Opened 2 years ago

Closed 2 years ago

#9104 closed defect (duplicate)

Volume Viewer: wrapped C/C++ object of type QScrollArea has been deleted

Reported by: michal.ponczek@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open U:\\\CovidSpikeCryoEMVarianstPDBEMDB31052023.cxs

Opened emdb 31071 as #7, grid size 384,384,384, pixel 1.1, shown at level
0.0872, step 2, values float32  
Opened emdb 32167 as #8, grid size 320,320,320, pixel 1.09, shown at level
0.000478, step 2, values float32  
Opened emdb 31783 as #9, grid size 384,384,384, pixel 1.1, shown at level
0.115, step 2, values float32  
Opened emdb 32854 as #10, grid size 360,360,360, pixel 1.09, shown at level
0.0263, step 2, values float32  
Opened emdb 21375 as #6, grid size 432,432,432, pixel 1.05, shown at level
0.0588, step 2, values float32  
Opened emdb 32854 as #11, grid size 360,360,360, pixel 1.09, shown at level
0.0109, step 2, values float32  
Opened emdb 30669 as #14, grid size 384,384,384, pixel 1.1, shown at level
0.123, step 2, values float32  
Log from Wed May 31 14:52:46 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6VSB fromDatabase pdbe

Summary of feedback from opening 6VSB fetched from pdbe  
---  
note | Fetching compressed mmCIF 6vsb from http://www.ebi.ac.uk/pdbe/entry-
files/download/6vsb.cif  
  
6vsb title:  
Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain
up [more info...]  
  
Chain information for 6vsb #1  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2 1-1208  
  
Non-standard residues in 6vsb #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> open 7EDH fromDatabase pdbe

Summary of feedback from opening 7EDH fetched from pdbe  
---  
note | Fetching compressed mmCIF 7edh from http://www.ebi.ac.uk/pdbe/entry-
files/download/7edh.cif  
  
7edh title:  
Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7), one RBD-up
conformation 3 [more info...]  
  
Chain information for 7edh #2  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2 16-1205  
  
Non-standard residues in 7edh #2  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> open 7VX1), fromDatabase pdbe

PDB identifiers are either 4 or 8 characters long, got "7VX1),"  

> open 7VX1 fromDatabase pdbe

Summary of feedback from opening 7VX1 fetched from pdbe  
---  
note | Fetching compressed mmCIF 7vx1 from http://www.ebi.ac.uk/pdbe/entry-
files/download/7vx1.cif  
  
7vx1 title:  
SARS-CoV-2 β variant spike protein in open state [more info...]  
  
Chain information for 7vx1 #3  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2 1-1206  
  

> open 7V7V fromDatabase pdbe

Summary of feedback from opening 7V7V fetched from pdbe  
---  
note | Fetching compressed mmCIF 7v7v from http://www.ebi.ac.uk/pdbe/entry-
files/download/7v7v.cif  
  
7v7v title:  
Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2), two RBD-up
conformation 3 [more info...]  
  
Chain information for 7v7v #4  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2 1-1206  
  
Non-standard residues in 7v7v #4  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> open 7WVN fromDatabase pdbe

Summary of feedback from opening 7WVN fetched from pdbe  
---  
note | Fetching compressed mmCIF 7wvn from http://www.ebi.ac.uk/pdbe/entry-
files/download/7wvn.cif  
  
7wvn title:  
SARS-CoV-2 ο S-open [more info...]  
  
Chain information for 7wvn #5  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2 1-1205  
  

> ui tool show Matchmaker

> matchmaker #!2-5 to #1

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 6vsb, chain C (#1) with 7edh, chain C (#2), sequence alignment
score = 5556.8  
RMSD between 586 pruned atom pairs is 1.233 angstroms; (across all 958 pairs:
2.731)  
  
Matchmaker 6vsb, chain B (#1) with 7vx1, chain A (#3), sequence alignment
score = 5613.3  
RMSD between 627 pruned atom pairs is 1.037 angstroms; (across all 966 pairs:
10.559)  
  
Matchmaker 6vsb, chain C (#1) with 7v7v, chain C (#4), sequence alignment
score = 5649.3  
RMSD between 535 pruned atom pairs is 1.116 angstroms; (across all 963 pairs:
11.142)  
  
Matchmaker 6vsb, chain C (#1) with 7wvn, chain C (#5), sequence alignment
score = 5476.8  
RMSD between 650 pruned atom pairs is 1.134 angstroms; (across all 965 pairs:
2.102)  
  

> open 21375 fromDatabase emdb

Summary of feedback from opening 21375 fetched from emdb  
---  
note | Fetching compressed map 21375 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-21375/map/emd_21375.map.gz  
  
Opened emdb 21375 as #6, grid size 432,432,432, pixel 1.05, shown at level
0.0501, step 2, values float32  

> transparency 70

> ui tool show "Hide Dust"

> surface dust #6 size 6.28

> volume #6 level 0.08391

> volume #6 level 0.0107

> volume #6 level 0.07265

> volume #6 level 0.08109

> open 31071 fromDatabase emdb

Summary of feedback from opening 31071 fetched from emdb  
---  
note | Fetching compressed map 31071 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-31071/map/emd_31071.map.gz  
  
Opened emdb 31071 as #7, grid size 384,384,384, pixel 1.1, shown at level
0.0872, step 2, values float32  

> open 32167 fromDatabase emdb

Summary of feedback from opening 32167 fetched from emdb  
---  
note | Fetching compressed map 32167 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-32167/map/emd_32167.map.gz  
  
Opened emdb 32167 as #8, grid size 320,320,320, pixel 1.09, shown at level
0.000478, step 2, values float32  

> open 31783

'31783' has no suffix  

> from emdb

Unknown command: from emdb  

> open 31783

'31783' has no suffix  

> from emdb

Unknown command: from emdb  

> open 31783

'31783' has no suffix  

> from emdb

Unknown command: from emdb  

> open 31783

'31783' has no suffix  

> from emdb

Unknown command: from emdb  

> open 31783

'31783' has no suffix  

> from emdb

Unknown command: from emdb  

> import 31783 from emdb

Unknown command: import 31783 from emdb  

> open 31783 fromDatabase emdb

Summary of feedback from opening 31783 fetched from emdb  
---  
note | Fetching compressed map 31783 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-31783/map/emd_31783.map.gz  
  
Opened emdb 31783 as #9, grid size 384,384,384, pixel 1.1, shown at level
0.115, step 2, values float32  

> open 32854 fromDatabase emdb

Summary of feedback from opening 32854 fetched from emdb  
---  
note | Fetching compressed map 32854 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-32854/map/emd_32854.map.gz  
  
Opened emdb 32854 as #10, grid size 360,360,360, pixel 1.09, shown at level
0.000895, step 2, values float32  

> open 7ejh fromDatabase pdbe

Summary of feedback from opening 7ejh fetched from pdbe  
---  
notes | Fetching compressed mmCIF 7ejh from http://www.ebi.ac.uk/pdbe/entry-
files/download/7ejh.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
Fetching CCD NAP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif  
Fetching CCD J66 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/J66/J66.cif  
  
7ejh title:  
Crystal structure of KRED mutant-F147L/L153Q/Y190P/L199A/M205F/M206F and
2-hydroxyisoindoline-1,3-dione complex [more info...]  
  
