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

[bhishem.thakur@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
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 "/Users/bt134/Desktop/DH1285 comparison with open occluded /chimera
> session .cxs"

Opened cryosparc_P23_J20_003_volume_map_sharp(1).mrc as #1, grid size
320,320,320, pixel 1.08, shown at level 1.03, step 1, values float32  
Opened cryosparc_P23_J20_003_volume_map_sharp(1).mrc as #2, grid size
320,320,320, pixel 1.08, shown at level 0.688, step 2, values float32  
Log from Tue Jan 17 11:54:39 2023UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/bt134/Desktop/DH1285 comparison with open occluded /DH1285
> comaprison with open occluded .cxs"

Opened cryosparc_P23_J20_003_volume_map_sharp(1).mrc as #1, grid size
320,320,320, pixel 1.08, shown at level 1.71, step 1, values float32  
Opened cryosparc_P23_J20_003_volume_map_sharp(1).mrc as #2, grid size
320,320,320, pixel 1.08, shown at level 0.688, step 2, values float32  
Log from Thu Jan 12 14:31:37 2023UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/bt134/Downloads/cryosparc_P23_J20_003_volume_map_sharp(1).mrc

Opened cryosparc_P23_J20_003_volume_map_sharp(1).mrc as #1, grid size
320,320,320, pixel 1.08, shown at level 0.688, step 2, values float32  

> volume #1 step 1

> volume #1 level 1.939

> volume #1 level 0.4885

> volume #1 level 1.167

> volume #1 level 0.7679

> open /Users/bt134/Downloads/cryosparc_P23_J20_003_volume_map_sharp(1).mrc

Opened cryosparc_P23_J20_003_volume_map_sharp(1).mrc as #2, grid size
320,320,320, pixel 1.08, shown at level 0.688, step 2, values float32  

> select add #1

2 models selected  

> select subtract #1

Nothing selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> fetch 7lok

Unknown command: fetch 7lok  

> open 7lok

Summary of feedback from opening 7lok fetched from pdb  
---  
notes | Fetching compressed mmCIF 7lok from
http://files.rcsb.org/download/7lok.cif  
Fetching CCD MPT from http://ligand-expo.rcsb.org/reports/M/MPT/MPT.cif  
Fetching CCD DPR from http://ligand-expo.rcsb.org/reports/D/DPR/DPR.cif  
Fetching CCD U2X from http://ligand-expo.rcsb.org/reports/U/U2X/U2X.cif  
  
7lok title:  
Structure of CD4 mimetic M48U1 in complex with BG505 SOSIP.664 HIV-1 Env
trimer and 17b Fab [more info...]  
  
Chain information for 7lok #3  
---  
Chain | Description | UniProt  
A C E | Envelope glycoprotein BG505 SOSIP.664 gp120 | Q2N0S6_9HIV1  
B D F | Envelope Glycoprotein BG505 SOSIP.664 gp41 | Q2N0S6_9HIV1  
G H I | M48U1 |  
J L | 17b Fab Light Chain |  
K M | 17b Fab Heavy Chain |  
  
Non-standard residues in 7lok #3  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
MPT — β-mercaptopropionic acid  
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)  
NH2 — amino group  
  

> hide atoms

> show atoms

> hide atoms

> show cartoons

> select add #3

14492 atoms, 14797 bonds, 15 pseudobonds, 2031 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.13059,0.74731,0.65151,-29.047,0.95008,0.28214,-0.13319,-21.609,-0.28336,0.6016,-0.74686,204.89

> view matrix models
> #3,-0.61262,0.78948,-0.037736,133.5,0.7766,0.59237,-0.21447,-27.631,-0.14696,-0.16069,-0.976,322.99

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.61262,0.78948,-0.037736,136.2,0.7766,0.59237,-0.21447,-12.734,-0.14696,-0.16069,-0.976,363.47

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.30261,-0.47521,-0.8262,288.19,-0.76262,0.39923,-0.50895,282.64,0.5717,0.78409,-0.24159,22.604

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.30261,-0.47521,-0.8262,280.48,-0.76262,0.39923,-0.50895,213.79,0.5717,0.78409,-0.24159,10.445

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.53096,-0.66403,-0.52644,230.71,-0.46506,0.29098,-0.83609,231.14,0.70837,0.68876,-0.15432,-8.7933

> view matrix models
> #3,-0.36264,-0.44608,-0.81824,373.41,0.60124,0.55886,-0.57113,-0.71067,0.71205,-0.69907,0.065536,152.34

> view matrix models
> #3,-0.027697,0.61513,-0.78794,172.38,0.81102,-0.44697,-0.37745,80.68,-0.58436,-0.64949,-0.48651,414.57

> view matrix models
> #3,-0.0010865,0.27036,-0.96276,241.02,0.96052,-0.26757,-0.076223,-8.8081,-0.27822,-0.92483,-0.2594,375.6

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.0010865,0.27036,-0.96276,232.81,0.96052,-0.26757,-0.076223,-43.965,-0.27822,-0.92483,-0.2594,326.67

> volume #1 level 1.712

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.90115,-0.2006,-0.3843,83.488,-0.10155,-0.95951,0.26273,160.88,-0.42144,-0.19774,-0.88503,335.16

> view matrix models
> #3,0.090864,-0.9901,0.10695,243.25,-0.86116,-0.13206,-0.49088,264.39,0.50015,-0.047498,-0.86464,175.52

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.090864,-0.9901,0.10695,255.24,-0.86116,-0.13206,-0.49088,296.98,0.50015,-0.047498,-0.86464,274.06

> view matrix models
> #3,0.090864,-0.9901,0.10695,259.61,-0.86116,-0.13206,-0.49088,349.66,0.50015,-0.047498,-0.86464,307.05

