selected
> select up
550 atoms, 558 bonds, 73 residues, 1 model selected
> mmaker #18 to sel
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 S1_hCOMMD4_AF-Q9H0A8-F1-model_v1.pdb 2.pdb, chain A (#15) with
S1_hCOMMD7_AF-F1QJA8-F1-model_v1.pdb 2.pdb, chain A (#18), sequence alignment
score = 132.4
RMSD between 58 pruned atom pairs is 0.927 angstroms; (across all 70 pairs:
2.467)
> show #18 models
> hide #15 models
> show #15 models
> view matrix models
> #15,-0.70913,-0.21871,-0.6703,428.71,0.58418,0.35009,-0.73224,148.37,0.39481,-0.91083,-0.12049,452.33
> select #18/A:173
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #7/A:127
16 atoms, 14 bonds, 2 residues, 2 models selected
> select up
304 atoms, 310 bonds, 37 residues, 2 models selected
> select up
1612 atoms, 1643 bonds, 200 residues, 2 models selected
> color sel tab04
> select clear
> save "D:/Work/CComplex Fits
> Umeå/Ccomplex_fits_COMMD_initial_positions_inner_ring_1done.cxs" includeMaps
> true
> show #!23 models
> show #!11 models
> select #23.1/B:29
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
59 atoms, 58 bonds, 8 residues, 1 model selected
> select up
635 atoms, 639 bonds, 83 residues, 1 model selected
> select up
1247 atoms, 1248 bonds, 169 residues, 1 model selected
> select down
635 atoms, 639 bonds, 83 residues, 1 model selected
> mmaker #17 to sel
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 6bp6, chain B (#23.1) with
S1_hCOMMD6_AF-Q7Z4G1-F1-model_v1.pdb.pdb, chain A (#17), sequence alignment
score = 124.5
RMSD between 42 pruned atom pairs is 0.965 angstroms; (across all 75 pairs:
4.438)
> show #17 models
> hide #17 models
> show #17 models
> select #23.1/A:87
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
214 atoms, 214 bonds, 28 residues, 1 model selected
> select up
612 atoms, 609 bonds, 86 residues, 1 model selected
> hide #15 models
> show #15 models
> mmaker #15 to sel
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 6bp6, chain A (#23.1) with S1_hCOMMD4_AF-Q9H0A8-F1-model_v1.pdb
2.pdb, chain A (#15), sequence alignment score = 144.2
RMSD between 47 pruned atom pairs is 1.035 angstroms; (across all 71 pairs:
3.477)
> hide #!23 models
> hide #!11 models
> select #5/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #15/A:161
16 atoms, 14 bonds, 2 residues, 2 models selected
> select up
176 atoms, 178 bonds, 22 residues, 2 models selected
> select up
1521 atoms, 1542 bonds, 199 residues, 2 models selected
> select up
16065 atoms, 16310 bonds, 2044 residues, 25 models selected
> select up
16065 atoms, 16310 bonds, 2044 residues, 25 models selected
> select down
1521 atoms, 1542 bonds, 199 residues, 2 models selected
> select down
176 atoms, 178 bonds, 22 residues, 2 models selected
> select up
1521 atoms, 1542 bonds, 199 residues, 2 models selected
> color sel tab06
> select clear
> select #17/A:66
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
149 atoms, 153 bonds, 17 residues, 1 model selected
> select up
675 atoms, 689 bonds, 85 residues, 1 model selected
> color sel tab08
> select #17/A:14
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!23 models
> show #!11 models
> select #23
1247 atoms, 1248 bonds, 2 pseudobonds, 169 residues, 3 models selected
> view matrix models #23,1,0,0,-2.1153,0,1,0,1.0274,0,0,1,-36.762
> view matrix models #23,1,0,0,-2.1599,0,1,0,1.5854,0,0,1,-35.736
> view matrix models
> #23,0.97599,0.075057,-0.20449,33.253,0.17471,0.29091,0.94066,-84.311,0.13009,-0.9538,0.27081,349.08
> view matrix models
> #23,0.96112,-0.21397,-0.17456,102.56,0.27521,0.69022,0.66922,-143.66,-0.022712,-0.69124,0.72227,210.41
> view matrix models
> #23,0.96112,-0.21397,-0.17456,100.75,0.27521,0.69022,0.66922,-135.68,-0.022712,-0.69124,0.72227,212.4
> view matrix models
> #23,0.86952,-0.18378,-0.45843,182.1,0.49103,0.2218,0.84243,-108.71,-0.053144,-0.95762,0.28311,391.55
> view matrix models
> #23,0.86952,-0.18378,-0.45843,184.33,0.49103,0.2218,0.84243,-113.56,-0.053144,-0.95762,0.28311,392.56
> save "D:/Work/CComplex Fits
> Umeå/Ccomplex_fits_COMMD_initial_positions_inner_ring_2done.cxs" includeMaps
> true
> fitmap sel inMap #1 search 50 radius 5
Found 49 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.306 (2), 0.2163 (1), 0.2153 (1), 0.2136 (1), 0.2121 (1), 0.2114 (1), 0.2106
(1), 0.2071 (1), 0.2059 (1), 0.2038 (1), 0.201 (1), 0.1985 (1), 0.1961 (1),
0.1959 (1), 0.1953 (1), 0.1947 (1), 0.1947 (1), 0.1944 (1), 0.1938 (1), 0.1926
(1), 0.1925 (1), 0.1887 (1), 0.1876 (1), 0.1861 (1), 0.1859 (1), 0.1852 (1),
0.1847 (1), 0.1846 (1), 0.1829 (1), 0.1813 (1), 0.1802 (1), 0.1802 (1), 0.1789
(1), 0.1781 (1), 0.1769 (1), 0.1766 (1), 0.1757 (1), 0.1733 (1), 0.1718 (1),
0.1704 (1), 0.17 (1), 0.1691 (1), 0.1658 (1), 0.1649 (1), 0.1612 (1), 0.1543
(1), 0.1522 (1), 0.1493 (1), 0.1339 (1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 1247 atoms
average map value = 0.306, steps = 236
shifted from previous position = 5.47
rotated from previous position = 42.8 degrees
atoms outside contour = 458, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.36031428 -0.44163704 -0.82166307 260.65440126
-0.32036561 -0.76866763 0.55363868 268.98292662
-0.87609332 0.46271660 0.13547660 232.58335626
Axis -0.56456754 0.33797678 0.75301739
Axis point 211.38915351 91.07320603 0.00000000
Rotation angle (degrees) 175.38133368
Shift along axis 118.89228335
Found 49 fits. List window not yet implemented.
> fitmap sel inMap #1 search 50 radius 5
Found 49 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.222 (1), 0.2172 (1), 0.213 (1), 0.2092 (1), 0.2089 (1), 0.2072 (1), 0.2063
(1), 0.2049 (1), 0.2032 (1), 0.2012 (1), 0.1985 (1), 0.1965 (2), 0.195 (1),
0.1938 (1), 0.1935 (1), 0.1922 (1), 0.1905 (1), 0.1905 (1), 0.1883 (1), 0.1877
(1), 0.1869 (1), 0.1859 (1), 0.1854 (1), 0.1843 (1), 0.1807 (1), 0.1802 (1),
0.1795 (1), 0.1792 (1), 0.1791 (1), 0.1787 (1), 0.1778 (1), 0.1759 (1), 0.174
(1), 0.1689 (1), 0.1688 (1), 0.1669 (1), 0.1665 (1), 0.1641 (1), 0.1639 (1),
0.1626 (1), 0.1611 (1), 0.1598 (1), 0.1593 (1), 0.159 (1), 0.1523 (1), 0.1497
(1), 0.1451 (1), 0.1431 (1), 0.127 (1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 1247 atoms
average map value = 0.222, steps = 140
shifted from previous position = 5.81
rotated from previous position = 21.8 degrees
atoms outside contour = 640, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.35239573 -0.39421588 -0.84877029 257.51847151
0.11051171 0.88307532 -0.45603179 238.95355274
0.92930319 -0.25450278 -0.26762647 182.38197875
Axis 0.10839109 -0.95632546 0.27146451
Axis point 62.95531520 0.00000000 222.38673141
Rotation angle (degrees) 111.62150148
Shift along axis -151.09442393
Found 49 fits. List window not yet implemented.