Chain information for 7ejh #11  
---  
Chain | Description | UniProt  
A B C D | 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase | Q6WVP7_LACKE
1-252  
  
Non-standard residues in 7ejh #11  
---  
J66 — 2-oxidanylisoindole-1,3-dione  
MG — magnesium ion  
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  
  

> select add #11

8491 atoms, 7840 bonds, 17 pseudobonds, 1805 residues, 2 models selected  

> select subtract #11

Nothing selected  

> close #11

> ui mousemode right "tape measure"

> marker segment #11 position 163.7,194.5,54.95 toPosition 188.6,317.2,256.1
> color yellow radius 0.275 label 237 labelHeight 23.7 labelColor yellow

> marker segment #11 position 170.1,174.2,64.59 toPosition 253.9,253.6,306.3
> color yellow radius 0.2733 label 267.9 labelHeight 26.79 labelColor yellow

> marker segment #11 position 182.8,162.8,70.84 toPosition 255.4,206.8,156.5
> color yellow radius 0.2733 label 120.6 labelHeight 12.06 labelColor yellow

> surface dust #6 size 6.28

> surface dust #7 size 6.6

> surface dust #8 size 6.56

[Repeated 4 time(s)]

> surface dust #9 size 6.6

> surface dust #10 size 6.56

> transparency 70

> marker delete #11

> ui tool show "Fit in Map"

> fitmap #6 inMap #7

Fit map emdb 21375 in map emdb 31071 using 52766 points  
correlation = 0.814, correlation about mean = 0.5495, overlap = 3770  
steps = 260, shift = 26.6, angle = 10.2 degrees  
  
Position of emdb 21375 (#6) relative to emdb 31071 (#7) coordinates:  
Matrix rotation and translation  
0.98423717 -0.17672381 -0.00677370 29.84551896  
0.17670951 0.98425945 -0.00266009 -51.25316675  
0.00713718 0.00142118 0.99997352 -17.21520217  
Axis 0.01153781 -0.03932619 0.99915981  
Axis point 306.04280747 142.55379027 0.00000000  
Rotation angle (degrees) 10.18722292  
Shift along axis -14.84079451  
  

> fitmap #6 inMap #8

Fit map emdb 21375 in map emdb 32167 using 52766 points  
correlation = 0.3376, correlation about mean = 0.1463, overlap = 556.3  
steps = 364, shift = 48.7, angle = 7.26 degrees  
  
Position of emdb 21375 (#6) relative to emdb 32167 (#8) coordinates:  
Matrix rotation and translation  
0.97695916 -0.19034227 0.09654340 -23.57600064  
0.18418830 0.98045439 0.06916542 -98.50470153  
-0.10782150 -0.04978962 0.99292271 5.33343526  
Axis -0.26856297 0.46139149 0.84557189  
Axis point 424.33554310 -224.05648632 0.00000000  
Rotation angle (degrees) 12.79514304  
Shift along axis -34.60778735  
  

> fitmap #6 inMap #8

Fit map emdb 21375 in map emdb 32167 using 52766 points  
correlation = 0.3411, correlation about mean = 0.1429, overlap = 563.8  
steps = 512, shift = 2.4, angle = 6.35 degrees  
  
Position of emdb 21375 (#6) relative to emdb 32167 (#8) coordinates:  
Matrix rotation and translation  
0.95642702 -0.28679111 0.05475594 10.42033617  
0.28432869 0.95749421 0.04860077 -111.88045961  
-0.06636677 -0.03091440 0.99731627 -10.47275394  
Axis -0.13495163 0.20556716 0.96929366  
Axis point 363.25609131 -35.11702812 0.00000000  
Rotation angle (degrees) 17.13392348  
Shift along axis -34.55636407  
  

> fitmap #6 inMap #10

Fit map emdb 21375 in map emdb 32854 using 52766 points  
correlation = 0.7923, correlation about mean = 0.6586, overlap = 2984  
steps = 424, shift = 28.4, angle = 26.9 degrees  
  
Position of emdb 21375 (#6) relative to emdb 32854 (#10) coordinates:  
Matrix rotation and translation  
0.73277046 -0.68021482 -0.01884818 189.98206036  
0.67978146 0.73299284 -0.02487318 -117.82593616  
0.03073468 0.00541369 0.99951292 -37.62896882  
Axis 0.02224952 -0.03642486 0.99908868  
Axis point 246.86979159 183.26281887 0.00000000  
Rotation angle (degrees) 42.89198574  
Shift along axis -29.07587344  
  

> fitmap #6 inMap #10

Fit map emdb 21375 in map emdb 32854 using 52766 points  
correlation = 0.7921, correlation about mean = 0.658, overlap = 2983  
steps = 40, shift = 0.0179, angle = 0.00148 degrees  
  
Position of emdb 21375 (#6) relative to emdb 32854 (#10) coordinates:  
Matrix rotation and translation  
0.73275311 -0.68023357 -0.01884582 189.98941729  
0.67980028 0.73297543 -0.02487148 -117.83058959  
0.03073194 0.00541326 0.99951300 -37.61077407  
Axis 0.02224735 -0.03642012 0.99908890  
Axis point 246.87246529 183.26056791 0.00000000  
Rotation angle (degrees) 42.89344481  
Shift along axis -29.05834257  
  

> select add #8

2 models selected  

> marker segment #11 position 135.6,195.1,192.1 toPosition 75.4,274.9,164.6
> color yellow radius 0.2733 label 103.7 labelHeight 10.37 labelColor yellow

> marker delete #11

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models #8,1,0,0,43.935,0,1,0,65.457,0,0,1,48.32

> fitmap #7 inMap #6

Fit map emdb 31071 in map emdb 21375 using 70538 points  
correlation = 0.8084, correlation about mean = 0.6265, overlap = 3427  
steps = 492, shift = 24.4, angle = 32.7 degrees  
  
Position of emdb 31071 (#7) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.98408886 0.17754028 0.00696894 -20.31585885  
-0.17755093 0.98411117 0.00093532 56.03163988  
-0.00669215 -0.00215778 0.99997528 17.14861648  
Axis -0.00870395 0.03844216 -0.99922292  
Axis point 306.02658326 142.58143808 0.00000000  
Rotation angle (degrees) 10.23486960  
Shift along axis -14.80448522  
  

> surface dust #8 size 6.51

> fitmap #8 inMap #6

Fit map emdb 32167 in map emdb 21375 using 39894 points  
correlation = 0.3516, correlation about mean = 0.07371, overlap = 594.4  
steps = 296, shift = 42.6, angle = 7.35 degrees  
  
Position of emdb 32167 (#8) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.75572722 0.64822441 0.09317445 -21.12972243  
-0.64112114 0.76133353 -0.09661744 228.74327561  
-0.13356662 0.01328032 0.99095085 72.81698103  
Axis 0.08365288 0.17259263 -0.98143465  
Axis point 311.64226056 145.67776707 0.00000000  
Rotation angle (degrees) 41.06142518  
Shift along axis -33.75326685  
  

> fitmap #8 inMap #6

Fit map emdb 32167 in map emdb 21375 using 39894 points  
correlation = 0.3516, correlation about mean = 0.0739, overlap = 594.4  
steps = 40, shift = 0.0145, angle = 0.00866 degrees  
  