> view matrix models
> #3,0.090864,-0.9901,0.10695,257.31,-0.86116,-0.13206,-0.49088,350.6,0.50015,-0.047498,-0.86464,312.26

> view matrix models
> #3,0.090864,-0.9901,0.10695,272.99,-0.86116,-0.13206,-0.49088,342.68,0.50015,-0.047498,-0.86464,238.71

> view matrix models
> #3,0.090864,-0.9901,0.10695,266.79,-0.86116,-0.13206,-0.49088,319.15,0.50015,-0.047498,-0.86464,196.96

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.20724,-0.97817,0.015569,260.87,-0.68268,-0.156,-0.71387,327.64,0.70071,0.13732,-0.70011,118.49

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.20724,-0.97817,0.015569,275.86,-0.68268,-0.156,-0.71387,388.79,0.70071,0.13732,-0.70011,130.94

> view matrix models
> #3,0.20724,-0.97817,0.015569,281.17,-0.68268,-0.156,-0.71387,393.4,0.70071,0.13732,-0.70011,143.19

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.090819,-0.98425,0.1517,279.96,-0.93738,-0.13592,-0.3207,372.65,0.33627,-0.11307,-0.93495,264.86

> ui tool show "Fit in Map"

> fitmap #3 inMap #1

Fit molecule 7lok (#3) to map cryosparc_P23_J20_003_volume_map_sharp(1).mrc
(#1) using 14492 atoms  
average map value = 0.8631, steps = 92  
shifted from previous position = 2.92  
rotated from previous position = 5.75 degrees  
atoms outside contour = 12937, contour level = 1.7124  
  
Position of 7lok (#3) relative to
cryosparc_P23_J20_003_volume_map_sharp(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.00427831 -0.99048182 0.13757708 294.85716881  
-0.95670082 -0.04409557 -0.28771359 355.62440780  
0.29104162 -0.13038917 -0.94778343 276.72337486  
Axis 0.70752461 -0.69016586 0.15192103  
Axis point 0.00000000 310.75016137 120.86150951  
Rotation angle (degrees) 173.61668886  
Shift along axis 5.21897801  
  

> hide #!1 models

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!1 models

> open 7tfo

Summary of feedback from opening 7tfo fetched from pdb  
---  
note | Fetching compressed mmCIF 7tfo from
http://files.rcsb.org/download/7tfo.cif  
  
7tfo title:  
Cryo-EM structure of HIV-1 Env trimer BG505 SOSIP.664 in complex with CD4bs
antibody Ab1573 [more info...]  
  
Chain information for 7tfo #4  
---  
Chain | Description | UniProt  
A B C | Envelope glycoprotein BG505 SOSIP.664 - gp120 | A0A6H1VH54_9PLVG  
H I P | CD4 binding site antibody Ab1573 - Fab heavy chain |  
J L Q | CD4 binding site antibody Ab1573 - Fab light chain |  
X Y Z | Envelope glycoprotein BG505 SOSIP.664 - gp41 | Q2N0S6_9HIV1  
  
Non-standard residues in 7tfo #4  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
MAN — alpha-D-mannopyranose (alpha-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)  
  

> hide #!4 atoms

> show #!4 cartoons

> select add #4

17774 atoms, 18180 bonds, 32 pseudobonds, 2304 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,21.275,0,1,0,-2.8096,0,0,1,-26.697

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.0037782,0.81227,-0.58328,148.8,0.35625,0.5461,0.75819,-114.37,0.93438,-0.20493,-0.29143,75.259

> view matrix models
> #4,0.30797,0.94606,-0.10066,-8.5884,0.55607,-0.093134,0.8259,-49.776,0.77198,-0.31033,-0.55475,165.4

> view matrix models
> #4,0.51546,0.81643,-0.26027,6.6054,0.52151,-0.057882,0.85128,-54.436,0.67994,-0.57454,-0.45561,208.82

> view matrix models
> #4,0.38124,0.8167,-0.4332,58.487,0.60405,0.13467,0.78548,-89.747,0.69984,-0.56114,-0.44198,200.89

> view matrix models
> #4,0.30468,0.77927,-0.54763,97.216,0.53424,0.33617,0.77561,-110.95,0.78851,-0.52888,-0.31389,158.69

> view matrix models
> #4,0.37216,0.72798,-0.5758,99.647,0.52265,0.3483,0.77815,-111.54,0.76703,-0.59054,-0.25085,161.97

> view matrix models
> #4,0.45454,0.79803,-0.39565,43.087,0.3688,0.23571,0.89913,-87.562,0.81079,-0.55461,-0.18717,137.64

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.45454,0.79803,-0.39565,27.846,0.3688,0.23571,0.89913,-86.062,0.81079,-0.55461,-0.18717,168.84

> view matrix models
> #4,0.45454,0.79803,-0.39565,30.673,0.3688,0.23571,0.89913,-75.67,0.81079,-0.55461,-0.18717,171.39

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.5229,0.74592,-0.41251,31.153,0.52868,0.095809,0.8434,-68.664,0.66864,-0.6591,-0.34425,239.78

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.5229,0.74592,-0.41251,30.976,0.52868,0.095809,0.8434,-69.399,0.66864,-0.6591,-0.34425,239.6

> fitmap #4 inMap #1

Fit molecule 7tfo (#4) to map cryosparc_P23_J20_003_volume_map_sharp(1).mrc
(#1) using 17774 atoms  
average map value = 0.9561, steps = 100  
shifted from previous position = 9.46  
rotated from previous position = 6.24 degrees  
atoms outside contour = 15526, contour level = 1.7124  
  