> show #!11 models
> view matrix models
> #17,0.15,0.49812,-0.85403,218.76,-0.43259,0.8098,0.39635,258.93,0.88903,0.30999,0.33695,229.68
> undo
> select #23
1247 atoms, 1248 bonds, 2 pseudobonds, 169 residues, 3 models selected
> view matrix models #23,1,0,0,3.18,0,1,0,3.9972,0,0,1,12.724
> view matrix models
> #23,0.32022,-0.88217,0.34529,323.71,0.52832,-0.13624,-0.83804,334.8,0.78634,0.45079,0.42244,-176.72
> view matrix models
> #23,-0.61154,-0.74574,-0.26435,613.74,0.78841,-0.60247,-0.12429,264.43,-0.066574,-0.28443,0.95638,110.03
> view matrix models
> #23,-0.61154,-0.74574,-0.26435,613.01,0.78841,-0.60247,-0.12429,266.64,-0.066574,-0.28443,0.95638,113.38
> view matrix models
> #23,-0.61154,-0.74574,-0.26435,613.67,0.78841,-0.60247,-0.12429,264.18,-0.066574,-0.28443,0.95638,117.25
> view matrix models
> #23,-0.61154,-0.74574,-0.26435,614.32,0.78841,-0.60247,-0.12429,260.72,-0.066574,-0.28443,0.95638,120.06
> view matrix models
> #23,-0.61154,-0.74574,-0.26435,611.12,0.78841,-0.60247,-0.12429,261.27,-0.066574,-0.28443,0.95638,121.33
> view matrix models
> #23,-0.62709,-0.71674,-0.30503,614.66,0.77328,-0.61995,-0.13303,270.89,-0.093756,-0.3193,0.94301,139.08
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 1247 atoms
average map value = 0.1863, steps = 88
shifted from previous position = 2.48e-13
rotated from previous position = 29.7 degrees
atoms outside contour = 786, contour level = 0.21812
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
-0.41799706 -0.70108123 -0.57772263 264.43745341
-0.32599938 0.70934654 -0.62494147 261.15156351
0.84794036 -0.07288654 -0.52505681 183.78855452
Axis 0.35069907 -0.90566838 0.23827494
Axis point 126.98530917 0.00000000 206.73904480
Rotation angle (degrees) 128.08673585
Shift along axis -99.98653675
> undo
> select #23.1/A:88
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #23.1/B:85
19 atoms, 18 bonds, 2 residues, 1 model selected
> select up
428 atoms, 428 bonds, 56 residues, 1 model selected
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 428 atoms
average map value = 0.2198, steps = 80
shifted from previous position = 2.98e-13
rotated from previous position = 14.4 degrees
atoms outside contour = 228, contour level = 0.21812
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
-0.48328130 -0.42792761 -0.76375196 262.29932395
-0.09486822 0.89285682 -0.44023472 245.50524534
0.87030983 -0.14030148 -0.47209772 182.57523189
Axis 0.17701272 -0.96438038 0.19656291
Axis point 92.60011132 0.00000000 199.39144265
Rotation angle (degrees) 122.09070253
Shift along axis -154.44260562
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 428 atoms
average map value = 0.1618, steps = 56
shifted from previous position = 3.48e-13
rotated from previous position = 16.5 degrees
atoms outside contour = 278, contour level = 0.21812
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
-0.34805111 -0.47948848 -0.80557503 259.61273734
-0.33484442 0.86620361 -0.37090492 253.93740294
0.87563670 0.14064836 -0.46203716 173.69245000
Axis 0.29011810 -0.95346851 0.08203223
Axis point 109.95360985 0.00000000 193.21413603
Rotation angle (degrees) 118.16045224
Shift along axis -152.55458560
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 428 atoms
average map value = 0.167, steps = 100
shifted from previous position = 3.83e-13
rotated from previous position = 53.9 degrees
atoms outside contour = 302, contour level = 0.21812
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
0.31319719 -0.50115818 -0.80668948 236.05920218
-0.81585578 0.29278916 -0.49865208 288.54468477
0.48609348 0.81431863 -0.31717206 167.96688383
Axis 0.70239314 -0.69159340 -0.16835214
Axis point 0.00000000 183.17399445 232.83712175
Rotation angle (degrees) 110.82978492
Shift along axis -62.02682102
> view matrix models
> #23.1,-0.3524,-0.39422,-0.84877,255.53,0.11051,0.88308,-0.45603,246.31,0.9293,-0.2545,-0.26763,177.74
> select up
1247 atoms, 1248 bonds, 169 residues, 1 model selected
> fitmap sel inMap #1 search 50 radius 1
Found 47 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.313 (1), 0.306 (2), 0.2391 (1), 0.228 (1), 0.2277 (1), 0.2235 (1), 0.219
(1), 0.2033 (1), 0.2029 (1), 0.202 (1), 0.2013 (2), 0.2007 (1), 0.2003 (1),
0.1986 (1), 0.1973 (2), 0.1955 (1), 0.1949 (1), 0.1947 (1), 0.1946 (1), 0.1945
(1), 0.1919 (1), 0.1899 (1), 0.1877 (1), 0.1853 (1), 0.177 (1), 0.1747 (1),
0.1742 (1), 0.1741 (1), 0.1672 (1), 0.1669 (1), 0.1657 (1), 0.1656 (1), 0.162
(1), 0.1614 (1), 0.1603 (1), 0.1584 (1), 0.158 (1), 0.1579 (1), 0.1571 (1),
0.1562 (1), 0.1543 (1), 0.1474 (1), 0.1472 (1), 0.143 (1), 0.1318 (1), 0.1246
(1), 0.1197 (1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 1247 atoms
average map value = 0.313, steps = 136
shifted from previous position = 4.37
rotated from previous position = 23.2 degrees
atoms outside contour = 436, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.32206739 -0.61194953 -0.72235052 258.19914301
-0.24874689 0.79089666 -0.55911310 264.51660975
0.91345365 -0.00038972 -0.40694252 178.98692451
Axis 0.31631770 -0.92610017 0.20562487
Axis point 107.73646112 0.00000000 215.65132791
Rotation angle (degrees) 117.97307863
Shift along axis -126.49175352
Found 47 fits. List window not yet implemented.
> view matrix models
> #23.1,-0.32207,-0.61195,-0.72235,253.36,-0.24875,0.7909,-0.55911,249.06,0.91345,-0.00038972,-0.40694,175.48
> view matrix models
> #23.1,-0.32207,-0.61195,-0.72235,265.44,-0.24875,0.7909,-0.55911,249.96,0.91345,-0.00038972,-0.40694,176.06
> view matrix models
> #23.1,-0.32207,-0.61195,-0.72235,263.49,-0.24875,0.7909,-0.55911,249.77,0.91345,-0.00038972,-0.40694,176.02
> view matrix models
> #23.1,-0.38095,-0.22848,-0.89592,255.54,0.33252,0.8703,-0.36333,235.45,0.86273,-0.43632,-0.25556,187.57
> view matrix models
> #23.1,-0.38095,-0.22848,-0.89592,253.75,0.33252,0.8703,-0.36333,235.22,0.86273,-0.43632,-0.25556,185.73
> view matrix models
> #23.1,-0.37322,-0.33418,-0.86546,256.32,0.22598,0.87203,-0.43417,237.87,0.8998,-0.35762,-0.24994,182.73
> fitmap sel inMap #1 search 50 radius 1
Found 49 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.306 (1), 0.2271 (1), 0.2238 (1), 0.2181 (1), 0.2166 (1), 0.2138 (1), 0.2113
(1), 0.2105 (1), 0.2061 (1), 0.2055 (1), 0.2025 (1), 0.2024 (1), 0.2009 (1),
0.2006 (1), 0.1995 (1), 0.1994 (1), 0.1984 (1), 0.198 (1), 0.1978 (1), 0.1968
(1), 0.1952 (1), 0.1936 (1), 0.1927 (1), 0.1918 (1), 0.1897 (1), 0.1861 (1),
0.1836 (1), 0.1816 (1), 0.1809 (1), 0.1806 (1), 0.1798 (1), 0.1784 (1), 0.1778
(1), 0.1698 (1), 0.1691 (1), 0.1681 (1), 0.1673 (1), 0.1665 (1), 0.1664 (1),
0.1658 (1), 0.1638 (1), 0.1616 (1), 0.1586 (1), 0.1565 (2), 0.1552 (1), 0.1521
(1), 0.1502 (1), 0.1469 (1), 0.1382 (1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 1247 atoms
average map value = 0.306, steps = 272
shifted from previous position = 4.36
rotated from previous position = 60.6 degrees
atoms outside contour = 460, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
0.37010035 0.58108473 0.72482150 195.62969215
-0.76006944 0.63801854 -0.12339713 272.80684301
-0.53415368 -0.50524534 0.67779565 227.51600187
Axis -0.20325108 0.67013034 -0.71387277
Axis point 351.59308847 51.23911907 0.00000000
Rotation angle (degrees) 69.94284989
Shift along axis -19.36328276
Found 49 fits. List window not yet implemented.
> fitmap sel inMap #1 search 50 radius 1
Found 49 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.306 (2), 0.2404 (1), 0.2208 (1), 0.2197 (1), 0.2152 (1), 0.2125 (1), 0.2118
(1), 0.2108 (1), 0.2093 (1), 0.2084 (1), 0.2059 (1), 0.2037 (1), 0.2012 (1),
0.1992 (1), 0.1966 (1), 0.1961 (1), 0.1956 (1), 0.1942 (1), 0.1936 (1), 0.1932
(1), 0.1916 (1), 0.1909 (1), 0.1887 (1), 0.1882 (1), 0.1865 (1), 0.1854 (1),
0.1853 (1), 0.1795 (1), 0.1786 (1), 0.1785 (1), 0.1783 (1), 0.1768 (1), 0.1762
(1), 0.1736 (1), 0.1725 (1), 0.1722 (1), 0.1691 (1), 0.1672 (1), 0.1651 (1),
0.1646 (1), 0.1627 (1), 0.1626 (1), 0.1577 (1), 0.1566 (1), 0.1557 (1), 0.1498
(1), 0.1437 (1), 0.1392 (1), 0.136 (1)
Best fit found:
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 1247 atoms
average map value = 0.306, steps = 116
shifted from previous position = 4.2
rotated from previous position = 20.8 degrees
atoms outside contour = 458, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
0.43592788 0.54402033 0.71694395 195.51899896
-0.63323305 0.75147746 -0.18519598 266.97820791
-0.63951761 -0.37326050 0.67208167 227.56022421
Axis -0.10413883 0.75112693 -0.65189220
Axis point 377.99069939 0.00000000 20.05792925
Rotation angle (degrees) 64.54871560
Shift along axis 31.82866451
Found 49 fits. List window not yet implemented.