Position of emdb 32167 (#8) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.75566115 0.64829857 0.09319433 -21.12244752  
-0.64117939 0.76126922 -0.09673758 228.78817549  
-0.13366081 0.01334655 0.99093726 72.83165476  
Axis 0.08378420 0.17265775 -0.98141200  
Axis point 311.66785167 145.68544886 0.00000000  
Rotation angle (degrees) 41.06770387  
Shift along axis -33.74553585  
  

> fitmap #10 inMap #6

Fit map emdb 32854 in map emdb 21375 using 56595 points  
correlation = 0.782, correlation about mean = 0.6542, overlap = 2671  
steps = 44, shift = 0.0405, angle = 0.0425 degrees  
  
Position of emdb 32854 (#10) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.73298056 0.67952602 0.03136703 -58.04396651  
-0.67997813 0.73321126 0.00556724 215.67146799  
-0.01921558 -0.02540957 0.99949243 38.44861242  
Axis -0.02276371 0.03717129 -0.99904960  
Axis point 246.81521078 183.37819986 0.00000000  
Rotation angle (degrees) 42.87480862  
Shift along axis -29.07398701  
  

> fitmap #10 inMap #6

Fit map emdb 32854 in map emdb 21375 using 56595 points  
correlation = 0.782, correlation about mean = 0.6543, overlap = 2671  
steps = 28, shift = 0.0103, angle = 0.00425 degrees  
  
Position of emdb 32854 (#10) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.73298701 0.67951699 0.03141180 -58.06046549  
-0.67996913 0.73322004 0.00550942 215.68233644  
-0.01928802 -0.02539739 0.99949134 38.46603190  
Axis -0.02271253 0.03725785 -0.99904754  
Axis point 246.82964207 183.40608215 0.00000000  
Rotation angle (degrees) 42.87421260  
Shift along axis -29.07483365  
  

> close #6

> open 21375 fromDatabase emdb

Opened emdb 21375 as #6, grid size 432,432,432, pixel 1.05, shown at level
0.0501, step 2, values float32  

> transparency 70

> surface dust #8 size 6.51

> surface dust #6 size 6.28

> fitmap #7 inMap #6

Fit map emdb 31071 in map emdb 21375 using 70538 points  
correlation = 0.8084, correlation about mean = 0.6264, overlap = 3428  
steps = 760, shift = 51, angle = 42.9 degrees  
  
Position of emdb 31071 (#7) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.98409143 0.17752232 0.00706258 -20.32287686  
-0.17753376 0.98411418 0.00102194 56.01934213  
-0.00676897 -0.00225953 0.99997454 17.18018700  
Axis -0.00923470 0.03892477 -0.99919947  
Axis point 306.01989378 142.67429865 0.00000000  
Rotation angle (degrees) 10.23408880  
Shift along axis -14.79821793  
  

> fitmap #8 inMap #6

Fit map emdb 32167 in map emdb 21375 using 39894 points  
correlation = 0.7241, correlation about mean = 0.6075, overlap = 1571  
steps = 1020, shift = 42.6, angle = 39.8 degrees  
  
Position of emdb 32167 (#8) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.79126628 0.60604011 0.08132069 -24.87331367  
-0.60236160 0.79542472 -0.06678336 205.63361942  
-0.10515788 0.00385896 0.99444805 64.65357397  
Axis 0.05767922 0.15225915 -0.98665610  
Axis point 301.80606934 141.76317947 0.00000000  
Rotation angle (degrees) 37.76123340  
Shift along axis -33.91591710  
  

> fitmap #10 inMap #6

Fit map emdb 32854 in map emdb 21375 using 56595 points  
correlation = 0.4601, correlation about mean = 0.1801, overlap = 1339  
steps = 1276, shift = 46.2, angle = 42.5 degrees  
  
Position of emdb 32854 (#10) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.73783644 0.67397405 0.03682882 -59.37169208  
-0.67461903 0.73812690 0.00760624 213.01626131  
-0.02205793 -0.03045758 0.99929264 29.83525559  
Axis -0.02818677 0.04360642 -0.99865108  
Axis point 245.41728430 184.34239609 0.00000000  
Rotation angle (degrees) 42.47025325  
Shift along axis -18.83263733  
  

> fitmap #9 inMap #6

Fit map emdb 31783 in map emdb 21375 using 70424 points  
correlation = 0.809, correlation about mean = 0.6793, overlap = 4130  
steps = 280, shift = 25.3, angle = 13.3 degrees  
  
Position of emdb 31783 (#9) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.97335058 0.22905573 -0.01105069 -25.69937027  
-0.22922082 0.97322255 -0.01719549 72.00079176  
0.00681606 0.01927028 0.99979108 9.12641470  
Axis 0.07926099 -0.03883467 -0.99609717  
Axis point 295.19600985 141.72337912 0.00000000  
Rotation angle (degrees) 13.29919509  
Shift along axis -13.92388054  
  

> select subtract #8

Nothing selected  

> fitmap #3 inMap #8

Fit molecule 7vx1 (#3) to map emdb 32167 (#8) using 25362 atoms  
average map value = 0.209, steps = 52  
shifted from previous position = 1.08  
rotated from previous position = 1.49 degrees  
atoms outside contour = 3880, contour level = 0.00047791  
  
Position of 7vx1 (#3) relative to emdb 32167 (#8) coordinates:  
Matrix rotation and translation  
-0.49016158 -0.86739098 -0.08587496 415.16204975  
0.85650848 -0.49758682 0.13711524 84.96328468  
-0.16166277 -0.00634401 0.98682567 30.85886364  
Axis -0.08285173 0.04376958 0.99560023  
Axis point 184.24557777 162.10693870 0.00000000  
Rotation angle (degrees) 120.03052832  
Shift along axis 0.04500340  
  

> fitmap #5 inMap #10

Fit molecule 7wvn (#5) to map emdb 32854 (#10) using 24805 atoms  
average map value = 0.1386, steps = 56  
shifted from previous position = 0.568  
rotated from previous position = 1.14 degrees  
atoms outside contour = 6260, contour level = 0.0008946  
  
Position of 7wvn (#5) relative to emdb 32854 (#10) coordinates:  
Matrix rotation and translation  
-0.48148599 -0.87644933 0.00279368 464.28041535  
0.87630624 -0.48134401 0.01988270 114.78436014  
-0.01608146 0.01202136 0.99979842 11.52025290  
Axis -0.00448483 0.01076810 0.99993196  
Axis point 198.24557527 194.68351847 0.00000000  
Rotation angle (degrees) 118.78444776  
Shift along axis 10.67326211  
  

> volume #6 level 0.0995

> volume #6 level 0.003652

> volume #6 level 0.1431

> ui tool show Matchmaker

> matchmaker #!3 to #4

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 7v7v, chain A (#4) with 7vx1, chain A (#3), sequence alignment
score = 5758.1  
RMSD between 507 pruned atom pairs is 1.259 angstroms; (across all 1019 pairs:
3.913)  
  

> matchmaker #!5 to #4

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 7v7v, chain A (#4) with 7wvn, chain B (#5), sequence alignment
score = 5521.2  
RMSD between 597 pruned atom pairs is 1.072 angstroms; (across all 1020 pairs:
15.297)  
  

> fitmap #5 inMap #10

Fit molecule 7wvn (#5) to map emdb 32854 (#10) using 24805 atoms  
average map value = 0.1386, steps = 60  
shifted from previous position = 1.49  
rotated from previous position = 2.04 degrees  
atoms outside contour = 6248, contour level = 0.0008946  
  