Position of 7tfo (#4) relative to
cryosparc_P23_J20_003_volume_map_sharp(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.54371381 0.71267947 -0.44324177 35.64510312  
0.47355633 0.17551029 0.86309938 -78.01313546  
0.69290670 -0.67917900 -0.24206650 212.88359113  
Axis -0.79892184 -0.58854085 -0.12386914  
Axis point 0.00000000 49.28160965 143.55590335  
Rotation angle (degrees) 105.15440794  
Shift along axis -8.93344293  
  

> set bgColor white

> volume #1 level 0.9043

> volume #1 level 2.644

> volume #1 level 0.8358

> hide #!1 models

> show #!1 models

> volume #1 level 1.918

> volume #1 level 1.247

> volume #1 level 1.082

> volume #1 level 0.8221

> volume #1 level 1.055

> volume #1 level 0.8221

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> volume #1 level 1.658

> volume #1 level 1.63

> volume #1 level 1.425

> open 6vy2

Summary of feedback from opening 6vy2 fetched from pdb  
---  
note | Fetching compressed mmCIF 6vy2 from
http://files.rcsb.org/download/6vy2.cif  
  
6vy2 title:  
Cryo-EM structure of M1214_N1 Fab in complex with CH505 TF chimeric SOSIP.664
Env trimer [more info...]  
  
Chain information for 6vy2 #5  
---  
Chain | Description | UniProt  
A C E | Glycoprotein 120 | A0A0A7I3C6_9HIV1  
B D F | Glycoprotein 41 | Q2N0S5_9HIV1  
H I J | M1214 N1 Fab heavy chain |  
L M N | M1214 N1 Fab light chain |  
  
Non-standard residues in 6vy2 #5  
---  
BMA — beta-D-mannopyranose  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  

> hide sel atoms

> show sel cartoons

> hide #!4 models

> select subtract #4

Nothing selected  

> hide #!1 models

> hide #!5 atoms

> show #!5 cartoons

> open 8vnl

Fetching url http://files.rcsb.org/download/8vnl.cif failed: HTTP Error 404:
Not Found  

> open 8v8l

Fetching url http://files.rcsb.org/download/8v8l.cif failed: HTTP Error 404:
Not Found  

> open 5v8l

Summary of feedback from opening 5v8l fetched from pdb  
---  
note | Fetching compressed mmCIF 5v8l from
http://files.rcsb.org/download/5v8l.cif  
  
5v8l title:  
BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibodies
3BNC117 and PGT145 [more info...]  
  
Chain information for 5v8l #6  
---  
Chain | Description | UniProt  
A C D | gp120 | Q2N0S6_9HIV1  
B E F | gp41 | Q2N0S6_9HIV1  
G H I | 3BNC117 antibody, heavy chain |  
J | PGT145 antibody, heavy chain |  
K L M | 3BNC117 antibody, light chain |  
N | PGT145 antibody, light chain |  
  
Non-standard residues in 5v8l #6  
---  
BMA — beta-D-mannopyranose  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  

> hide #!5-6 atoms

> show #!5-6 cartoons

> select add #6

22934 atoms, 23602 bonds, 9 pseudobonds, 2792 residues, 2 models selected  

> view matrix models #6,1,0,0,2.7674,0,1,0,-0.58143,0,0,1,6.101

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.83822,0.54276,-0.052973,-57.331,0.543,-0.83966,-0.011001,237.01,-0.050451,-0.019543,-0.99854,364.05

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.83822,0.54276,-0.052973,-41.917,0.543,-0.83966,-0.011001,233.62,-0.050451,-0.019543,-0.99854,400.19

> view matrix models
> #6,0.83822,0.54276,-0.052973,-42.608,0.543,-0.83966,-0.011001,247.45,-0.050451,-0.019543,-0.99854,413.89

> view matrix models
> #6,0.83822,0.54276,-0.052973,-37.988,0.543,-0.83966,-0.011001,252.46,-0.050451,-0.019543,-0.99854,395.8

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.81773,0.57117,-0.071342,-36.146,0.56228,-0.76611,0.31133,179.61,0.12317,-0.2947,-0.94762,404.62

> show #!1 models

> view matrix models
> #6,0.93544,-0.0021275,0.35349,-26.128,-0.22413,-0.77685,0.58844,284.08,0.27336,-0.62968,-0.72717,399.7

> hide #!5 models

> view matrix models
> #6,0.88426,0.16271,0.43774,-61.295,-0.15468,-0.78239,0.60328,269.27,0.44064,-0.60116,-0.66666,352.04

> view matrix models
> #6,-0.27146,0.48864,-0.82918,317.93,-0.90391,-0.42531,0.045284,442.8,-0.33053,0.7618,0.55715,36.831

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.27146,0.48864,-0.82918,264.53,-0.90391,-0.42531,0.045284,503.94,-0.33053,0.7618,0.55715,65.052

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.38041,-0.034453,-0.92418,398.26,-0.17127,-0.9794,0.10701,455.53,-0.90882,0.19899,0.36667,312.27

> view matrix models
> #6,-0.40058,0.21012,-0.89184,351.41,-0.089608,-0.97767,-0.19009,490.85,-0.91187,0.0037677,0.41047,341.32

> view matrix models
> #6,-0.37739,0.16691,-0.91089,358.24,-0.012339,-0.98444,-0.17528,474.77,-0.92597,-0.054909,0.37358,361.2

> view matrix models
> #6,-0.39271,0.23464,-0.88923,344.93,0.012474,-0.96546,-0.26026,481.19,-0.91958,-0.1133,0.37622,370.3

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.39271,0.23464,-0.88923,410.36,0.012474,-0.96546,-0.26026,405.19,-0.91958,-0.1133,0.37622,335.97

> view matrix models
> #6,-0.39271,0.23464,-0.88923,383.24,0.012474,-0.96546,-0.26026,403.09,-0.91958,-0.1133,0.37622,321.95