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 1247 atoms
average map value = 0.1698, steps = 80
shifted from previous position = 1.27e-13
rotated from previous position = 12.3 degrees
atoms outside contour = 829, contour level = 0.21812
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
-0.45521413 -0.06675968 -0.88787569 255.18568870
0.47295589 0.82674202 -0.30464768 230.28881714
0.75438240 -0.55860601 -0.34477022 195.01510636
Axis -0.14534943 -0.93992300 0.30889851
Axis point 30.15798223 0.00000000 206.33811830
Rotation angle (degrees) 119.11874140
Shift along axis -193.30497428
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 1247 atoms
average map value = 0.1505, steps = 80
shifted from previous position = 2.86e-13
rotated from previous position = 40 degrees
atoms outside contour = 885, contour level = 0.21812
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
-0.08001457 0.30547268 -0.94883301 232.51127052
0.89653194 0.43811779 0.06544615 217.87016383
0.43569272 -0.84542246 -0.30892178 213.79619305
Axis -0.51767737 -0.78687269 0.33591892
Axis point -64.41747442 0.00000000 198.35153810
Rotation angle (degrees) 118.38600120
Shift along axis -219.98371793
> view matrix models
> #23.1,-0.051885,-0.43846,-0.89725,253.41,0.74246,0.58393,-0.32828,221.67,0.66787,-0.68321,0.29524,196.58
> view matrix models
> #23.1,-0.10816,-0.40164,-0.90939,253.37,0.60304,0.70073,-0.38121,221.16,0.79035,-0.58963,0.16642,193.74
> view matrix models
> #23.1,-0.10816,-0.40164,-0.90939,252.08,0.60304,0.70073,-0.38121,231.28,0.79035,-0.58963,0.16642,178.19
> view matrix models
> #23.1,-0.72774,-0.32187,-0.60564,255.04,0.38751,0.53563,-0.75029,244.91,0.5659,-0.7807,-0.26507,193.64
> view matrix models
> #23.1,-0.72774,-0.32187,-0.60564,262.53,0.38751,0.53563,-0.75029,248.42,0.5659,-0.7807,-0.26507,200.41
> view matrix models
> #23.1,-0.72774,-0.32187,-0.60564,258.51,0.38751,0.53563,-0.75029,250.36,0.5659,-0.7807,-0.26507,201.14
> view matrix models
> #23.1,-0.68886,-0.5287,-0.49594,262.45,0.18684,0.53153,-0.82618,254.74,0.70041,-0.66178,-0.26736,195.53
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) using 1247 atoms
average map value = 0.1952, steps = 56
shifted from previous position = 6.36e-14
rotated from previous position = 12.4 degrees
atoms outside contour = 729, contour level = 0.21812
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
gaussian (#11) coordinates:
Matrix rotation and translation
-0.62440427 -0.48280603 -0.61401756 261.06169509
0.39097457 0.48734461 -0.78079064 248.26807100
0.67620868 -0.72759430 -0.11553512 195.52266568
Axis 0.03411840 -0.82750922 0.56041451
Axis point 64.90170222 -0.00000000 258.30227538
Rotation angle (degrees) 128.77747703
Shift along axis -86.96337232
> view matrix models
> #23.1,-0.59343,-0.52211,-0.61257,261.72,0.34077,0.52651,-0.77888,247.87,0.72919,-0.67096,-0.13453,193.28
> view matrix models
> #23.1,-0.63376,-0.35712,-0.68616,258.52,0.32974,0.67769,-0.65727,241.79,0.69973,-0.64281,-0.31173,195.48
> view matrix models
> #23.1,-0.32785,-0.42006,-0.84621,257.91,0.40066,0.74935,-0.52721,236.66,0.85556,-0.51189,-0.077375,185.75
> view matrix models
> #23.1,-0.32069,-0.4398,-0.83889,258.28,0.37225,0.75588,-0.53859,237.08,0.87097,-0.485,-0.078689,184.73
> view matrix models
> #23.1,-0.32069,-0.4398,-0.83889,258.71,0.37225,0.75588,-0.53859,240.71,0.87097,-0.485,-0.078689,183.78
> view matrix models
> #23.1,-0.29026,-0.50548,-0.81255,259.8,0.27048,0.77114,-0.57635,242.4,0.91793,-0.38707,-0.087114,180.26
> view matrix models
> #23.1,-0.29026,-0.50548,-0.81255,260.93,0.27048,0.77114,-0.57635,243.19,0.91793,-0.38707,-0.087114,180.88
> view matrix models
> #23.1,-0.29026,-0.50548,-0.81255,259.19,0.27048,0.77114,-0.57635,243.86,0.91793,-0.38707,-0.087114,182.19
> show #2 models
> hide #2 models
> save "D:/Work/CComplex Fits
> Umeå/Ccomplex_fits_COMMD_initial_positions_inner_ring_2done.cxs" includeMaps
> true
——— End of log from Tue Jan 25 17:26:46 2022 ———
opened ChimeraX session
> mmaker #18 to #17
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 S1_hCOMMD6_AF-Q7Z4G1-F1-model_v1.pdb.pdb, chain A (#17) with
S1_hCOMMD7_AF-F1QJA8-F1-model_v1.pdb 2.pdb, chain A (#18), sequence alignment
score = 149.8
RMSD between 59 pruned atom pairs is 0.891 angstroms; (across all 69 pairs:
3.007)
> select clear
> select #23.1/B:87
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #23.1/A:84
15 atoms, 13 bonds, 2 residues, 1 model selected
> select up
428 atoms, 428 bonds, 56 residues, 1 model selected
> ui tool show "Fit in Map"
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 428 atoms
average map value = 0.2731, steps = 84
shifted from previous position = 3.62e-13
rotated from previous position = 24.9 degrees
atoms outside contour = 186, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.08634421 -0.70664098 -0.70228420 255.60488989
-0.06563374 0.70742010 -0.70373928 257.94054256
0.99410104 -0.01467035 -0.10746107 171.58716182
Axis 0.35519823 -0.87444523 0.33042360
Axis point 92.13173790 0.00000000 260.93099679
Rotation angle (degrees) 104.07504690
Shift along axis -78.06802383
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 428 atoms
average map value = 0.2731, steps = 84
shifted from previous position = 3.62e-13
rotated from previous position = 24.9 degrees
atoms outside contour = 186, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.08634421 -0.70664098 -0.70228420 255.60488989
-0.06563374 0.70742010 -0.70373928 257.94054256
0.99410104 -0.01467035 -0.10746107 171.58716182
Axis 0.35519823 -0.87444523 0.33042360
Axis point 92.13173790 0.00000000 260.93099679
Rotation angle (degrees) 104.07504690
Shift along axis -78.06802383
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 428 atoms
average map value = 0.2731, steps = 84
shifted from previous position = 3.62e-13
rotated from previous position = 24.9 degrees
atoms outside contour = 186, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.08634421 -0.70664098 -0.70228420 255.60488989
-0.06563374 0.70742010 -0.70373928 257.94054256
0.99410104 -0.01467035 -0.10746107 171.58716182
Axis 0.35519823 -0.87444523 0.33042360
Axis point 92.13173790 0.00000000 260.93099679
Rotation angle (degrees) 104.07504690
Shift along axis -78.06802383
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 428 atoms
average map value = 0.2396, steps = 80
shifted from previous position = 1.73e-13
rotated from previous position = 11.5 degrees
atoms outside contour = 204, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.27814552 -0.69857723 -0.65926081 260.94211860
-0.09991005 0.70366277 -0.70347471 259.13132106
0.95532876 -0.12980163 -0.26551548 177.98881788
Axis 0.31606480 -0.88955704 0.32983528
Axis point 101.98414246 0.00000000 240.91489352
Rotation angle (degrees) 114.83453271
Shift along axis -89.33048202
> ui mousemode right "translate selected models"
> view matrix models
> #23.1,-0.29026,-0.50548,-0.81255,260.94,0.27048,0.77114,-0.57635,242.6,0.91793,-0.38707,-0.087114,181.14
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 428 atoms
average map value = 0.2569, steps = 68
shifted from previous position = 2.27e-13
rotated from previous position = 15.8 degrees
atoms outside contour = 187, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.12136896 -0.57825538 -0.80677767 256.87308914
0.06778187 0.80606074 -0.58793846 248.88008051
0.99029045 -0.12604246 -0.05863546 171.57291295
Axis 0.23509382 -0.91466394 0.32881724
Axis point 66.30982592 0.00000000 258.52501161
Rotation angle (degrees) 100.77611712
Shift along axis -110.83622703
> view matrix models
> #23.1,-0.17694,-0.62509,-0.76023,258.46,0.07871,0.76096,-0.64401,250.86,0.98107,-0.17379,-0.085445,173.52
> view matrix models
> #23.1,-0.25548,-0.52654,-0.81086,257.5,0.18466,0.79667,-0.57551,247.14,0.94901,-0.29677,-0.1063,177.98
> view matrix models
> #23.1,-0.66608,-0.31651,-0.67539,255.75,0.35849,0.65821,-0.662,249.78,0.65408,-0.68307,-0.32496,197.25
> select clear
> select #11
2 models selected
> select clear
> select clear
> select clear
Drag select of 1 residues
> select up
29 atoms, 29 bonds, 4 residues, 1 model selected
> select up
612 atoms, 609 bonds, 86 residues, 1 model selected
> mmaker #17 to sel
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 6bp6, chain A (#23.1) with
S1_hCOMMD6_AF-Q7Z4G1-F1-model_v1.pdb.pdb, chain A (#17), sequence alignment
score = 125.7
RMSD between 43 pruned atom pairs is 1.006 angstroms; (across all 71 pairs:
4.078)
> select #23.1/B:85
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
214 atoms, 214 bonds, 28 residues, 1 model selected
> select up
635 atoms, 639 bonds, 83 residues, 1 model selected
> show #4 models
> hide #4 models
> show #2 models
> hide #3 models
> show #3 models
> select clear
> hide #2 models
> show #2 models
Drag select of 2 residues
> select up
38 atoms, 37 bonds, 5 residues, 1 model selected
> select up
635 atoms, 639 bonds, 83 residues, 1 model selected
> mmaker #12 to sel
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 6bp6, chain B (#23.1) with S1_hCOMMD1_AF-Q8N668-F1-model_v1.pdb
2.pdb, chain A (#12), sequence alignment score = 119.5
RMSD between 61 pruned atom pairs is 0.960 angstroms; (across all 75 pairs:
3.267)
> show #12 models
> hide #!23 models
> select #2/A:70
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #12 models
> show #12 models
Drag select of 11 cryosparc_P4_J86_006_volume_map_sharp.mrc gaussian , 1
residues
> select up
146 atoms, 147 bonds, 18 residues, 2 models selected
> select up
1491 atoms, 1518 bonds, 190 residues, 2 models selected
> color sel tab12
> select #17/A:52
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
37 atoms, 37 bonds, 5 residues, 1 model selected
> select up
675 atoms, 689 bonds, 85 residues, 1 model selected
> color sel tab14
> 6
Unknown command: 6
> color sel tab16
> select clear
> save "D:/Work/CComplex Fits
> Umeå/Ccomplex_fits_COMMD_initial_positions_inner_ring_3done.cxs" includeMaps
> true
> show #!23 models
> select #23
1247 atoms, 1248 bonds, 2 pseudobonds, 169 residues, 3 models selected
> view matrix models
> #23,-0.64546,-0.71493,-0.26883,609.56,0.76092,-0.63239,-0.14518,255.89,-0.066215,-0.29826,0.95218,108.56
> view matrix models