Position of 7wvn (#5) relative to emdb 32854 (#10) coordinates:  
Matrix rotation and translation  
-0.48165466 -0.87635625 0.00291617 464.28303022  
0.87621756 -0.48151288 0.01970095 114.88069877  
-0.01586088 0.01204426 0.99980166 11.43709108  
Axis -0.00436854 0.01071327 0.99993307  
Axis point 198.22467568 194.70277142 0.00000000  
Rotation angle (degrees) 118.79537538  
Shift along axis 10.63883597  
  

> volume #6 level 0.05884

> volume #10 level 0.007864

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> select add #5

24805 atoms, 25423 bonds, 21 pseudobonds, 3162 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.23458,-0.97069,0.052251,356.16,0.97157,0.23588,0.020179,-15.792,-0.031913,0.046032,0.99843,3.6441

> ui mousemode right "translate selected atoms"

> fitmap #5 inMap #10

Fit molecule 7wvn (#5) to map emdb 32854 (#10) using 24805 atoms  
average map value = 0.3783, steps = 236  
shifted from previous position = 18.4  
rotated from previous position = 24.2 degrees  
atoms outside contour = 1620, contour level = 0.0078638  
  
Position of 7wvn (#5) relative to emdb 32854 (#10) coordinates:  
Matrix rotation and translation  
-0.17648090 -0.95524325 0.23741275 382.71706727  
0.96241900 -0.21804155 -0.16188745 85.03646373  
0.20640774 0.19992050 0.95782443 -75.96071155  
Axis 0.18537698 0.01588582 0.98253907  
Axis point 163.84782141 199.30669714 0.00000000  
Rotation angle (degrees) 102.61208106  
Shift along axis -2.33655673  
  

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> volume #10 level 0.02321

> fitmap #5 inMap #10

Fit molecule 7wvn (#5) to map emdb 32854 (#10) using 24805 atoms  
average map value = 0.1689, steps = 88  
shifted from previous position = 7.28  
rotated from previous position = 2.47 degrees  
atoms outside contour = 7273, contour level = 0.023208  
  
Position of 7wvn (#5) relative to emdb 32854 (#10) coordinates:  
Matrix rotation and translation  
-0.21808145 -0.94519613 0.24299128 389.29117293  
0.95388891 -0.25906110 -0.15160244 100.05725542  
0.20624362 0.19872500 0.95810852 -74.06958006  
Axis 0.18137800 0.01902567 0.98322940  
Axis point 162.46123092 202.55824920 0.00000000  
Rotation angle (degrees) 105.04140554  
Shift along axis -0.31487915  
  

> fitmap #5 inMap #10

Fit molecule 7wvn (#5) to map emdb 32854 (#10) using 24805 atoms  
average map value = 0.169, steps = 92  
shifted from previous position = 7.36  
rotated from previous position = 0.0381 degrees  
atoms outside contour = 7298, contour level = 0.023208  
  
Position of 7wvn (#5) relative to emdb 32854 (#10) coordinates:  
Matrix rotation and translation  
-0.21744976 -0.94534679 0.24297130 396.34104608  
0.95405819 -0.25842389 -0.15162477 99.24017211  
0.20612758 0.19883799 0.95811005 -72.37268560  
Axis 0.18141603 0.01907205 0.98322148  
Axis point 166.14498826 204.78144830 0.00000000  
Rotation angle (degrees) 105.00372229  
Shift along axis 2.63695421  
  

> volume #10 level 0.05083

> volume #10 level 0.1613

> volume #10 level 0.02628

> fitmap #5 inMap #10

Fit molecule 7wvn (#5) to map emdb 32854 (#10) using 24805 atoms  
average map value = 0.3783, steps = 104  
shifted from previous position = 8.62  
rotated from previous position = 2.44 degrees  
atoms outside contour = 2769, contour level = 0.026277  
  
Position of 7wvn (#5) relative to emdb 32854 (#10) coordinates:  
Matrix rotation and translation  
-0.17649210 -0.95523547 0.23743575 394.25746645  
0.96243513 -0.21803862 -0.16179547 97.02890458  
0.20632294 0.19996088 0.95783427 -67.11907558  
Axis 0.18535052 0.01594105 0.98254316  
Axis point 163.96644585 209.10476609 0.00000000  
Rotation angle (degrees) 102.61203483  
Shift along axis 8.67517810  
  

> fitmap #5 inMap #10

Fit molecule 7wvn (#5) to map emdb 32854 (#10) using 24805 atoms  
average map value = 0.1392, steps = 84  
shifted from previous position = 3.51  
rotated from previous position = 0.963 degrees  
atoms outside contour = 10254, contour level = 0.026277  
  
Position of 7wvn (#5) relative to emdb 32854 (#10) coordinates:  
Matrix rotation and translation  
-0.19276811 -0.95171203 0.23892399 396.08659700  
0.95972359 -0.23358164 -0.15610971 103.35509726  
0.20437974 0.19920802 0.95840758 -66.33914045  
Axis 0.18273082 0.01776522 0.98300246  
Axis point 162.85260052 210.35386048 0.00000000  
Rotation angle (degrees) 103.53097974  
Shift along axis 9.00181676  
  

> select up

24805 atoms, 25423 bonds, 21 pseudobonds, 3162 residues, 2 models selected  

> open 32854 fromDatabase emdb

Opened emdb 32854 as #11, grid size 360,360,360, pixel 1.09, shown at level
0.000895, step 2, values float32  

> transparency 70

> open 7wvn fromDatabase pdbe

7wvn title:  
SARS-CoV-2 ο S-open [more info...]  
  
Chain information for 7wvn #12  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2 1-1205  
  

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!10 models

> show #!10 models

> show #!5 models

> hide #!5 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> surface dust #11 size 6.56

> volume #11 level 0.001726

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

143301 atoms, 146780 bonds, 140 pseudobonds, 18401 residues, 12 models
selected  

> show (#!12 & sel) target ab

> select ::name="BMA"::name="NAG"

3105 atoms, 3189 bonds, 222 residues, 3 models selected  

> show #11-12 target ab

> transparency 60

> volume #11 color #ffff8766

> volume #11 color #ff9f8c66

> volume #11 color #ffc0b566

> volume #11 color #ffe9de66

> show #!5 models

> hide #!5 models

> volume #11 level 0.007864

> volume #11 level 0.01093

> open 7ej4 fromDatabase pdbe

Summary of feedback from opening 7ej4 fetched from pdbe  
---  
note | Fetching compressed mmCIF 7ej4 from http://www.ebi.ac.uk/pdbe/entry-
files/download/7ej4.cif  
  
7ej4 title:  
Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody
RBD-chAb-25 [more info...]  
  