> view matrix models
> #6,-0.39271,0.23464,-0.88923,396.29,0.012474,-0.96546,-0.26026,407.1,-0.91958,-0.1133,0.37622,306.7

> view matrix models
> #6,-0.39271,0.23464,-0.88923,394.52,0.012474,-0.96546,-0.26026,406.53,-0.91958,-0.1133,0.37622,307.07

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.7262,0.19202,-0.66013,426.6,-0.026658,-0.96735,-0.25205,412.94,-0.68697,-0.16544,0.7076,215.08

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.7262,0.19202,-0.66013,416.86,-0.026658,-0.96735,-0.25205,412.7,-0.68697,-0.16544,0.7076,216.96

> view matrix models
> #6,-0.7262,0.19202,-0.66013,418.89,-0.026658,-0.96735,-0.25205,411.27,-0.68697,-0.16544,0.7076,212.85

> fitmap #6 inMap #1

Fit molecule 5v8l (#6) to map cryosparc_P23_J20_003_volume_map_sharp(1).mrc
(#1) using 22934 atoms  
average map value = 0.7309, steps = 328  
shifted from previous position = 26.7  
rotated from previous position = 41.3 degrees  
atoms outside contour = 19690, contour level = 1.4248  
  
Position of 5v8l (#6) relative to
cryosparc_P23_J20_003_volume_map_sharp(1).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.92617797 0.37283589 -0.05646020 288.34680479  
-0.36321411 -0.92228717 -0.13214338 443.94385354  
-0.10134031 -0.10188115 0.98962132 23.03661996  
Axis 0.04100364 0.06081006 -0.99730679  
Axis point 187.12330200 195.08765485 0.00000000  
Rotation angle (degrees) 158.34488025  
Shift along axis 15.84494024  
  

> volume #1 level 1.096

> hide #!6 models

> show #!6 models

> hide #!1 models

> show #!1 models

> volume #1 level 1.945

> volume #1 level 1.438

> show #!5 models

> hide #!6 models

> select add #5

44360 atoms, 45642 bonds, 12 pseudobonds, 5414 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.41858,-0.62244,-0.66134,557.43,-0.28967,0.78167,-0.55235,215.24,0.86075,-0.039634,-0.50749,125.62,#6,0.68078,0.48538,-0.54859,145.18,0.040346,-0.77265,-0.63355,466,-0.73138,0.40917,-0.54558,344.52

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.41858,-0.62244,-0.66134,542.7,-0.28967,0.78167,-0.55235,253.35,0.86075,-0.039634,-0.50749,48.842,#6,0.68078,0.48538,-0.54859,130.44,0.040346,-0.77265,-0.63355,504.11,-0.73138,0.40917,-0.54558,267.75

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.7761,-0.62622,-0.074338,502.48,-0.52664,0.70846,-0.46981,301.95,0.34687,-0.32547,-0.87963,289.56,#6,0.95379,0.29577,0.053002,-1.0196,0.27805,-0.80189,-0.52882,453.79,-0.11391,0.51912,-0.84708,224.82

> view matrix models
> #5,-0.72529,-0.65625,-0.20805,524.52,-0.6358,0.75441,-0.16314,254.68,0.26402,0.013955,-0.96442,252.51,#6,0.93119,0.35603,-0.078223,19.254,0.33139,-0.91621,-0.22524,402.5,-0.15186,0.18382,-0.97116,312.62

> view matrix models
> #5,-0.60873,-0.79156,0.05364,476.88,-0.79036,0.59915,-0.12789,312.56,0.069098,-0.12025,-0.99034,326.49,#6,0.84587,0.49762,0.19205,-48.82,0.52736,-0.83423,-0.16112,347.71,0.08004,0.23756,-0.96807,270.22

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.60873,-0.79156,0.05364,502.54,-0.79036,0.59915,-0.12789,250.97,0.069098,-0.12025,-0.99034,385.68,#6,0.84587,0.49762,0.19205,-23.161,0.52736,-0.83423,-0.16112,286.11,0.08004,0.23756,-0.96807,329.41

> view matrix models
> #5,-0.60873,-0.79156,0.05364,477.29,-0.79036,0.59915,-0.12789,254.49,0.069098,-0.12025,-0.99034,413.68,#6,0.84587,0.49762,0.19205,-48.404,0.52736,-0.83423,-0.16112,289.64,0.08004,0.23756,-0.96807,357.41

> view matrix models
> #5,-0.60873,-0.79156,0.05364,465.86,-0.79036,0.59915,-0.12789,245.63,0.069098,-0.12025,-0.99034,372.92,#6,0.84587,0.49762,0.19205,-59.842,0.52736,-0.83423,-0.16112,280.78,0.08004,0.23756,-0.96807,316.65

> view matrix models
> #5,-0.60873,-0.79156,0.05364,460.19,-0.79036,0.59915,-0.12789,241.91,0.069098,-0.12025,-0.99034,375.93,#6,0.84587,0.49762,0.19205,-65.511,0.52736,-0.83423,-0.16112,277.06,0.08004,0.23756,-0.96807,319.66

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.66001,-0.6547,0.36844,380.16,-0.57262,0.75588,0.3174,75.733,-0.4863,-0.0014912,-0.87379,444.21,#6,0.81175,0.32021,0.48839,-92.316,0.22364,-0.94297,0.24655,253.5,0.53949,-0.090912,-0.83707,283.2

> fitmap #5 inMap #1

Fit molecule 6vy2 (#5) to map cryosparc_P23_J20_003_volume_map_sharp(1).mrc
(#1) using 21426 atoms  
average map value = 0.749, steps = 312  
shifted from previous position = 11.6  
rotated from previous position = 32 degrees  
atoms outside contour = 18851, contour level = 1.4385  
  