> #23,-0.70311,-0.52826,-0.476,610.88,-0.21429,-0.48087,0.8502,254.5,-0.67803,0.69979,0.2249,114.81
> view matrix models
> #23,-0.70311,-0.52826,-0.476,611.41,-0.21429,-0.48087,0.8502,251.46,-0.67803,0.69979,0.2249,108.96
> select #23.1/B:74
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #23.1/A:73
15 atoms, 13 bonds, 2 residues, 1 model selected
> select up
428 atoms, 428 bonds, 56 residues, 1 model selected
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 428 atoms
average map value = 0.2119, steps = 72
shifted from previous position = 3.74e-13
rotated from previous position = 30.1 degrees
atoms outside contour = 225, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.20891693 -0.35848038 -0.90986014 266.03936882
0.54652969 0.72873737 -0.41260999 238.83294420
0.81096178 -0.58346685 0.04367466 181.07105849
Axis -0.08753878 -0.88166587 0.46368336
Axis point 7.32903783 0.00000000 268.23584060
Rotation angle (degrees) 102.60641195
Shift along axis -149.89998115
> view matrix models
> #23.1,-0.77502,-0.089657,-0.62555,250.01,0.41472,0.67473,-0.61052,247.66,0.47681,-0.73259,-0.48575,203.83
> view matrix models
> #23.1,-0.77502,-0.089657,-0.62555,246.93,0.41472,0.67473,-0.61052,248.05,0.47681,-0.73259,-0.48575,202.57
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 428 atoms
average map value = 0.2394, steps = 56
shifted from previous position = 2.76e-13
rotated from previous position = 9.8 degrees
atoms outside contour = 218, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.72274279 -0.10752914 -0.68270078 249.28745703
0.52238007 0.56177762 -0.64150202 250.20702672
0.45250626 -0.82027025 -0.34984961 198.08029974
Axis -0.13641110 -0.86623246 0.48065928
Axis point 46.15675618 0.00000000 217.59853532
Rotation angle (degrees) 139.06097901
Shift along axis -155.53388978
> view matrix models
> #23.1,-0.77502,-0.089657,-0.62555,248.22,0.41472,0.67473,-0.61052,250.76,0.47681,-0.73259,-0.48575,201.91
> view matrix models
> #23.1,-0.77154,-0.18735,-0.60797,250.82,0.30145,0.7339,-0.60871,250.75,0.56023,-0.65291,-0.50975,198.58
> show #4 models
> hide #4 models
> select #23.1/B:9
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
114 atoms, 115 bonds, 13 residues, 1 model selected
> select up
635 atoms, 639 bonds, 83 residues, 1 model selected
> show #4 models
> hide #4 models
> show #4 models
> mmaker #14 to sel
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 6bp6, chain B (#23.1) with S1_hCOMMD3_AF-Q9UBI1-F1-model_v1.pdb
2.pdb, chain A (#14), sequence alignment score = 141.5
RMSD between 36 pruned atom pairs is 0.896 angstroms; (across all 74 pairs:
4.567)
> show #14 models
> show #8 models
> hide #8 models
> show #8 models
> hide #4 models
> show #4 models
> hide #14 models
> show #14 models
> select #23.1/A:84
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
214 atoms, 214 bonds, 28 residues, 1 model selected
> select up
612 atoms, 609 bonds, 86 residues, 1 model selected
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> mmaker #20 to sel
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 6bp6, chain A (#23.1) with S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb
2.pdb, chain A (#20), sequence alignment score = 381.7
RMSD between 69 pruned atom pairs is 0.546 angstroms; (across all 73 pairs:
0.873)
> show #20 models
> show #19 models
> select #19
557 atoms, 563 bonds, 70 residues, 1 model selected
> hide #19 models
> ~select #19
Nothing selected
> save "D:/Work/CComplex Fits
> Umeå/Ccomplex_fits_COMMD_initial_positions_inner_ring_4done.cxs" includeMaps
> true
> select #23
1247 atoms, 1248 bonds, 2 pseudobonds, 169 residues, 3 models selected
> view matrix models
> #23,-0.70311,-0.52826,-0.476,603.32,-0.21429,-0.48087,0.8502,218.25,-0.67803,0.69979,0.2249,134.88
> view matrix models
> #23,-0.76941,-0.26466,-0.58135,566.46,-0.63023,0.16638,0.75837,154.39,-0.10399,0.94988,-0.29481,32.839
> view matrix models
> #23,-0.76941,-0.26466,-0.58135,569.41,-0.63023,0.16638,0.75837,160.99,-0.10399,0.94988,-0.29481,37.318
> view matrix models
> #23,-0.76941,-0.26466,-0.58135,576.33,-0.63023,0.16638,0.75837,160.24,-0.10399,0.94988,-0.29481,37.839
> view matrix models
> #23,-0.73414,-0.26585,-0.6248,576.58,-0.67348,0.16794,0.71988,176.47,-0.086446,0.94927,-0.30234,35.426
> view matrix models
> #23,-0.71968,-0.51235,-0.46857,611.29,-0.67989,0.38323,0.62521,137.22,-0.14075,0.76853,-0.62414,154.25
> view matrix models
> #23,-0.4115,-0.68387,-0.60248,612.39,-0.91127,0.29696,0.28532,273.67,-0.016213,0.66643,-0.74539,175.62
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 1247 atoms
average map value = 0.2039, steps = 84
shifted from previous position = 3.09e-13
rotated from previous position = 23.9 degrees
atoms outside contour = 697, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.50411372 -0.01799874 -0.86344972 262.91897657
0.48621344 0.82037388 -0.30097015 241.43319811
0.71376876 -0.57154408 -0.40481046 196.34461226
Axis -0.16126579 -0.94004395 0.30051741
Axis point 35.75279260 0.00000000 202.93019553
Rotation angle (degrees) 122.97514361
Shift along axis -210.35268033
> select #23.1/B:84
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #23.1/A:87
15 atoms, 13 bonds, 2 residues, 1 model selected
> select up
428 atoms, 428 bonds, 56 residues, 1 model selected
Fit molecule 6bp6 (#23.1) to map cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) using 428 atoms
average map value = 0.2964, steps = 92
shifted from previous position = 3.61e-13
rotated from previous position = 36.1 degrees
atoms outside contour = 169, contour level = 0.19008
Position of 6bp6 (#23.1) relative to cryosparc_P4_J86_006_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.36164264 0.06540500 -0.93001978 271.02708451
0.43690740 0.89310958 -0.10708431 237.96835618
0.82360580 -0.44505883 -0.35156239 199.88268548
Axis -0.18528003 -0.96134999 0.20366025
Axis point 29.01190160 0.00000000 201.47417933
Rotation angle (degrees) 114.20783295
Shift along axis -238.27862651
> undo
> select #23
1247 atoms, 1248 bonds, 2 pseudobonds, 169 residues, 3 models selected
> view matrix models
> #23,-0.32469,-0.62034,-0.71397,596,-0.93572,0.10066,0.33807,322.32,-0.13785,0.77785,-0.61315,149.11
> view matrix models
> #23,-0.32469,-0.62034,-0.71397,596.12,-0.93572,0.10066,0.33807,322.18,-0.13785,0.77785,-0.61315,148.82
> select #23.1/A:41
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
86 atoms, 86 bonds, 11 residues, 1 model selected
> select up
612 atoms, 609 bonds, 86 residues, 1 model selected
> mmaker #16 to sel
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 6bp6, chain A (#23.1) with S1_hCOMMD5_AF-Q9GZQ3-F1-model_v1.pdb
2.pdb, chain A (#16), sequence alignment score = 142.8
RMSD between 34 pruned atom pairs is 0.696 angstroms; (across all 73 pairs:
6.538)
> show #16 models
> select #23.1/B:62
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
214 atoms, 214 bonds, 28 residues, 1 model selected
> select up
635 atoms, 639 bonds, 83 residues, 1 model selected
> show #9 models
> show #21 models
> hide #21 models
> show #19 models
> hide #19 models
> mmaker #21 to sel
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 6bp6, chain B (#23.1) with S1_hCOMMD10_AF-Q9Y6G5-F1-model_v1.pdb
2.pdb, chain A (#21), sequence alignment score = 124.9
RMSD between 57 pruned atom pairs is 0.858 angstroms; (across all 72 pairs:
3.885)
> show #21 models
> hide #!23 models
> show #19 models
> select #13/A:170
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
152 atoms, 153 bonds, 19 residues, 1 model selected
> select up
650 atoms, 660 bonds, 79 residues, 1 model selected
> mmaker #23 to sel
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 S1_hCOMMD2_AF-Q86X83-F1-model_v1.pdb 2.pdb, chain A (#13) with
6bp6, chain A (#23.1), sequence alignment score = 127.5
RMSD between 50 pruned atom pairs is 0.999 angstroms; (across all 76 pairs:
4.725)
> show #!23 models
> select #23.1/B:88
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
214 atoms, 214 bonds, 28 residues, 1 model selected
> select up
635 atoms, 639 bonds, 83 residues, 1 model selected
> mmaker #19 to sel
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 6bp6, chain B (#23.1) with S1_hCOMMD8_AF-Q9NX08-F1-model_v1.pdb
2.pdb, chain A (#19), sequence alignment score = 141.6
RMSD between 58 pruned atom pairs is 0.860 angstroms; (across all 70 pairs:
2.366)
> hide #!23 models
> save "D:/Work/CComplex Fits
> Umeå/Ccomplex_fits_COMMD_initial_positions_inner_ring_5done.cxs" includeMaps
> true
> hide #!11 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #19 models
> hide #20 models
> hide #21 models
Drag select of 190 residues
> color sel tab01
> hide #12 models
> hide #2 models
> show #3 models
> show #13 models
Drag select of 199 residues
> color sel tab03
> select clear
> hide #13 models
> show #14 models
> hide #3 models
> show #4 models
Drag select of 195 residues
> color sel tab05
> select clear
> hide #4 models
> show #5 models
> hide #14 models
> show #15 models
Drag select of 199 residues
> color sel tab07
> select clear
> hide #15 models
> show #16 models
> hide #5 models
> show #6 models
Drag select of 224 residues
> color sel tab09
> select clear
> hide #6 models
> hide #16 models
> show #17 models
> hide #17 models
> show #18 models
> show #7 models
Drag select of 200 residues
> color sel tab11
> hide #7 models
> show #8 models
> hide #18 models
> show #19 models
Drag select of 183 residues
> color sel tab13
> select clear
> hide #19 models
> show #20 models
> hide #8 models
> show #9 models
Drag select of 198 residues
> color sel tab15
> hide #9 models
> show #10 models
> hide #20 models
> show #21 models
Drag select of 202 residues
> color sel tab17
> color sel tab19
> show #20 models
> hide #21 models
> hide #10 models
> show #9 models
Drag select of 198 residues
> color sel tab17
> select clear
> hide #9 models
> show #8 models
> show #19 models
> hide #20 models
> show #!11 models
> show #12 models
> hide #12 models
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #7 models
> show #18 models
> select #19/A:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
75 atoms, 76 bonds, 9 residues, 1 model selected
> select up
557 atoms, 563 bonds, 70 residues, 1 model selected