Chain information for 7ej4 #13  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2 1-1208  
H I J | RBD-chAb-25, Heavy chain |  
L M N | RBD-chAb-25, Light chain |  
  
Non-standard residues in 7ej4 #13  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> select add #13

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> select subtract #13

3105 atoms, 3189 bonds, 222 residues, 3 models selected  

> select add #13

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> select subtract #13

3105 atoms, 3189 bonds, 222 residues, 3 models selected  

> select add #13

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> select subtract #13

3105 atoms, 3189 bonds, 222 residues, 3 models selected  

> select add #13

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> hide (#!13 & sel) target a

> show (#!13 & sel) target ab

> ui tool show Matchmaker

> matchmaker #!13 to #1

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 6vsb, chain B (#1) with 7ej4, chain C (#13), sequence alignment
score = 5691.9  
RMSD between 522 pruned atom pairs is 1.272 angstroms; (across all 959 pairs:
15.249)  
  

> select subtract #13

3105 atoms, 3189 bonds, 222 residues, 3 models selected  

> select add #13

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> hide #!13 models

> select add #12

57950 atoms, 59433 bonds, 44 pseudobonds, 7184 residues, 7 models selected  

> select subtract #12

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> select add #12

57950 atoms, 59433 bonds, 44 pseudobonds, 7184 residues, 7 models selected  

> select subtract #12

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> matchmaker #!12 to #1

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 6vsb, chain C (#1) with 7wvn, chain C (#12), sequence alignment
score = 5476.8  
RMSD between 650 pruned atom pairs is 1.134 angstroms; (across all 965 pairs:
2.102)  
  

> hide #!11 models

> show #!11 models

> fitmap #10 inMap #6

Fit map emdb 32854 in map emdb 21375 using 34103 points  
correlation = 0.5348, correlation about mean = 0.139, overlap = 1325  
steps = 40, shift = 0.0116, angle = 0.00879 degrees  
  
Position of emdb 32854 (#10) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.73793009 0.67386859 0.03688230 -59.37680395  
-0.67451588 0.73822082 0.00763892 212.97248473  
-0.02207965 -0.03051469 0.99929042 29.86218461  
Axis -0.02825749 0.04366866 -0.99864636  
Axis point 245.41632863 184.34679472 0.00000000  
Rotation angle (degrees) 42.46238866  
Shift along axis -18.84369912  
  

> select add #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 7 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,1,0,0,20.895,0,1,0,35.562,0,0,1,32.616,#2,0.98407,0.1775,0.01025,-0.33614,-0.17749,0.98412,-0.0025384,91.598,-0.010538,0.00067862,0.99994,49.993,#4,0.97714,0.21134,-0.023152,-0.030626,-0.21192,0.97692,-0.026813,104.17,0.016951,0.031106,0.99937,37.087,#11,1,0,0,20.895,0,1,0,35.562,0,0,1,32.616,#13,0.39239,0.91905,-0.037193,-19.09,0.90201,-0.3924,-0.18003,197.31,-0.18005,0.037093,-0.98296,516.55

> fitmap #10 inMap #6

Fit map emdb 32854 in map emdb 21375 using 34103 points  
correlation = 0.5349, correlation about mean = 0.1393, overlap = 1325  
steps = 28, shift = 0.0152, angle = 0.00685 degrees  
  
Position of emdb 32854 (#10) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.73791322 0.67388244 0.03696657 -59.39450158  
-0.67453048 0.73820833 0.00755616 212.99116534  
-0.02219707 -0.03051087 0.99928794 29.87028480  
Axis -0.02819264 0.04381691 -0.99864170  
Axis point 245.42647806 184.37666159 0.00000000  
Rotation angle (degrees) 42.46373977  
Shift along axis -18.82261070  
  

> view matrix models
> #1,0.89492,0.44622,-0.001735,-50.891,-0.44622,0.89493,0.00034263,146.74,0.0017056,0.00046757,1,32.178,#2,0.80149,0.59798,0.0063057,-44.917,-0.59795,0.80151,-0.0065029,206.37,-0.0089427,0.0014415,0.99996,49.544,#4,0.77987,0.62499,-0.034418,-39.01,-0.62566,0.77998,-0.013322,217.48,0.018519,0.031923,0.99932,36.645,#11,0.89492,0.44622,-0.001735,-50.891,-0.44622,0.89493,0.00034263,146.74,0.0017056,0.00046757,1,32.178,#13,0.75396,0.64732,-0.11191,-15.341,0.63208,-0.76125,-0.14485,309.5,-0.17896,0.038477,-0.9831,516.12

> view matrix models
> #1,0.89492,0.44622,-0.001735,-39.775,-0.44622,0.89493,0.00034263,152.88,0.0017056,0.00046757,1,32.399,#2,0.80149,0.59798,0.0063057,-33.802,-0.59795,0.80151,-0.0065029,212.51,-0.0089427,0.0014415,0.99996,49.766,#4,0.77987,0.62499,-0.034418,-27.894,-0.62566,0.77998,-0.013322,223.62,0.018519,0.031923,0.99932,36.866,#11,0.89492,0.44622,-0.001735,-39.775,-0.44622,0.89493,0.00034263,152.88,0.0017056,0.00046757,1,32.399,#13,0.75396,0.64732,-0.11191,-4.2249,0.63208,-0.76125,-0.14485,315.64,-0.17896,0.038477,-0.9831,516.34

> show #!6 models

> hide #!6 models

> show #!6 models

> fitmap #10 inMap #6

Fit map emdb 32854 in map emdb 21375 using 34103 points  
correlation = 0.5348, correlation about mean = 0.1391, overlap = 1325  
steps = 40, shift = 0.0116, angle = 0.00388 degrees  
  
Position of emdb 32854 (#10) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.73792097 0.67387648 0.03692066 -59.38430273  
-0.67452420 0.73821356 0.00760530 212.98176200  
-0.02213030 -0.03051599 0.99928926 29.86909453  
Axis -0.02823316 0.04373395 -0.99864420  
Axis point 245.42133014 184.36008990 0.00000000  
Rotation angle (degrees) 42.46313305  
Shift along axis -18.83745716  
  

> fitmap #10 inMap #6

Fit map emdb 32854 in map emdb 21375 using 34103 points  
correlation = 0.5349, correlation about mean = 0.1396, overlap = 1325  
steps = 28, shift = 0.0238, angle = 0.00838 degrees  
  
Position of emdb 32854 (#10) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.73788217 0.67391288 0.03703155 -59.40957781  
-0.67456220 0.73817967 0.00752411 213.01166663  
-0.02226534 -0.03053199 0.99928577 29.87600814  
Axis -0.02818314 0.04391339 -0.99863773  
Axis point 245.42926330 184.40217579 0.00000000  
Rotation angle (degrees) 42.46636522  
Shift along axis -18.80689612  
  

> select subtract #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> select add #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 7 models selected  

> select subtract #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> select add #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 7 models selected  

> select subtract #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> select add #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 7 models selected  

> select subtract #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> fitmap #10 inMap #6

Fit map emdb 32854 in map emdb 21375 using 34103 points  
correlation = 0.5348, correlation about mean = 0.139, overlap = 1325  
steps = 40, shift = 0.0275, angle = 0.0123 degrees  
  
Position of emdb 32854 (#10) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.73792843 0.67387228 0.03684813 -59.37049913  
-0.67451810 0.73821899 0.00761976 212.97690089  
-0.02206725 -0.03047757 0.99929183 29.85230001  
Axis -0.02821577 0.04363409 -0.99864906  
Axis point 245.42372754 184.33874647 0.00000000  
Rotation angle (degrees) 42.46247702  
Shift along axis -18.84373335  
  

> fitmap #10 inMap #6

Fit map emdb 32854 in map emdb 21375 using 34103 points  
correlation = 0.5348, correlation about mean = 0.1391, overlap = 1325  
steps = 36, shift = 0.00351, angle = 0.00299 degrees  
  