Position of 6vy2 (#5) relative to
cryosparc_P23_J20_003_volume_map_sharp(1).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.58594272 -0.81035179 -0.00105156 464.54135065  
-0.81035082 0.58594365 -0.00125882 219.85835353  
0.00163624 0.00011454 -0.99999865 373.50331866  
Axis 0.45500358 -0.89048955 0.00032125  
Axis point 288.28171996 0.00000000 186.98511115  
Rotation angle (degrees) 179.91353073  
Shift along axis 15.70639529  
  

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> select subtract #5

22934 atoms, 23602 bonds, 9 pseudobonds, 2792 residues, 2 models selected  

> select subtract #6

Nothing selected  

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!1 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 #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!5 models

> volume #1 level 1.055

> volume #1 level 1.836

> volume #1 level 1.589

> volume #1 level 1.055

> select add #4/L:24

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

50 atoms, 49 bonds, 8 residues, 1 model selected  

> select up

834 atoms, 857 bonds, 110 residues, 1 model selected  

> select add #4/H:37

841 atoms, 863 bonds, 111 residues, 1 model selected  

> select up

899 atoms, 924 bonds, 117 residues, 1 model selected  

> select up

1748 atoms, 1790 bonds, 232 residues, 1 model selected  

> show sel surfaces

> volume #1 level 1.137

> hide #!4 models

> save /Users/bt134/Desktop/image52.png supersample 3

> save /Users/bt134/Desktop/image53.png supersample 3

> show #!4 models

> save /Users/bt134/Desktop/image54.png supersample 3

> save /Users/bt134/Desktop/image55.png supersample 3

> save /Users/bt134/Desktop/image56.png supersample 3

> show #!5 models

> hide #!1 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> view matrix models
> #4,0.56043,0.72703,-0.39667,22.426,0.50885,0.075623,0.85753,-65.82,0.65344,-0.68243,-0.32757,234.66

> fitmap #5 inMap #1

Fit molecule 6vy2 (#5) to map cryosparc_P23_J20_003_volume_map_sharp(1).mrc
(#1) using 21426 atoms  
average map value = 0.7489, steps = 28  
shifted from previous position = 0.0152  
rotated from previous position = 0.0243 degrees  
atoms outside contour = 16749, contour level = 1.1371  
  
Position of 6vy2 (#5) relative to
cryosparc_P23_J20_003_volume_map_sharp(1).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.58562853 -0.81057907 -0.00088562 464.50423501  
-0.81057802 0.58562920 -0.00130624 219.98392524  
0.00157746 -0.00004711 -0.99999875 373.54964392  
Axis 0.45517626 -0.89040128 0.00037998  
Axis point 288.33533095 0.00000000 186.99937360  
Rotation angle (degrees) 179.92075242  
Shift along axis 15.69927142  
  

> show #!1 models

> fitmap #5 inMap #1

Fit molecule 6vy2 (#5) to map cryosparc_P23_J20_003_volume_map_sharp(1).mrc
(#1) using 21426 atoms  
average map value = 0.749, steps = 36  
shifted from previous position = 0.0133  
rotated from previous position = 0.0117 degrees  
atoms outside contour = 16752, contour level = 1.1371  
  
Position of 6vy2 (#5) relative to
cryosparc_P23_J20_003_volume_map_sharp(1).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.58554404 -0.81063992 -0.00104586 464.51942382  
-0.81063875 0.58554497 -0.00138061 220.02525704  
0.00173157 0.00003941 -0.99999850 373.49976636  
Axis 0.45522254 -0.89037761 0.00037658  
Axis point 288.34220229 0.00000000 186.99671048  
Rotation angle (degrees) 179.91063598  
Shift along axis 15.69479960  
  

> fitmap #5 inMap #1

Fit molecule 6vy2 (#5) to map cryosparc_P23_J20_003_volume_map_sharp(1).mrc
(#1) using 21426 atoms  
average map value = 0.749, steps = 28  
shifted from previous position = 0.0143  
rotated from previous position = 0.00855 degrees  
atoms outside contour = 16753, contour level = 1.1371  
  
Position of 6vy2 (#5) relative to
cryosparc_P23_J20_003_volume_map_sharp(1).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.58556603 -0.81062419 -0.00092494 464.49219300  
-0.81062315 0.58556676 -0.00129746 220.01422539  
0.00159336 -0.00000997 -0.99999873 373.53916227  
Axis 0.45521057 -0.89038374 0.00036709  
Axis point 288.33914721 -0.00000000 186.99653520  
Rotation angle (degrees) 179.91897413  
Shift along axis 15.68178759  
  

> hide #!1 models

> view matrix models
> #4,0.56057,0.7334,-0.38455,19.232,0.50041,0.069998,0.86296,-64.392,0.65981,-0.67618,-0.32776,232.57

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.56057,0.7334,-0.38455,19.725,0.50041,0.069998,0.86296,-66.522,0.65981,-0.67618,-0.32776,234.27

> select add #4

17774 atoms, 18180 bonds, 32 pseudobonds, 2304 residues, 4 models selected  

> select subtract #4

2 models selected  

> show #!1 models

> volume #1 level 1.712

> hide #!1 models

> save /Users/bt134/Desktop/image53.png supersample 3

> show #!1 models

> save /Users/bt134/Desktop/image54.png supersample 3

> hide #!1 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> save /Users/bt134/Desktop/image55.png supersample 3

> hide #!4 models

> show #!5 models

> show #!4 models

> hide #!4 models

> save /Users/bt134/Desktop/image56.png supersample 3

> show #!4 models

> show #!1 models

> save /Users/bt134/Desktop/image57.png supersample 3

> hide #!4 models

> hide #!5 models

> save /Users/bt134/Desktop/image53.png supersample 3

> show #!5 models

> hide #!5 models

> save "/Users/bt134/Desktop/DH1285 comaprison with open occluded .cxs"

——— End of log from Thu Jan 12 14:31:37 2023 ———

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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  
  

Populating font family aliases took 310 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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.  
  