> mmaker #23 to sel
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 S1_hCOMMD8_AF-Q9NX08-F1-model_v1.pdb 2.pdb, chain A (#19) with
6bp6, chain A (#23.1), sequence alignment score = 147.6
RMSD between 56 pruned atom pairs is 0.714 angstroms; (across all 70 pairs:
2.463)
> show #!23 models
> select #11
2 models selected
> select clear
> select #11
2 models selected
> select clear
> select #18/A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
75 atoms, 75 bonds, 9 residues, 1 model selected
> select up
571 atoms, 581 bonds, 70 residues, 1 model selected
> select clear
> select #18/A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
75 atoms, 75 bonds, 9 residues, 1 model selected
> select up
571 atoms, 581 bonds, 70 residues, 1 model selected
> mmaker #19 to sel
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 S1_hCOMMD7_AF-F1QJA8-F1-model_v1.pdb 2.pdb, chain A (#18) with
S1_hCOMMD8_AF-Q9NX08-F1-model_v1.pdb 2.pdb, chain A (#19), sequence alignment
score = 129
RMSD between 54 pruned atom pairs is 1.006 angstroms; (across all 70 pairs:
2.836)
Drag select of 2 residues
> select up
38 atoms, 37 bonds, 5 residues, 1 model selected
> select up
612 atoms, 609 bonds, 86 residues, 1 model selected
> mmaker #18 to sel
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 6bp6, chain A (#23.1) with S1_hCOMMD7_AF-F1QJA8-F1-model_v1.pdb
2.pdb, chain A (#18), sequence alignment score = 107.2
RMSD between 40 pruned atom pairs is 0.858 angstroms; (across all 70 pairs:
3.840)
> select clear
> hide #!23 models
> hide #19 models
> hide #!11 models
> show #19 models
> hide #7 models
> hide #8 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> show #20 models
> show #21 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> save "D:/Work/CComplex Fits
> Umeå/Ccomplex_fits_COMMD_initial_positions_inner_ring_5done.cxs" includeMaps
> true
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\segma\Desktop\movie2.mp4
Movie saved to \C:Users\\...\Desktop\movie2.mp4
> show #!11 models
> show #10 models
> select #20
608 atoms, 613 bonds, 80 residues, 1 model selected
> select #9
919 atoms, 930 bonds, 118 residues, 1 model selected
> view matrix models
> #9,-0.37904,-0.89585,-0.23192,581.49,-0.46973,-0.029676,0.88231,123.85,-0.7973,0.44337,-0.40955,381.48
> view matrix models
> #9,-0.37904,-0.89585,-0.23192,580.04,-0.46973,-0.029676,0.88231,127.31,-0.7973,0.44337,-0.40955,379.08
> view matrix models
> #9,-0.37904,-0.89585,-0.23192,580.85,-0.46973,-0.029676,0.88231,127.14,-0.7973,0.44337,-0.40955,373.75
> view matrix models
> #9,-0.37904,-0.89585,-0.23192,578.35,-0.46973,-0.029676,0.88231,122.46,-0.7973,0.44337,-0.40955,375.07
> view matrix models
> #9,-0.45627,-0.88545,-0.088343,562.09,-0.42327,0.12863,0.89683,66.57,-0.78273,0.44659,-0.43347,376.07
> view matrix models
> #9,-0.52268,-0.84792,-0.088493,568.5,-0.31296,0.094288,0.94507,37.817,-0.79301,0.52167,-0.31465,332.22
> view matrix models
> #9,-0.52268,-0.84792,-0.088493,568.19,-0.31296,0.094288,0.94507,38.897,-0.79301,0.52167,-0.31465,330.16
> view matrix models
> #9,-0.52268,-0.84792,-0.088493,566.73,-0.31296,0.094288,0.94507,36.814,-0.79301,0.52167,-0.31465,330.72
> view matrix models
> #9,-0.49543,-0.86851,-0.015511,549.03,-0.28286,0.14442,0.94823,15.695,-0.82131,0.47417,-0.31721,350.58
> view matrix models
> #9,-0.49543,-0.86851,-0.015511,547.88,-0.28286,0.14442,0.94823,17.975,-0.82131,0.47417,-0.31721,348.41
> view matrix models
> #9,-0.49543,-0.86851,-0.015511,546.67,-0.28286,0.14442,0.94823,17.24,-0.82131,0.47417,-0.31721,349.06
> view matrix models
> #9,-0.49543,-0.86851,-0.015511,545.78,-0.28286,0.14442,0.94823,17.117,-0.82131,0.47417,-0.31721,349.06
> select clear
> volume #11 level 0.1167
> select #9/A:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
106 atoms, 106 bonds, 13 residues, 1 model selected
> select up
919 atoms, 930 bonds, 118 residues, 1 model selected
Fit molecule S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 919 atoms
average map value = 0.09377, steps = 84
shifted from previous position = 1.66e-13
rotated from previous position = 33 degrees
atoms outside contour = 781, contour level = 0.19008
Position of S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.71891584 -0.66764252 -0.19342560 587.24418497
-0.02588748 -0.25236123 0.96728675 54.61969897
-0.69461488 0.70040512 0.16414291 150.85602016
Axis -0.31145260 0.58489116 0.74893231
Axis point 313.44512902 54.86789722 0.00000000
Rotation angle (degrees) 154.63098072
Shift along axis -37.97120303
> view matrix models
> #9,-0.71892,-0.66764,-0.19343,589.76,-0.025887,-0.25236,0.96729,53.287,-0.69461,0.70041,0.16414,154.06
Fit molecule S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 919 atoms
average map value = 0.1101, steps = 56
shifted from previous position = 5.68e-14
rotated from previous position = 12.8 degrees
atoms outside contour = 769, contour level = 0.19008
Position of S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.82774324 -0.49693816 -0.26056394 586.46183182
-0.14269008 -0.26268508 0.95427255 87.18398186
-0.54266071 0.82707259 0.14652766 88.05694662
Axis -0.27042399 0.59973081 0.75312271
Axis point 300.23797978 54.11127504 0.00000000
Rotation angle (degrees) 166.39740342
Shift along axis -39.98874103
> view matrix models
> #9,-0.82774,-0.49694,-0.26056,585.33,-0.14269,-0.26269,0.95427,85.886,-0.54266,0.82707,0.14653,89.044
Fit molecule S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 919 atoms
average map value = 0.1046, steps = 52
shifted from previous position = 2.84e-14
rotated from previous position = 5.63 degrees
atoms outside contour = 776, contour level = 0.19008
Position of S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.87816849 -0.41852241 -0.23164429 570.47839329
-0.13531707 -0.24712818 0.95948786 78.85222588
-0.45881302 0.87393747 0.16038696 53.35617880
Axis -0.22935698 0.60902976 0.75926156
Axis point 286.81670690 52.76781068 0.00000000
Rotation angle (degrees) 169.25137164
Shift along axis -42.30855328
Fit molecule S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 919 atoms
average map value = 0.1046, steps = 40
shifted from previous position = 3.98e-13
rotated from previous position = 0.0292 degrees
atoms outside contour = 776, contour level = 0.19008
Position of S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.87812827 -0.41862455 -0.23161217 570.48820390
-0.13504510 -0.24754019 0.95941997 78.90964917
-0.45897009 0.87377193 0.16083885 53.33592761
Axis -0.22935948 0.60884868 0.75940603
Axis point 286.80815166 52.84916814 0.00000000
Rotation angle (degrees) 169.23907557
Shift along axis -42.29921919
> view matrix models
> #9,-0.87813,-0.41862,-0.23161,569.98,-0.13505,-0.24754,0.95942,81.897,-0.45897,0.87377,0.16084,56.768
Fit molecule S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 919 atoms
average map value = 0.1052, steps = 48
shifted from previous position = 1.24e-13
rotated from previous position = 12.6 degrees
atoms outside contour = 791, contour level = 0.19008
Position of S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.85605435 -0.44331999 -0.26577871 578.78994237
-0.26166769 -0.07174709 0.96248760 65.78304956
-0.44575886 0.89348743 -0.05458310 96.85784172
Axis -0.26051447 0.67952640 0.68583969
Axis point 303.29448995 12.47113094 0.00000000
Rotation angle (degrees) 172.38993109
Shift along axis -39.65288461
> view matrix models
> #9,-0.85605,-0.44332,-0.26578,579.22,-0.26167,-0.071747,0.96249,62.254,-0.44576,0.89349,-0.054583,93.694
> view matrix models
> #9,-0.85605,-0.44332,-0.26578,581.38,-0.26167,-0.071747,0.96249,61.339,-0.44576,0.89349,-0.054583,94.224
Fit molecule S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 919 atoms
average map value = 0.1099, steps = 48
shifted from previous position = 4.02e-14
rotated from previous position = 4.42 degrees
atoms outside contour = 784, contour level = 0.19008
Position of S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.81437871 -0.49007716 -0.31082420 593.67706652
-0.30433550 -0.09538826 0.94777686 81.16740211
-0.49413279 0.86644418 -0.07146570 116.81358890
Axis -0.29754687 0.67061471 0.67951583
Axis point 316.86184532 12.29056096 0.00000000
Rotation angle (degrees) 172.14468175
Shift along axis -42.83801796
Fit molecule S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 919 atoms
average map value = 0.1099, steps = 28
shifted from previous position = 1.17e-13
rotated from previous position = 0.0463 degrees
atoms outside contour = 785, contour level = 0.19008
Position of S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.81473095 -0.48956362 -0.31071036 593.60213081
-0.30444810 -0.09487154 0.94779257 81.05571698
-0.49348235 0.86679115 -0.07175192 116.62964711
Axis -0.29729626 0.67082076 0.67942214
Axis point 316.78787638 12.20452366 0.00000000
Rotation angle (degrees) 172.17024208
Shift along axis -42.86107339
> view matrix models
> #9,-0.9181,-0.35364,-0.17897,553.62,-0.05189,-0.34041,0.93884,85.672,-0.39294,0.87124,0.29418,8.5636
Fit molecule S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 919 atoms
average map value = 0.1094, steps = 84
shifted from previous position = 3.66e-13
rotated from previous position = 10.6 degrees
atoms outside contour = 791, contour level = 0.19008
Position of S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.85639692 -0.38589405 -0.34303071 584.03799057
-0.20672372 -0.35253202 0.91268093 132.20002825
-0.47312747 0.85252977 0.22213388 49.07668374
Axis -0.26215857 0.56700450 0.78088333
Axis point 294.55321816 69.41970659 0.00000000
Rotation angle (degrees) 173.41235980
Shift along axis -39.82939024
> view matrix models
> #9,-0.8564,-0.38589,-0.34303,582.56,-0.20672,-0.35253,0.91268,135.3,-0.47313,0.85253,0.22213,49.72
> view matrix models
> #9,-0.90764,-0.33097,-0.25816,561.59,-0.075006,-0.47726,0.87556,144.15,-0.41299,0.81405,0.40835,3.1739
Fit molecule S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) to map
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) using 919 atoms
average map value = 0.1153, steps = 64
shifted from previous position = 1.66e-13
rotated from previous position = 20.8 degrees
atoms outside contour = 770, contour level = 0.19008