Position of emdb 32854 (#10) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.73792199 0.67387725 0.03688624 -59.37807480  
-0.67452346 0.73821445 0.00758471 212.98542571  
-0.02211879 -0.03047756 0.99929069 29.85922179  
Axis -0.02818952 0.04370006 -0.99864691  
Axis point 245.42939994 184.35218665 0.00000000  
Rotation angle (degrees) 42.46299115  
Shift along axis -18.83750361  
  

> select add #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 7 models selected  

> select subtract #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> select add #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 7 models selected  

> select subtract #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> select add #9

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 7 models selected  

> select subtract #9

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> select add #10

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 7 models selected  

> select subtract #10

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 5 models selected  

> select add #10

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 7 models selected  

> show #!10 models

> select add #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 9 models selected  

> select subtract #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 7 models selected  

> select add #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 9 models selected  

> select subtract #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 7 models selected  

> select add #11

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 9 models selected  

> open 30669 fromDatabase emdb

Summary of feedback from opening 30669 fetched from emdb  
---  
note | Fetching compressed map 30669 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-30669/map/emd_30669.map.gz  
  
Opened emdb 30669 as #14, grid size 384,384,384, pixel 1.1, shown at level
0.123, step 2, values float32  

> select subtract #10

33145 atoms, 34010 bonds, 23 pseudobonds, 4022 residues, 7 models selected  

> fitmap #10 inMap #14

Fit map emdb 32854 in map emdb 30669 using 34103 points  
correlation = 0.4156, correlation about mean = 0.07219, overlap = 1185  
steps = 216, shift = 10.3, angle = 15.8 degrees  
  
Position of emdb 32854 (#10) relative to emdb 30669 (#14) coordinates:  
Matrix rotation and translation  
0.76896420 0.62825526 -0.11827671 -24.48965733  
-0.63766011 0.74054991 -0.21207408 242.75194013  
-0.04564685 0.23849772 0.97006969 -4.36236134  
Axis 0.33483045 -0.05397295 -0.94073136  
Axis point 319.32563472 147.24406517 0.00000000  
Rotation angle (degrees) 42.28630845  
Shift along axis -17.19811093  
  

> select subtract #13

3105 atoms, 3189 bonds, 222 residues, 5 models selected  

> select add #2

25306 atoms, 25959 bonds, 23 pseudobonds, 3068 residues, 6 models selected  

> select add #1

47306 atoms, 48506 bonds, 62 pseudobonds, 5973 residues, 7 models selected  

> select subtract #2

24030 atoms, 24630 bonds, 39 pseudobonds, 3050 residues, 5 models selected  

> select subtract #1

1176 atoms, 1212 bonds, 84 residues, 3 models selected  

> select add #4

25304 atoms, 25975 bonds, 21 pseudobonds, 3173 residues, 4 models selected  

> select subtract #4

2 models selected  

> select add #14.1

3 models selected  

> ui mousemode right "translate selected atoms"

> select clear

> select add #14

2 models selected  

> select subtract #14

Nothing selected  

> select add #14

2 models selected  

> ui mousemode right "move picked models"

> ui mousemode right "translate selected atoms"

[Repeated 1 time(s)]

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected atoms"

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models #14,1,0,0,0.02389,0,1,0,-0.31419,0,0,1,0.26561

> ui mousemode right "rotate selected models"

> view matrix models
> #14,-0.82047,0.50374,0.27031,219.25,0.54921,0.82582,0.12804,-109.8,-0.15873,0.25351,-0.95422,428.45

> fitmap #10 inMap #14

Fit map emdb 32854 in map emdb 30669 using 34103 points  
correlation = 0.742, correlation about mean = 0.42, overlap = 3484  
steps = 576, shift = 18, angle = 41.1 degrees  
  
Position of emdb 32854 (#10) relative to emdb 30669 (#14) coordinates:  
Matrix rotation and translation  
-0.64853686 -0.74868035 -0.13739604 512.71061066  
-0.75966197 0.64801563 0.05467564 221.09928968  
0.04810020 0.13983372 -0.98900602 389.09388293  
Axis 0.41661471 -0.90749426 -0.05372484  
Axis point 296.13502073 0.00000000 202.56904902  
Rotation angle (degrees) 174.13398932  
Shift along axis -7.94756215  
  

> undo

[Repeated 1 time(s)]

> view matrix models
> #14,-0.77424,0.55049,0.31227,191.46,0.61933,0.76059,0.19478,-126.84,-0.13028,0.3442,-0.92981,399.83

> fitmap #10 inMap #7

Fit map emdb 32854 in map emdb 31071 using 34103 points  
correlation = 0.7344, correlation about mean = 0.4402, overlap = 3850  
steps = 536, shift = 22.5, angle = 40.2 degrees  
  
Position of emdb 32854 (#10) relative to emdb 31071 (#7) coordinates:  
Matrix rotation and translation  
0.84068165 0.54080228 0.02805799 -66.44444960  
-0.54119954 0.84084953 0.00866712 151.13902126  
-0.01890535 -0.02247126 0.99956872 22.59260434  
Axis -0.02873955 0.04334538 -0.99864669  
Axis point 224.58894888 189.77518654 0.00000000  
Rotation angle (degrees) 32.80176094  
Shift along axis -14.10126745  
  

> fitmap #14 inMap #6

Fit map emdb 30669 in map emdb 21375 using 70700 points  
correlation = 0.7557, correlation about mean = 0.588, overlap = 2954  
steps = 680, shift = 25.1, angle = 46.2 degrees  
  
Position of emdb 30669 (#14) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
-0.98847426 -0.11769750 0.09521519 437.22545702  
-0.11155960 0.99146802 0.06742121 26.98409809  
-0.10233812 0.05602196 -0.99317091 466.09713075  
Axis -0.05757862 0.99785946 0.03100313  
Axis point 230.96652851 0.00000000 221.73619805  
Rotation angle (degrees) 174.31907084  
Shift along axis 16.20196889  
  

> fitmap #10 inMap #6

Fit map emdb 32854 in map emdb 21375 using 34103 points  
correlation = 0.8228, correlation about mean = 0.596, overlap = 2658  
steps = 84, shift = 0.298, angle = 0.322 degrees  
  
Position of emdb 32854 (#10) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.73298018 0.67952984 0.03129305 -58.05027631  
-0.67997931 0.73321047 0.00552710 215.68076322  
-0.01918856 -0.02532988 0.99949497 38.42906952  
Axis -0.02267569 0.03709711 -0.99905436  
Axis point 246.82222577 183.38562557 0.00000000  
Rotation angle (degrees) 42.87475091  
Shift along axis -29.07526545  
  

> select subtract #14

Nothing selected  

> hide #!11 models

> show #!11 models

> hide #!11 models

> hide #!12 models

> hide #!10 models

> hide #14.1 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!11 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!6 models

> hide #!11 models

> show #!11 models

> hide #10.1 models

> hide #!11 models

> hide #!10 models

> show #!10 models

> show #!11 models

> show #10.1 models

> hide #10.1 models

> show #10.1 models

> fitmap #10 inMap #6

Fit map emdb 32854 in map emdb 21375 using 34103 points  
correlation = 0.8229, correlation about mean = 0.5963, overlap = 2658  
steps = 44, shift = 0.0169, angle = 0.00941 degrees  
  