> show #!4 models

> volume #1 level 1.069

> hide #!4 models

> show #!4 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> hide #!5 models

> show #!3 models

> select add #3

14492 atoms, 14797 bonds, 15 pseudobonds, 2031 residues, 2 models selected  

> color sel bypolymer

> color sel byhetero

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmp_kape63b/ante.in.mol2 -fi
mol2 -o
/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmp_kape63b/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
(HIS) ``  
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`  
(HIS) ``  
(HIS) `Info: Finished reading file
(/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmp_kape63b/ante.in.mol2);
atoms read (19), bonds read (18).`  
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HIS) ``  
(HIS) ``  
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(HIS) `Info: Total number of electrons: 78; net charge: -3`  
(HIS) ``  
(HIS) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(HIS) ``  
(HIS) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(HIS) ``  
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(HIS) ``  
Charges for residue HIS determined  
Assigning partial charges to residue DPR (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmpmfw_b5o5/ante.in.mol2 -fi
mol2 -o
/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmpmfw_b5o5/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(DPR) ``  
(DPR) `Welcome to antechamber 20.0: molecular input file processor.`  
(DPR) ``  
(DPR) `Info: Finished reading file
(/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmpmfw_b5o5/ante.in.mol2);
atoms read (26), bonds read (26).`  
(DPR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(DPR) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(DPR) ``  
(DPR) ``  
(DPR) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(DPR) `Info: Total number of electrons: 92; net charge: 0`  
(DPR) ``  
(DPR) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(DPR) ``  
(DPR) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(DPR) ``  
(DPR) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(DPR) ``  
Charges for residue DPR determined  
Assigning partial charges to residue MPT (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmp7q4e6sy6/ante.in.mol2 -fi
mol2 -o
/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmp7q4e6sy6/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(MPT) ``  
(MPT) `Welcome to antechamber 20.0: molecular input file processor.`  
(MPT) ``  
(MPT) `Info: Finished reading file
(/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmp7q4e6sy6/ante.in.mol2);
atoms read (15), bonds read (14).`  
(MPT) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(MPT) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(MPT) ``  
(MPT) ``  
(MPT) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(MPT) `Info: Total number of electrons: 48; net charge: 0`  
(MPT) ``  
(MPT) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(MPT) ``  
(MPT) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(MPT) ``  
(MPT) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(MPT) ``  
Charges for residue MPT determined  
Assigning partial charges to residue U2X (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmppely1l6s/ante.in.mol2 -fi
mol2 -o
/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmppely1l6s/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(U2X) ``  
(U2X) `Welcome to antechamber 20.0: molecular input file processor.`  
(U2X) ``  
(U2X) `Info: Finished reading file
(/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmppely1l6s/ante.in.mol2);
atoms read (52), bonds read (53).`  
(U2X) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(U2X) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(U2X) ``  
(U2X) ``  
(U2X) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(U2X) `Info: Total number of electrons: 180; net charge: 0`  
(U2X) ``  
(U2X) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(U2X) ``  
(U2X) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(U2X) ``  
(U2X) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(U2X) ``  
Charges for residue U2X determined  
Assigning partial charges to residue MPT+CYS (net charge +0) with am1-bcc
method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmpzmzp28vx/ante.in.mol2 -fi
mol2 -o
/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmpzmzp28vx/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(MPT+CYS) ``  
(MPT+CYS) `Welcome to antechamber 20.0: molecular input file processor.`  
(MPT+CYS) ``  
(MPT+CYS) `Info: Finished reading file
(/var/folders/91/zk_5t7ss6j52jf5cfv13_d6w0000gp/T/tmpzmzp28vx/ante.in.mol2);
atoms read (37), bonds read (36).`  
(MPT+CYS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(MPT+CYS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(MPT+CYS) ``  
(MPT+CYS) ``  
(MPT+CYS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(MPT+CYS) `Info: Total number of electrons: 156; net charge: 0`  
(MPT+CYS) ``  
(MPT+CYS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(MPT+CYS) ``  
(MPT+CYS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(MPT+CYS) ``  
(MPT+CYS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(MPT+CYS) ``  
Charges for residue MPT+CYS determined  
Coulombic values for 7lok_A SES surface #3.2: minimum, -19.44, mean -0.81,
maximum 12.82  
Coulombic values for 7lok_B SES surface #3.3: minimum, -20.70, mean -0.89,
maximum 10.01  
Coulombic values for 7lok_C SES surface #3.4: minimum, -16.44, mean -0.71,
maximum 12.49  
Coulombic values for 7lok_D SES surface #3.5: minimum, -16.36, mean -0.63,
maximum 9.71  
Coulombic values for 7lok_E SES surface #3.6: minimum, -39.79, mean -8.55,
maximum 4.16  
Coulombic values for 7lok_F SES surface #3.7: minimum, -22.72, mean -2.58,
maximum 6.30  
Coulombic values for 7lok_G SES surface #3.8: minimum, -2.30, mean 2.50,
maximum 8.79  
Coulombic values for 7lok_H SES surface #3.9: minimum, -2.38, mean 2.57,
maximum 8.79  
Coulombic values for 7lok_I SES surface #3.10: minimum, -23.65, mean -6.58,
maximum 1.90  
Coulombic values for 7lok_J SES surface #3.11: minimum, -10.76, mean 0.02,
maximum 10.01  
Coulombic values for 7lok_K SES surface #3.12: minimum, -21.20, mean -1.72,
maximum 12.83  
Coulombic values for 7lok_L SES surface #3.13: minimum, -10.02, mean 0.28,
maximum 9.67  
Coulombic values for 7lok_M SES surface #3.14: minimum, -17.87, mean -1.51,
maximum 12.40  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select subtract #3