Position of S1_hCOMMD9_AF-Q9P000-F1-model_v1.pdb 1.pdb (#9) relative to
cryosparc_P4_J86_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98999584 -0.14001432 0.01744130 469.48899805
0.08992796 -0.53088281 0.84266032 125.68811362
-0.10872525 0.83579871 0.53816298 -105.34888270
Axis -0.02615233 0.48087081 0.87640134
Axis point 227.65057303 109.34776791 0.00000000
Rotation angle (degrees) 172.46189711
Shift along axis -44.16639030
> select clear
> save "D:/Work/CComplex Fits
> Umeå/Ccomplex_fits_COMMD_rigid_body_fitted_ring.cxs"
——— End of log from Wed Jan 26 19:10:28 2022 ———
opened ChimeraX session
> combine #2,12 name COMMD1
Unknown command: combine #2,12 name COMMD1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD_proteins.pdb relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD1.pdb models #2,12
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD_[NUMBER]_Nt.pdb models
> #2-6 relModel #1
No model chosen to save relative to
> save /data/data_epk/Commander_fits/Rigid_body/[NUMBER].pdb models #2-6
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD1_Nt.pdb models #2
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD2_Nt.pdb models #3
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD3_Nt.pdb models #4
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD4_Nt.pdb models #5
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD5_Nt.pdb models #6
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD7_Nt.pdb models #7
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD8_Nt.pdb models #8
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD9_Nt.pdb models #9
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD10_Nt.pdb models #10
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD1_Ct.pdb models #12
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD2_Ct.pdb models #13
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD3_Ct.pdb models #14
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD4_Ct.pdb models #15
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD5_Ct.pdb models #16
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD6_Ct.pdb models #17
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD7_Ct.pdb models #18
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD8_Ct.pdb models #19
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD9_Ct.pdb models #20
> relModel #1
> save /data/data_epk/Commander_fits/Rigid_body/COMMD10_Ct.pdb models #21
> relModel #1
> open /data/data_epk/Commander_fits/Rigid_body/COMMD1.pdb
Summary of feedback from opening
/data/data_epk/Commander_fits/Rigid_body/COMMD1.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
599 messages similar to the above omitted
Ignored bad PDB record found on line 1504
Chain information for COMMD1.pdb #24
---
Chain | Description
A | No description available
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #18 models
> hide #17 models
> hide #19 models
> hide #20 models
> hide #21 models
> hide #24 models
> show #24 models
> close #24
> open /data/data_epk/Commander_fits/Rigid_body/COMMD1.pdb
Summary of feedback from opening
/data/data_epk/Commander_fits/Rigid_body/COMMD1.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
599 messages similar to the above omitted
Ignored bad PDB record found on line 1504
Chain information for COMMD1.pdb #24
---
Chain | Description
A | No description available
> open /data/data_epk/Commander_fits/Rigid_body/COMMD2.pdb
Summary of feedback from opening
/data/data_epk/Commander_fits/Rigid_body/COMMD2.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
645 messages similar to the above omitted
Chain information for COMMD2.pdb #25
---
Chain | Description
A | No description available
> open /data/data_epk/Commander_fits/Rigid_body/COMMD3.pdb
Summary of feedback from opening
/data/data_epk/Commander_fits/Rigid_body/COMMD3.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
614 messages similar to the above omitted
Chain information for COMMD3.pdb #26
---
Chain | Description
A | No description available
> open /data/data_epk/Commander_fits/Rigid_body/COMMD4.pdb
Summary of feedback from opening
/data/data_epk/Commander_fits/Rigid_body/COMMD4.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
545 messages similar to the above omitted
Chain information for COMMD4.pdb #27
---
Chain | Description
A | No description available
> open /data/data_epk/Commander_fits/Rigid_body/COMMD5.pdb
Summary of feedback from opening
/data/data_epk/Commander_fits/Rigid_body/COMMD5.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
610 messages similar to the above omitted
Chain information for COMMD5.pdb #28
---
Chain | Description
A | No description available
> open /data/data_epk/Commander_fits/Rigid_body/COMMD6.pdb
Chain information for COMMD6.pdb #29
---
Chain | Description
A | No description available
> open /data/data_epk/Commander_fits/Rigid_body/COMMD7.pdb
Summary of feedback from opening
/data/data_epk/Commander_fits/Rigid_body/COMMD7.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
566 messages similar to the above omitted
Chain information for COMMD7.pdb #30
---
Chain | Description
A | No description available
> open /data/data_epk/Commander_fits/Rigid_body/COMMD8.pdb
Summary of feedback from opening
/data/data_epk/Commander_fits/Rigid_body/COMMD8.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
552 messages similar to the above omitted
Chain information for COMMD8.pdb #31
---
Chain | Description
A | No description available
> open /data/data_epk/Commander_fits/Rigid_body/COMMD9.pdb
Summary of feedback from opening
/data/data_epk/Commander_fits/Rigid_body/COMMD9.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
603 messages similar to the above omitted
Chain information for COMMD9.pdb #32
---
Chain | Description
A | No description available
> open /data/data_epk/Commander_fits/Rigid_body/COMMD10.pdb
Summary of feedback from opening
/data/data_epk/Commander_fits/Rigid_body/COMMD10.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
581 messages similar to the above omitted
Chain information for COMMD10.pdb #33
---
Chain | Description
A | No description available
> close #12-21
> close #2-10
> close #22-23
> save
> /data/data_epk/Commander_fits/Rigid_body/Ccomplex_fits_COMMD_rigid_body_fitted_ring_combined_COMMD_MODELS.cxs
> includeMaps true
——— End of log from Thu Jan 27 15:53:10 2022 ———
opened ChimeraX session
> close #24-33
> open /data/data_epk/Commander_fits/Rigid_body/COMMD_chainID_corrected.pdb
Chain information for COMMD_chainID_corrected.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
> select #2
14818 atoms, 15071 bonds, 1875 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> save
> /data/data_epk/Commander_fits/flexible_fitting/Starting_point_for_ISOLDE.cxs
> save
> /data/data_epk/Commander_fits/flexible_fitting/Starting_point_for_ISOLDE.cxs
> includeMaps true
——— End of log from Fri Jan 28 14:24:25 2022 ———
opened ChimeraX session
> ui tool show ISOLDE
> set selectionWidth 4
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 292 residues in model #2 to IUPAC-IUB
standards.
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.
Done loading forcefield
> hide atoms
> isolde tutorial
> alphafold match #2
Fetching compressed AlphaFold Q9P000 from
https://alphafold.ebi.ac.uk/files/AF-Q9P000-F1-model_v1.cif
Fetching compressed AlphaFold Q9Y6G5 from
https://alphafold.ebi.ac.uk/files/AF-Q9Y6G5-F1-model_v1.cif
Fetching compressed AlphaFold Q9UBI1 from
https://alphafold.ebi.ac.uk/files/AF-Q9UBI1-F1-model_v1.cif
Fetching compressed AlphaFold Q9GZQ3 from
https://alphafold.ebi.ac.uk/files/AF-Q9GZQ3-F1-model_v1.cif
Fetching compressed AlphaFold Q86X83 from
https://alphafold.ebi.ac.uk/files/AF-Q86X83-F1-model_v1.cif
Fetching compressed AlphaFold Q8N668 from
https://alphafold.ebi.ac.uk/files/AF-Q8N668-F1-model_v1.cif
Fetching compressed AlphaFold F1QJA8 from
https://alphafold.ebi.ac.uk/files/AF-F1QJA8-F1-model_v1.cif
Fetching compressed AlphaFold Q9H0A8 from
https://alphafold.ebi.ac.uk/files/AF-Q9H0A8-F1-model_v1.cif
Fetching compressed AlphaFold Q7Z4G1 from
https://alphafold.ebi.ac.uk/files/AF-Q7Z4G1-F1-model_v1.cif
Fetching compressed AlphaFold Q9NX08 from
https://alphafold.ebi.ac.uk/files/AF-Q9NX08-F1-model_v1.cif
10 AlphaFold models found using sequence similarity searches: Q9P000 (chain
A), Q9Y6G5 (chain B), Q9UBI1 (chain C), Q9GZQ3 (chain D), Q86X83 (chain E),
Q8N668 (chain F), F1QJA8 (chain G), Q9H0A8 (chain H), Q7Z4G1 (chain I), Q9NX08
(chain J)
AlphaFold chains matching COMMD_chainID_corrected.pdb
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
F | COMD1_HUMAN | Q8N668 | 21.26 | 190 | 190 | 100
E | COMD2_HUMAN | Q86X83 | 16.41 | 199 | 199 | 100
C | COMD3_HUMAN | Q9UBI1 | 3.48 | 195 | 195 | 100
H | COMD4_HUMAN | Q9H0A8 | 9.10 | 199 | 199 | 100
D | COMD5_HUMAN | Q9GZQ3 | 9.75 | 224 | 224 | 100
I | COMD6_HUMAN | Q7Z4G1 | 0.00 | 85 | 85 | 100
J | COMD8_HUMAN | Q9NX08 | 12.37 | 183 | 183 | 100
A | COMD9_HUMAN | Q9P000 | 6.42 | 198 | 198 | 100
B | COMDA_HUMAN | Q9Y6G5 | 12.01 | 202 | 202 | 100
G | F1QJA8_DANRE | F1QJA8 | 14.18 | 200 | 200 | 100
Opened 10 AlphaFold models
> combine #3
> isolde select #4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 292 residues in model #4 to IUPAC-IUB
standards.
> hide #3 models
> hide #!2 models
Opened cryosparc_P4_J86_006_volume_map_sharp.mrc as #4.1.1.1, grid size
568,568,568, pixel 0.82, shown at step 1, values float32
> hide #!11 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> select #3.1
1527 atoms, 1544 bonds, 198 residues, 1 model selected
> ui tool show "Selection Inspector"
> isolde restrain torsions #2/A templateResidues #3/A adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 26 residues in
model #3.1 to IUPAC-IUB standards.
> isolde restrain torsions #2/B templateResidues #3/B adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 34 residues in
model #3.2 to IUPAC-IUB standards.
> isolde restrain torsions #2/C templateResidues #3/C adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 32 residues in
model #3.3 to IUPAC-IUB standards.
> isolde restrain torsions #2/D templateResidues #3/D adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 34 residues in
model #3.4 to IUPAC-IUB standards.