Position of emdb 32854 (#10) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.73299895 0.67950264 0.03144366 -58.06496150  
-0.67995704 0.73323069 0.00558462 215.66375476  
-0.01926069 -0.02547386 0.99948992 38.48187415  
Axis -0.02282437 0.03726180 -0.99904485  
Axis point 246.80900511 183.40921397 0.00000000  
Rotation angle (degrees) 42.87332178  
Shift along axis -29.08380132  
  

> fitmap #11 inMap #6

Fit map emdb 32854 in map emdb 21375 using 39740 points  
correlation = 0.8083, correlation about mean = 0.6132, overlap = 2667  
steps = 428, shift = 14.5, angle = 16.4 degrees  
  
Position of emdb 32854 (#11) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.73305674 0.67943913 0.03146872 -58.07091159  
-0.67989286 0.73329069 0.00551851 215.65154205  
-0.01932623 -0.02544074 0.99948950 38.48267478  
Axis -0.02275356 0.03733185 -0.99904385  
Axis point 246.82925127 183.41871220 0.00000000  
Rotation angle (degrees) 42.86837904  
Shift along axis -29.07388850  
  

> fitmap #11 inMap #6

Fit map emdb 32854 in map emdb 21375 using 39740 points  
correlation = 0.8082, correlation about mean = 0.6128, overlap = 2667  
steps = 28, shift = 0.0186, angle = 0.00763 degrees  
  
Position of emdb 32854 (#11) relative to emdb 21375 (#6) coordinates:  
Matrix rotation and translation  
0.73298570 0.67951905 0.03139787 -58.05747847  
-0.67997163 0.73321741 0.00555081 215.67240203  
-0.01924958 -0.02541832 0.99949155 38.44439366  
Axis -0.02275827 0.03721925 -0.99904794  
Axis point 246.81444737 183.39707444 0.00000000  
Rotation angle (degrees) 42.87437006  
Shift along axis -29.05933904  
  

> transparency 60

> show #!12 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> ui tool show Matchmaker

> matchmaker #!12 to #5

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 7wvn, chain B (#5) with 7wvn, chain B (#12), sequence alignment
score = 6198.7  
RMSD between 1057 pruned atom pairs is 0.000 angstroms; (across all 1057
pairs: 0.000)  
  

> fitmap #12 inMap #10

Fit molecule 7wvn (#12) to map emdb 32854 (#10) using 24805 atoms  
average map value = 0.1182, steps = 72  
shifted from previous position = 4.87  
rotated from previous position = 2.05 degrees  
atoms outside contour = 11946, contour level = 0.026277  
  
Position of 7wvn (#12) relative to emdb 32854 (#10) coordinates:  
Matrix rotation and translation  
0.99823455 -0.05927239 -0.00381641 13.04921872  
0.05929933 0.99821294 0.00738287 -12.61999614  
0.00337199 -0.00759615 0.99996546 -15.23193994  
Axis -0.12510655 -0.06003844 0.99032507  
Axis point 234.38600494 179.48985854 0.00000000  
Rotation angle (degrees) 3.43206690  
Shift along axis -15.95942981  
  

> fitmap #5 inMap #11

Fit molecule 7wvn (#5) to map emdb 32854 (#11) using 24805 atoms  
average map value = 0.1182, steps = 76  
shifted from previous position = 4.87  
rotated from previous position = 2.05 degrees  
atoms outside contour = 10202, contour level = 0.010933  
  
Position of 7wvn (#5) relative to emdb 32854 (#11) coordinates:  
Matrix rotation and translation  
-0.23405347 -0.94136638 0.24299859 400.86342263  
0.95167828 -0.27294746 -0.14074137 111.05022347  
0.19881504 0.19831548 0.95976224 -70.78133234  
Axis 0.17625464 0.02296829 0.98407660  
Axis point 164.19059485 209.92641746 0.00000000  
Rotation angle (degrees) 105.87975311  
Shift along axis 3.55042019  
  

> show #!1 models

> show #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> show #!3 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> show #!7 models

> show #!8 models

> show #!13 models

> show #!14 models

> show #14.1 models

> fitmap #6 inMap #11

Fit map emdb 21375 in map emdb 32854 using 75563 points  
correlation = 0.7775, correlation about mean = 0.6954, overlap = 3019  
steps = 40, shift = 0.0255, angle = 0.0377 degrees  
  
Position of emdb 21375 (#6) relative to emdb 32854 (#11) coordinates:  
Matrix rotation and translation  
0.73282594 -0.68015425 -0.01887694 189.96005714  
0.67971871 0.73304881 -0.02493834 -117.81459413  
0.03079964 0.00544445 0.99951075 -37.65689213  
Axis 0.02232192 -0.03649686 0.99908444  
Axis point 246.86749274 183.27113295 0.00000000  
Rotation angle (degrees) 42.88738553  
Shift along axis -29.08227949  
  

> fitmap #6 inMap #11

Fit map emdb 21375 in map emdb 32854 using 75563 points  
correlation = 0.7775, correlation about mean = 0.6954, overlap = 3019  
steps = 40, shift = 0.00959, angle = 0.00545 degrees  
  
Position of emdb 21375 (#6) relative to emdb 32854 (#11) coordinates:  
Matrix rotation and translation  
0.73278675 -0.68019442 -0.01895070 189.98568068  
0.67975913 0.73301203 -0.02491763 -117.81883817  
0.03083992 0.00537740 0.99950987 -37.64770555  
Axis 0.02225608 -0.03657842 0.99908292  
Axis point 246.87472607 183.27786715 0.00000000  
Rotation angle (degrees) 42.89062063  
Shift along axis -29.07521500  
  

> fitmap #7 inMap #11

Fit map emdb 31071 in map emdb 32854 using 70538 points  
correlation = 0.6882, correlation about mean = 0.5656, overlap = 3839  
steps = 60, shift = 0.233, angle = 0.223 degrees  
  
Position of emdb 31071 (#7) relative to emdb 32854 (#11) coordinates:  
Matrix rotation and translation  
0.84093001 -0.54088750 -0.01665618 137.59409197  
0.54051189 0.84103707 -0.02243968 -90.64385492  
0.02614581 0.00986733 0.99960944 -21.90920496  
Axis 0.02983852 -0.03953161 0.99877270  
Axis point 224.37592021 189.18190708 0.00000000  
Rotation angle (degrees) 32.77654803  
Shift along axis -14.19341397  
  

> fitmap #8 inMap #11

Fit map emdb 32167 in map emdb 32854 using 39894 points  
correlation = 0.6448, correlation about mean = 0.5049, overlap = 1819  
steps = 64, shift = 0.174, angle = 0.244 degrees  
  
Position of emdb 32167 (#8) relative to emdb 32854 (#11) coordinates:  
Matrix rotation and translation  
0.99204247 -0.09305294 0.08481087 30.06689052  
0.09515814 0.99523813 -0.02111855 15.36965707  
-0.08244187 0.02902094 0.99617324 26.54829899  
Axis 0.19529961 0.65147050 0.73310589  
Axis point 92.54038573 241.01459698 0.00000000  
Rotation angle (degrees) 7.37515370  
Shift along axis 35.34764468  
  

> fitmap #8 inMap #11

Fit map emdb 32167 in map emdb 32854 using 39894 points  
correlation = 0.6449, correlation about mean = 0.5051, overlap = 1819  
steps = 40, shift = 0.023, angle = 0.011 degrees  
  