13 models selected  

> volume #1 level 1.712

> volume #1 level 0.7673

> volume #1 level 1.041

> select add #3

14492 atoms, 14797 bonds, 15 pseudobonds, 2031 residues, 2 models selected  

> show sel surfaces

> surface

> select subtract #3

13 models selected  

> hide #!1 models

> coulombic #!3

Coulombic values for 7lok_A SES surface #3.2: minimum, -19.44, mean -0.81,
maximum 12.82  
Coulombic values for 7lok_B SES surface #3.3: minimum, -20.70, mean -0.89,
maximum 10.01  
Coulombic values for 7lok_C SES surface #3.4: minimum, -16.44, mean -0.71,
maximum 12.49  
Coulombic values for 7lok_D SES surface #3.5: minimum, -16.36, mean -0.63,
maximum 9.71  
Coulombic values for 7lok_E SES surface #3.6: minimum, -39.79, mean -8.55,
maximum 4.16  
Coulombic values for 7lok_F SES surface #3.7: minimum, -22.72, mean -2.58,
maximum 6.30  
Coulombic values for 7lok_G SES surface #3.8: minimum, -2.30, mean 2.50,
maximum 8.79  
Coulombic values for 7lok_H SES surface #3.9: minimum, -2.38, mean 2.57,
maximum 8.79  
Coulombic values for 7lok_I SES surface #3.10: minimum, -23.65, mean -6.58,
maximum 1.90  
Coulombic values for 7lok_J SES surface #3.11: minimum, -10.76, mean 0.02,
maximum 10.01  
Coulombic values for 7lok_K SES surface #3.12: minimum, -21.20, mean -1.72,
maximum 12.83  
Coulombic values for 7lok_L SES surface #3.13: minimum, -10.02, mean 0.28,
maximum 9.67  
Coulombic values for 7lok_M SES surface #3.14: minimum, -17.87, mean -1.51,
maximum 12.40  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic #!3

Coulombic values for 7lok_A SES surface #3.2: minimum, -19.44, mean -0.81,
maximum 12.82  
Coulombic values for 7lok_B SES surface #3.3: minimum, -20.70, mean -0.89,
maximum 10.01  
Coulombic values for 7lok_C SES surface #3.4: minimum, -16.44, mean -0.71,
maximum 12.49  
Coulombic values for 7lok_D SES surface #3.5: minimum, -16.36, mean -0.63,
maximum 9.71  
Coulombic values for 7lok_E SES surface #3.6: minimum, -39.79, mean -8.55,
maximum 4.16  
Coulombic values for 7lok_F SES surface #3.7: minimum, -22.72, mean -2.58,
maximum 6.30  
Coulombic values for 7lok_G SES surface #3.8: minimum, -2.30, mean 2.50,
maximum 8.79  
Coulombic values for 7lok_H SES surface #3.9: minimum, -2.38, mean 2.57,
maximum 8.79  
Coulombic values for 7lok_I SES surface #3.10: minimum, -23.65, mean -6.58,
maximum 1.90  
Coulombic values for 7lok_J SES surface #3.11: minimum, -10.76, mean 0.02,
maximum 10.01  
Coulombic values for 7lok_K SES surface #3.12: minimum, -21.20, mean -1.72,
maximum 12.83  
Coulombic values for 7lok_L SES surface #3.13: minimum, -10.02, mean 0.28,
maximum 9.67  
Coulombic values for 7lok_M SES surface #3.14: minimum, -17.87, mean -1.51,
maximum 12.40  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select add #3

14492 atoms, 14797 bonds, 15 pseudobonds, 2031 residues, 2 models selected  

> mlp sel

Map values for surface "7lok_A SES surface": minimum -27.73, mean -4.474,
maximum 23.6  
Map values for surface "7lok_B SES surface": minimum -28.14, mean -2.653,
maximum 22.8  
Map values for surface "7lok_C SES surface": minimum -27.38, mean -4.204,
maximum 23.62  
Map values for surface "7lok_D SES surface": minimum -27.86, mean -2.494,
maximum 22.56  
Map values for surface "7lok_E SES surface": minimum -27.97, mean -9.859,
maximum 7.163  
Map values for surface "7lok_F SES surface": minimum -25.55, mean -9.252,
maximum 5.033  
Map values for surface "7lok_G SES surface": minimum -24.08, mean 16.82,
maximum 161.2  
Map values for surface "7lok_H SES surface": minimum -24.53, mean 16.84,
maximum 147.7  
Map values for surface "7lok_I SES surface": minimum -24.56, mean 15.64,
maximum 149.4  
Map values for surface "7lok_J SES surface": minimum -27.04, mean -5.444,
maximum 23.4  
Map values for surface "7lok_K SES surface": minimum -26.83, mean -4.048,
maximum 24.19  
Map values for surface "7lok_L SES surface": minimum -25.95, mean -4.671,
maximum 22.4  
Map values for surface "7lok_M SES surface": minimum -27.43, mean -4.131,
maximum 23.08  
To also show corresponding color key, enter the above mlp command and add key
true  

> color sel bychain

> show #!1 models

> volume #1 level 0.8495

> volume #1 level 0.9728

> select subtract #3

13 models selected  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!4 models