> isolde restrain torsions #2/E templateResidues #3/E adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 36 residues in
model #3.5 to IUPAC-IUB standards.
> isolde restrain torsions #2/F templateResidues #3/F adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 31 residues in
model #3.6 to IUPAC-IUB standards.
> isolde restrain torsions #2/G templateResidues #3/G adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 30 residues in
model #3.7 to IUPAC-IUB standards.
> isolde restrain torsions #2/H templateResidues #3/H adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 27 residues in
model #3.8 to IUPAC-IUB standards.
> isolde restrain torsions #2/I templateResidues #3/I adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 12 residues in
model #3.9 to IUPAC-IUB standards.
> isolde restrain torsions #2/J templateResidues #3/J adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 30 residues in
model #3.10 to IUPAC-IUB standards.
> isolde restrain distances #2/A templateAtoms #3/A adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]Fetching compressed Alphafold Q9P000 PAE from
https://alphafold.ebi.ac.uk/files/AF-Q9P000-F1-predicted_aligned_error_v1.json
RMSD between 133 pruned atom pairs is 1.606 angstroms; (across all 198 pairs:
5.259)
RMSD between 18 pruned atom pairs is 2.523 angstroms; (across all 65 pairs:
27.588)
RMSD between 10 pruned atom pairs is 2.404 angstroms; (across all 47 pairs:
23.195)
RMSD between 7 pruned atom pairs is 2.229 angstroms; (across all 37 pairs:
26.217)
RMSD between 7 pruned atom pairs is 2.621 angstroms; (across all 30 pairs:
25.204)
RMSD between 8 pruned atom pairs is 3.070 angstroms; (across all 23 pairs:
27.763)
RMSD between 4 pruned atom pairs is 3.507 angstroms; (across all 15 pairs:
28.444)
RMSD between 4 pruned atom pairs is 2.667 angstroms; (across all 11 pairs:
30.874)
No further alignments of 3 or more residues found.
> isolde restrain distances #2/B templateAtoms #3/B adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]Fetching compressed Alphafold Q9Y6G5 PAE from
https://alphafold.ebi.ac.uk/files/AF-Q9Y6G5-F1-predicted_aligned_error_v1.json
RMSD between 106 pruned atom pairs is 0.001 angstroms; (across all 202 pairs:
12.010)
RMSD between 10 pruned atom pairs is 3.199 angstroms; (across all 96 pairs:
32.696)
RMSD between 8 pruned atom pairs is 2.954 angstroms; (across all 86 pairs:
35.266)
RMSD between 8 pruned atom pairs is 3.414 angstroms; (across all 78 pairs:
29.609)
RMSD between 5 pruned atom pairs is 3.451 angstroms; (across all 70 pairs:
33.857)
RMSD between 10 pruned atom pairs is 3.631 angstroms; (across all 65 pairs:
33.368)
RMSD between 6 pruned atom pairs is 3.539 angstroms; (across all 55 pairs:
31.620)
RMSD between 5 pruned atom pairs is 2.704 angstroms; (across all 49 pairs:
44.650)
RMSD between 5 pruned atom pairs is 1.872 angstroms; (across all 44 pairs:
34.841)
RMSD between 7 pruned atom pairs is 3.036 angstroms; (across all 39 pairs:
34.423)
RMSD between 4 pruned atom pairs is 3.992 angstroms; (across all 32 pairs:
32.659)
RMSD between 5 pruned atom pairs is 3.409 angstroms; (across all 28 pairs:
32.791)
RMSD between 6 pruned atom pairs is 2.969 angstroms; (across all 23 pairs:
42.316)
RMSD between 4 pruned atom pairs is 3.857 angstroms; (across all 17 pairs:
36.749)
RMSD between 5 pruned atom pairs is 2.192 angstroms; (across all 13 pairs:
34.618)
No further alignments of 3 or more residues found.
> isolde restrain distances #2/C templateAtoms #3/C adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]Fetching compressed Alphafold Q9UBI1 PAE from
https://alphafold.ebi.ac.uk/files/AF-Q9UBI1-F1-predicted_aligned_error_v1.json
RMSD between 186 pruned atom pairs is 2.736 angstroms; (across all 195 pairs:
2.992)
RMSD between 9 pruned atom pairs is 0.001 angstroms; (across all 9 pairs:
0.001)
> isolde restrain distances #2/D templateAtoms #3/D adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]Fetching compressed Alphafold Q9GZQ3 PAE from
https://alphafold.ebi.ac.uk/files/AF-Q9GZQ3-F1-predicted_aligned_error_v1.json
RMSD between 89 pruned atom pairs is 3.005 angstroms; (across all 224 pairs:
8.313)
RMSD between 8 pruned atom pairs is 3.276 angstroms; (across all 135 pairs:
33.538)
RMSD between 8 pruned atom pairs is 3.713 angstroms; (across all 127 pairs:
34.533)
RMSD between 8 pruned atom pairs is 3.504 angstroms; (across all 119 pairs:
39.664)
RMSD between 7 pruned atom pairs is 3.706 angstroms; (across all 111 pairs:
38.313)
RMSD between 8 pruned atom pairs is 3.731 angstroms; (across all 104 pairs:
37.867)
RMSD between 6 pruned atom pairs is 3.772 angstroms; (across all 96 pairs:
37.400)
RMSD between 7 pruned atom pairs is 3.232 angstroms; (across all 90 pairs:
38.997)
RMSD between 6 pruned atom pairs is 3.711 angstroms; (across all 83 pairs:
43.917)
RMSD between 4 pruned atom pairs is 3.149 angstroms; (across all 77 pairs:
38.302)
RMSD between 7 pruned atom pairs is 3.213 angstroms; (across all 73 pairs:
45.968)
RMSD between 4 pruned atom pairs is 3.117 angstroms; (across all 66 pairs:
42.689)
RMSD between 5 pruned atom pairs is 3.824 angstroms; (across all 62 pairs:
43.809)
RMSD between 4 pruned atom pairs is 2.967 angstroms; (across all 57 pairs:
39.475)
RMSD between 5 pruned atom pairs is 3.317 angstroms; (across all 53 pairs:
38.714)
RMSD between 4 pruned atom pairs is 3.249 angstroms; (across all 48 pairs:
52.275)
RMSD between 4 pruned atom pairs is 2.856 angstroms; (across all 44 pairs:
45.750)
RMSD between 4 pruned atom pairs is 3.792 angstroms; (across all 40 pairs:
41.551)
RMSD between 3 pruned atom pairs is 3.530 angstroms; (across all 36 pairs:
41.313)
RMSD between 4 pruned atom pairs is 2.389 angstroms; (across all 33 pairs:
42.402)
RMSD between 4 pruned atom pairs is 2.268 angstroms; (across all 29 pairs:
43.122)
RMSD between 3 pruned atom pairs is 2.503 angstroms; (across all 25 pairs:
48.333)
RMSD between 3 pruned atom pairs is 1.648 angstroms; (across all 22 pairs:
44.007)
RMSD between 4 pruned atom pairs is 1.088 angstroms; (across all 19 pairs:
61.942)
RMSD between 3 pruned atom pairs is 3.906 angstroms; (across all 15 pairs:
39.542)
No further alignments of 3 or more residues found.
> isolde restrain distances #2/E templateAtoms #3/E adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]Fetching compressed Alphafold Q86X83 PAE from
https://alphafold.ebi.ac.uk/files/AF-Q86X83-F1-predicted_aligned_error_v1.json
RMSD between 102 pruned atom pairs is 0.001 angstroms; (across all 199 pairs:
16.407)
RMSD between 12 pruned atom pairs is 3.391 angstroms; (across all 97 pairs:
23.107)
RMSD between 10 pruned atom pairs is 3.297 angstroms; (across all 85 pairs:
27.278)
RMSD between 8 pruned atom pairs is 2.935 angstroms; (across all 75 pairs:
24.315)
RMSD between 7 pruned atom pairs is 3.397 angstroms; (across all 67 pairs:
33.067)
RMSD between 8 pruned atom pairs is 2.564 angstroms; (across all 60 pairs:
38.187)
RMSD between 6 pruned atom pairs is 3.206 angstroms; (across all 52 pairs:
28.019)
RMSD between 5 pruned atom pairs is 2.775 angstroms; (across all 46 pairs:
32.466)
RMSD between 7 pruned atom pairs is 3.908 angstroms; (across all 41 pairs:
36.314)
RMSD between 4 pruned atom pairs is 2.084 angstroms; (across all 34 pairs:
33.069)
RMSD between 3 pruned atom pairs is 2.145 angstroms; (across all 30 pairs:
32.680)
RMSD between 4 pruned atom pairs is 1.361 angstroms; (across all 27 pairs:
30.597)
RMSD between 6 pruned atom pairs is 3.505 angstroms; (across all 23 pairs:
37.438)
RMSD between 4 pruned atom pairs is 3.845 angstroms; (across all 17 pairs:
32.128)
RMSD between 3 pruned atom pairs is 3.099 angstroms; (across all 13 pairs:
43.892)
RMSD between 3 pruned atom pairs is 1.738 angstroms; (across all 10 pairs:
46.828)
RMSD between 3 pruned atom pairs is 2.751 angstroms; (across all 7 pairs:
41.834)
No further alignments of 3 or more residues found.
> isolde restrain distances #2/F templateAtoms #3/F adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]Fetching compressed Alphafold Q8N668 PAE from
https://alphafold.ebi.ac.uk/files/AF-Q8N668-F1-predicted_aligned_error_v1.json
RMSD between 100 pruned atom pairs is 0.001 angstroms; (across all 190 pairs:
21.265)
RMSD between 13 pruned atom pairs is 2.256 angstroms; (across all 90 pairs:
28.699)
RMSD between 9 pruned atom pairs is 3.312 angstroms; (across all 77 pairs:
24.917)
RMSD between 6 pruned atom pairs is 1.906 angstroms; (across all 68 pairs:
34.599)
RMSD between 8 pruned atom pairs is 3.063 angstroms; (across all 62 pairs:
31.308)
RMSD between 7 pruned atom pairs is 2.714 angstroms; (across all 54 pairs:
33.952)
RMSD between 10 pruned atom pairs is 2.800 angstroms; (across all 47 pairs:
37.114)
RMSD between 9 pruned atom pairs is 2.703 angstroms; (across all 37 pairs:
31.556)
RMSD between 6 pruned atom pairs is 3.973 angstroms; (across all 28 pairs:
36.248)
RMSD between 6 pruned atom pairs is 2.734 angstroms; (across all 22 pairs:
47.378)
RMSD between 4 pruned atom pairs is 2.789 angstroms; (across all 16 pairs:
40.125)
RMSD between 4 pruned atom pairs is 3.666 angstroms; (across all 12 pairs:
24.693)
No further alignments of 3 or more residues found.