Position of emdb 32167 (#8) relative to emdb 32854 (#11) coordinates:  
Matrix rotation and translation  
0.99206355 -0.09297934 0.08464485 30.06011754  
0.09507538 0.99524708 -0.02106921 15.37972200  
-0.08228354 0.02894964 0.99618840 26.52150452  
Axis 0.19509528 0.65109334 0.73349526  
Axis point 92.25612920 241.28907035 0.00000000  
Rotation angle (degrees) 7.36505954  
Shift along axis 35.33161944  
  

> fitmap #9 inMap #11

Fit map emdb 31783 in map emdb 32854 using 70424 points  
correlation = 0.7327, correlation about mean = 0.6547, overlap = 4992  
steps = 64, shift = 0.258, angle = 0.251 degrees  
  
Position of emdb 31783 (#9) relative to emdb 32854 (#11) coordinates:  
Matrix rotation and translation  
0.86905710 -0.49433252 -0.01936760 122.65452502  
0.49305351 0.86868279 -0.04783773 -82.20180655  
0.04047205 0.03202445 0.99866734 -30.15682817  
Axis 0.08047246 -0.06029693 0.99493139  
Axis point 219.80992378 192.36711077 0.00000000  
Rotation angle (degrees) 29.74944567  
Shift along axis -15.17714660  
  

> fitmap #9 inMap #11

Fit map emdb 31783 in map emdb 32854 using 70424 points  
correlation = 0.7327, correlation about mean = 0.6547, overlap = 4992  
steps = 116, shift = 0.0102, angle = 0.00608 degrees  
  
Position of emdb 31783 (#9) relative to emdb 32854 (#11) coordinates:  
Matrix rotation and translation  
0.86906145 -0.49432681 -0.01931844 122.64774204  
0.49304559 0.86868213 -0.04793118 -82.18820189  
0.04047525 0.03213027 0.99866381 -30.17999385  
Axis 0.08067328 -0.06025064 0.99491793  
Axis point 219.78600166 192.37056557 0.00000000  
Rotation angle (degrees) 29.74943651  
Shift along axis -15.18032990  
  

> fitmap #10 inMap #11

Fit map emdb 32854 in map emdb 32854 using 34103 points  
correlation = 1, correlation about mean = 1, overlap = 5184  
steps = 48, shift = 0.0192, angle = 0.00787 degrees  
  
Position of emdb 32854 (#10) relative to emdb 32854 (#11) coordinates:  
Matrix rotation and translation  
0.99999999 -0.00004742 -0.00010964 0.03550283  
0.00004744 0.99999999 0.00011639 -0.03760402  
0.00010963 -0.00011639 0.99999999 0.00901053  
Axis -0.69786787 -0.65734819 0.28438319  
Axis point 0.00000000 71.26012066 308.94903104  
Rotation angle (degrees) 0.00955578  
Shift along axis 0.00250509  
  

> hide #10.1 models

> show #10.1 models

> hide #10.1 models

> show #10.1 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> show #!8 models

> hide #8.1 models

> show #8.1 models

> hide #8.1 models

> hide #!8 models

> hide #!10 models

> hide #!9 models

> hide #10.1 models

> show #10.1 models

> hide #!11 models

> hide #10.1 models

> hide #!10 models

> matchmaker #!1 to #5

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 7wvn, chain C (#5) with 6vsb, chain C (#1), sequence alignment
score = 5476.8  
RMSD between 650 pruned atom pairs is 1.134 angstroms; (across all 965 pairs:
2.102)  
  

> matchmaker #!2 to #5

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 7wvn, chain C (#5) with 7edh, chain C (#2), sequence alignment
score = 5432.3  
RMSD between 618 pruned atom pairs is 1.211 angstroms; (across all 996 pairs:
3.253)  
  

> matchmaker #!3 to #5

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 7wvn, chain B (#5) with 7vx1, chain A (#3), sequence alignment
score = 5790.2  
RMSD between 423 pruned atom pairs is 1.031 angstroms; (across all 1044 pairs:
12.767)  
  

> matchmaker #!4 to #5

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 7wvn, chain B (#5) with 7v7v, chain A (#4), sequence alignment
score = 5521.2  
RMSD between 597 pruned atom pairs is 1.072 angstroms; (across all 1020 pairs:
15.297)  
  

> matchmaker #!12 to #5

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 7wvn, chain B (#5) with 7wvn, chain B (#12), sequence alignment
score = 6198.7  
RMSD between 1057 pruned atom pairs is 0.000 angstroms; (across all 1057
pairs: 0.000)  
  

> matchmaker #!13 to #5

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 7wvn, chain B (#5) with 7ej4, chain C (#13), sequence alignment
score = 5537.7  
RMSD between 640 pruned atom pairs is 1.194 angstroms; (across all 1004 pairs:
17.261)  
  

> show #!10 models

> show #10.1 models

> show #!8 models

> show #8.1 models

> hide #8.1 models

> show #8.1 models

> show #!9 models

> show #!6 models

> hide #!6 models

> show #!6 models

> show #!7 models

> show #!11 models

> show #!12 models

> show #!13 models

> show #!14 models

> hide #!14 models

> hide #!13 models

> show #!13 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> select add #14

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.98847,-0.1177,0.095215,438.14,-0.11156,0.99147,0.067421,20.041,-0.10234,0.056022,-0.99317,441.36

> fitmap #14 inMap #11

Fit map emdb 30669 in map emdb 32854 using 70700 points  
correlation = 0.4309, correlation about mean = 0.2043, overlap = 1789  
steps = 116, shift = 15.2, angle = 2.85 degrees  
  
Position of emdb 30669 (#14) relative to emdb 32854 (#11) coordinates:  
Matrix rotation and translation  
-0.60923809 -0.79218711 0.03561637 483.80438329  
-0.78052443 0.60698952 0.14948356 198.97201747  
-0.14003771 0.06327163 -0.98812253 431.03519549  
Axis -0.43981744 0.89611416 0.05949816  
Axis point 302.55896006 0.00000000 195.75824874  
Rotation angle (degrees) 174.37548215  
Shift along axis -8.83816310  
  

> select clear

> save U:/CovidSpikeCryoEMVarianstPDBEMDB31052023.cxs

> save U:/CovidSpikeCryoEMVarianstPDBEMDB31052023.cxs includeMaps true

——— End of log from Wed May 31 14:52:46 2023 ———

opened ChimeraX session  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\map\volume_viewer.py",
line 1530, in <lambda>  
QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))  
RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted  
  
RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted  
  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\map\volume_viewer.py",
line 1530, in  
QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 531.79
OpenGL renderer: NVIDIA GeForce GTX 1060 6GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: pl_PL.cp1250
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: ATComputers
Model: OPTIMUS 
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 34,296,348,672
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-8400 CPU @ 2.80GHz
OSLanguage: pl-PL

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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-StarMap: 1.1.70
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    pyqtgraph: 0.13.1
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    Send2Trash: 1.8.0
    SEQCROW: 1.5.9
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Volume Viewer: wrapped C/C++ object of type QScrollArea has been deleted

comment:2 by Tom Goddard, 2 years ago

Resolution: → duplicate
Status: assigned → closed

This error was fixed more than a year ago. Get the current ChimeraX (version 1.6.1) to avoid it. I think the error happens when the Volume Viewer panel is shown and you try to open a session that has no volumes. You can probably avoid it by closing the Volume Viewer panel before you open the new session.

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