> save /Users/bt134/Desktop/image1.png supersample 3

> hide #!1 models

> save /Users/bt134/Desktop/image2.png supersample 3

> show #!1 models

> hide #!4 models

> save /Users/bt134/Desktop/image3.png supersample 3

> show #!4 models

> volume #1 level 0.9317

> hide #!4 models

> show #!4 models

> hide #!1 models

> hide #!4 cartoons

> show #!4 cartoons

> style #!4 stick

Changed 17774 atom styles  

> hide #!4 cartoons

> show #!4 atoms

> hide surfaces

> hide #!4 cartoons

> select add #4

17774 atoms, 18180 bonds, 32 pseudobonds, 2304 residues, 2 models selected  

> show sel cartoons

> hide sticks

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show sel atoms

> hide sel atoms

> select subtract #4

12 models selected  

> save /Users/bt134/Desktop/image4.png supersample 3

> show #!3 models

> hide #!3 models

> show #!5 models

> hide #!5 models

> save /Users/bt134/Desktop/image5.png supersample 3

> show #!5 models

> hide #!4 models

> select add #5

21426 atoms, 22040 bonds, 3 pseudobonds, 2622 residues, 2 models selected  

> color sel bychain

> select subtract #5

12 models selected  

> save /Users/bt134/Desktop/image6.png supersample 3

> show #!4 models

> set bgColor white

> save /Users/bt134/Desktop/image7.png supersample 3

> show #!1 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> volume #1 level 1.274

> volume #1 level 1.534

> ui tool show "Fit in Map"

> fitmap #4 inMap #1

Fit molecule 7tfo (#4) to map cryosparc_P23_J20_003_volume_map_sharp(1).mrc
(#1) using 17774 atoms  
average map value = 0.9561, steps = 100  
shifted from previous position = 2.67  
rotated from previous position = 6.35 degrees  
atoms outside contour = 14499, contour level = 1.5344  
  
Position of 7tfo (#4) relative to
cryosparc_P23_J20_003_volume_map_sharp(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.54379815 0.71263251 -0.44321380 35.63858772  
0.47340022 0.17559377 0.86316804 -78.01106927  
0.69294719 -0.67920669 -0.24187282 212.85373229  
Axis -0.79893125 -0.58851750 -0.12391940  
Axis point 0.00000000 49.28937720 143.54802473  
Rotation angle (degrees) 105.14367884  
Shift along axis -8.93860919  
  

> fitmap #5 inMap #1

Fit molecule 6vy2 (#5) to map cryosparc_P23_J20_003_volume_map_sharp(1).mrc
(#1) using 21426 atoms  
average map value = 0.749, steps = 36  
shifted from previous position = 0.00649  
rotated from previous position = 0.00512 degrees  
atoms outside contour = 19346, contour level = 1.5344  
  
Position of 6vy2 (#5) relative to
cryosparc_P23_J20_003_volume_map_sharp(1).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.58559245 -0.81060512 -0.00090287 464.48906233  
-0.81060421 0.58559315 -0.00121715 219.98187151  
0.00151534 0.00001912 -0.99999885 373.54950000  
Axis 0.45519609 -0.89039115 0.00033637  
Axis point 288.33294792 0.00000000 186.99067929  
Rotation angle (degrees) 179.92219505  
Shift along axis 15.68934332  
  

> volume #1 level 1.904

> save /Users/bt134/Desktop/image8.png supersample 3

> save /Users/bt134/Desktop/image9.png supersample 3

> hide #!5 models

> hide #!1 models

> select add #4

17774 atoms, 18180 bonds, 32 pseudobonds, 2304 residues, 2 models selected  

> mlp sel

Map values for surface "7tfo_A SES surface": minimum -29.5, mean -4.546,
maximum 26.78  
Map values for surface "7tfo_B SES surface": minimum -29.92, mean -4.413,
maximum 24.84  
Map values for surface "7tfo_C SES surface": minimum -29.32, mean -4.1,
maximum 26.15  
Map values for surface "7tfo_H SES surface": minimum -26.36, mean -4.587,
maximum 22.48  
Map values for surface "7tfo_I SES surface": minimum -25.09, mean -4.363,
maximum 22.18  
Map values for surface "7tfo_J SES surface": minimum -27.25, mean -5.031,
maximum 24.46  
Map values for surface "7tfo_L SES surface": minimum -32.59, mean -5.135,
maximum 22.79  
Map values for surface "7tfo_P SES surface": minimum -25.2, mean -3.991,
maximum 23.62  
Map values for surface "7tfo_Q SES surface": minimum -29.16, mean -5.854,
maximum 23.3  
Map values for surface "7tfo_X SES surface": minimum -27.85, mean -2.548,
maximum 23.3  
Map values for surface "7tfo_Y SES surface": minimum -25.82, mean -2.922,
maximum 22.35  
Map values for surface "7tfo_Z SES surface": minimum -26.84, mean -2.754,
maximum 22.98  
To also show corresponding color key, enter the above mlp command and add key
true  

> show sel surfaces

> color sel bychain

> show #!1 models

> volume #1 level 1.233

> volume #1 level 1.028

> set bgColor white

> hide #!4 models

> select subtract #4

12 models selected  

> save /Users/bt134/Desktop/image10.png supersample 3

> show #!4 models

> hide #!1 models

> save /Users/bt134/Desktop/image11.png supersample 3

> show #!1 models

> save /Users/bt134/Desktop/image10.png supersample 3

> hide #!1 models

> show #!1 models

> hide #!4 models

> save "/Users/bt134/Desktop/DH1285 comparison with open occluded /chimera
> session .cxs"

——— End of log from Tue Jan 17 11:54:39 2023 ———

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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  
  

Populating font family aliases took 294 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.5.1 (21G83)
      Kernel Version: Darwin 21.6.0
      Time since boot: 54 days 4:25

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    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-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
    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
    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: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    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

[Tom Goddard]

This was fixed 7 months ago. The fix is in the current ChimeraX 1.5.

Duplicate of #7103.