> isolde restrain distances #2/G templateAtoms #3/G adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]Fetching compressed Alphafold F1QJA8 PAE from
https://alphafold.ebi.ac.uk/files/AF-F1QJA8-F1-predicted_aligned_error_v1.json
RMSD between 130 pruned atom pairs is 0.001 angstroms; (across all 200 pairs:
14.184)
RMSD between 9 pruned atom pairs is 3.130 angstroms; (across all 70 pairs:
29.026)
RMSD between 10 pruned atom pairs is 3.539 angstroms; (across all 61 pairs:
23.408)
RMSD between 6 pruned atom pairs is 3.330 angstroms; (across all 51 pairs:
22.114)
RMSD between 11 pruned atom pairs is 3.711 angstroms; (across all 45 pairs:
27.809)
RMSD between 8 pruned atom pairs is 3.073 angstroms; (across all 34 pairs:
25.811)
RMSD between 4 pruned atom pairs is 2.705 angstroms; (across all 26 pairs:
23.132)
RMSD between 4 pruned atom pairs is 3.123 angstroms; (across all 22 pairs:
20.882)
RMSD between 3 pruned atom pairs is 3.379 angstroms; (across all 18 pairs:
20.455)
RMSD between 4 pruned atom pairs is 3.680 angstroms; (across all 15 pairs:
22.081)
RMSD between 3 pruned atom pairs is 3.114 angstroms; (across all 11 pairs:
23.206)
No further alignments of 3 or more residues found.
> isolde restrain distances #2/H templateAtoms #3/H adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]Fetching compressed Alphafold Q9H0A8 PAE from
https://alphafold.ebi.ac.uk/files/AF-Q9H0A8-F1-predicted_aligned_error_v1.json
RMSD between 142 pruned atom pairs is 1.416 angstroms; (across all 199 pairs:
7.038)
RMSD between 5 pruned atom pairs is 3.569 angstroms; (across all 57 pairs:
22.515)
RMSD between 5 pruned atom pairs is 3.010 angstroms; (across all 52 pairs:
24.324)
RMSD between 6 pruned atom pairs is 3.459 angstroms; (across all 47 pairs:
29.104)
RMSD between 5 pruned atom pairs is 3.252 angstroms; (across all 41 pairs:
22.785)
RMSD between 9 pruned atom pairs is 3.224 angstroms; (across all 36 pairs:
32.851)
RMSD between 5 pruned atom pairs is 3.899 angstroms; (across all 27 pairs:
23.251)
RMSD between 3 pruned atom pairs is 0.712 angstroms; (across all 22 pairs:
28.004)
RMSD between 6 pruned atom pairs is 2.824 angstroms; (across all 19 pairs:
22.701)
RMSD between 4 pruned atom pairs is 2.322 angstroms; (across all 13 pairs:
20.955)
RMSD between 3 pruned atom pairs is 3.525 angstroms; (across all 9 pairs:
25.790)
No further alignments of 3 or more residues found.
> isolde restrain distances #2/I templateAtoms #3/I adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]Fetching compressed Alphafold Q7Z4G1 PAE from
https://alphafold.ebi.ac.uk/files/AF-Q7Z4G1-F1-predicted_aligned_error_v1.json
RMSD between 85 pruned atom pairs is 0.001 angstroms; (across all 85 pairs:
0.001)
> isolde restrain distances #2/J templateAtoms #3/J adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]Fetching compressed Alphafold Q9NX08 PAE from
https://alphafold.ebi.ac.uk/files/AF-Q9NX08-F1-predicted_aligned_error_v1.json
RMSD between 92 pruned atom pairs is 0.450 angstroms; (across all 183 pairs:
12.063)
RMSD between 19 pruned atom pairs is 0.982 angstroms; (across all 91 pairs:
27.800)
RMSD between 9 pruned atom pairs is 2.910 angstroms; (across all 72 pairs:
33.673)
RMSD between 6 pruned atom pairs is 3.396 angstroms; (across all 63 pairs:
30.506)
RMSD between 5 pruned atom pairs is 2.421 angstroms; (across all 57 pairs:
34.730)
RMSD between 9 pruned atom pairs is 3.965 angstroms; (across all 52 pairs:
41.446)
RMSD between 5 pruned atom pairs is 2.794 angstroms; (across all 43 pairs:
37.269)
RMSD between 5 pruned atom pairs is 3.822 angstroms; (across all 38 pairs:
34.487)
RMSD between 5 pruned atom pairs is 2.524 angstroms; (across all 33 pairs:
53.929)
RMSD between 4 pruned atom pairs is 2.606 angstroms; (across all 28 pairs:
36.257)
RMSD between 3 pruned atom pairs is 2.718 angstroms; (across all 24 pairs:
45.702)
RMSD between 4 pruned atom pairs is 2.053 angstroms; (across all 21 pairs:
38.181)
RMSD between 3 pruned atom pairs is 3.411 angstroms; (across all 17 pairs:
36.994)
RMSD between 4 pruned atom pairs is 2.573 angstroms; (across all 14 pairs:
41.462)
RMSD between 3 pruned atom pairs is 2.402 angstroms; (across all 10 pairs:
55.526)
No further alignments of 3 or more residues found.
> addh #2
Summary of feedback from adding hydrogens to COMMD_chainID_corrected.pdb #2.2
---
notes | No usable SEQRES records for COMMD_chainID_corrected.pdb (#2.2) chain
A; guessing termini instead
No usable SEQRES records for COMMD_chainID_corrected.pdb (#2.2) chain B;
guessing termini instead
No usable SEQRES records for COMMD_chainID_corrected.pdb (#2.2) chain C;
guessing termini instead
No usable SEQRES records for COMMD_chainID_corrected.pdb (#2.2) chain D;
guessing termini instead
No usable SEQRES records for COMMD_chainID_corrected.pdb (#2.2) chain E;
guessing termini instead
5 messages similar to the above omitted
Chain-initial residues that are actual N termini: COMMD_chainID_corrected.pdb
#2.2/A MET 1, COMMD_chainID_corrected.pdb #2.2/B MET 1,
COMMD_chainID_corrected.pdb #2.2/C MET 1, COMMD_chainID_corrected.pdb #2.2/D
MET 1, COMMD_chainID_corrected.pdb #2.2/E MET 1, COMMD_chainID_corrected.pdb
#2.2/F MET 1, COMMD_chainID_corrected.pdb #2.2/G MET 1,
COMMD_chainID_corrected.pdb #2.2/H MET 1, COMMD_chainID_corrected.pdb #2.2/I
MET 1, COMMD_chainID_corrected.pdb #2.2/J MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: COMMD_chainID_corrected.pdb
#2.2/A LYS 198, COMMD_chainID_corrected.pdb #2.2/B THR 202,
COMMD_chainID_corrected.pdb #2.2/C LEU 195, COMMD_chainID_corrected.pdb #2.2/D
ASP 224, COMMD_chainID_corrected.pdb #2.2/E LYS 199,
COMMD_chainID_corrected.pdb #2.2/F ASN 190, COMMD_chainID_corrected.pdb #2.2/G
SER 200, COMMD_chainID_corrected.pdb #2.2/H GLY 199,
COMMD_chainID_corrected.pdb #2.2/I VAL 85, COMMD_chainID_corrected.pdb #2.2/J
LYS 183
Chain-final residues that are not actual C termini:
1745 hydrogen bonds
15026 hydrogens added
> select #2
29844 atoms, 30097 bonds, 1875 residues, 10 models selected
ISOLDE: stopped sim
Traceback (most recent call last):
File "/home/epkumpu/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "/home/epkumpu/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2784, in start_sim
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,
File "/home/epkumpu/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 576, in __init__
mobile_atoms = self.expand_mobile_selection(selected_atoms, expansion_mode)
File "/home/epkumpu/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 971, in
expand_mobile_selection
sel = selections.expand_selection_along_chains(core_atoms,
File "/home/epkumpu/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/selections.py", line 39, in
expand_selection_along_chains
raise TypeError('Selected atoms must all be in the same model!')
TypeError: Selected atoms must all be in the same model!
TypeError: Selected atoms must all be in the same model!
File "/home/epkumpu/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/selections.py", line 39, in
expand_selection_along_chains
raise TypeError('Selected atoms must all be in the same model!')
See log for complete Python traceback.
> select #2.2
29844 atoms, 30097 bonds, 1875 residues, 7 models selected
ISOLDE: stopped sim
Traceback (most recent call last):
File "/home/epkumpu/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "/home/epkumpu/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2784, in start_sim
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,
File "/home/epkumpu/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 576, in __init__
mobile_atoms = self.expand_mobile_selection(selected_atoms, expansion_mode)
File "/home/epkumpu/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 971, in
expand_mobile_selection
sel = selections.expand_selection_along_chains(core_atoms,
File "/home/epkumpu/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/selections.py", line 39, in
expand_selection_along_chains
raise TypeError('Selected atoms must all be in the same model!')
TypeError: Selected atoms must all be in the same model!
TypeError: Selected atoms must all be in the same model!
File "/home/epkumpu/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/selections.py", line 39, in
expand_selection_along_chains
raise TypeError('Selected atoms must all be in the same model!')
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 460.91.03
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 30BAS0PF00
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 Intel(R) Xeon(R) Silver 4108 CPU @ 1.80GHz
Cache Size: 11264 KB
Memory:
total used free shared buff/cache available
Mem: 125G 5.7G 110G 281M 9.4G 118G
Swap: 126G 0B 126G
Graphics:
65:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1)
Subsystem: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06]
Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-Clipper: 0.17.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (4)
comment:1 by , 4 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE vs. submodels |
comment:2 by , 4 years ago
follow-up: 3 comment:3 by , 4 years ago
Actually, even better would be a session file - if you still have the ChimeraX session open, do "save problem_session.cxs" and send me the result (I'll of course keep it confidential).
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 31 January 2022 19:51
Cc: esa-pekka.kumpula@helsinki.fi <esa-pekka.kumpula@helsinki.fi>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #6050: ISOLDE vs. submodels
#6050: ISOLDE vs. submodels
------------------------------------------+---------------------------
Reporter: esa-pekka.kumpula@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
------------------------------------------+---------------------------
Comment (by Tristan Croll):
Could you share the model file with me, so I can try and figure out what's
going on?
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6050#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:4 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
Could you share the model file with me, so I can try and figure out what's going on?