id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16055	Crash moving window between screens	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-14.6.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 22895 fromDatabase emdb format ccp4

Summary of feedback from opening 22895 fetched from emdb  
---  
notes | Fetching compressed map 22895 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22895/map/emd_22895.map.gz  
Fetching map header 22895 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22895/header/emd-22895.xml  
  
Opened emdb 22895 as #1, grid size 300,300,300, pixel 2.17, shown at level
0.05, step 2, values float32  

> close session

> open 7ao8 fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 7ao8 fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
notes | Fetching compressed 7ao8 bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/7ao8-assembly-1.cif.gz  
Fetching CCD IHP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/IHP/IHP.cif  
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif  
Fetching CCD K from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/K/K.cif  
  
7ao8 bioassembly 1 title:  
Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex [more info...]  
  
Chain information for 7ao8 bioassembly 1 #1  
---  
Chain | Description  
A | Methyl-CpG-binding domain protein 2  
B C | Metastasis-associated protein MTA1  
D E | Histone deacetylase 1  
  
Non-standard residues in 7ao8 bioassembly 1 #1  
---  
IHP — (IHP)  
K — (K)  
ZN — (ZN)  
  
Opened 1 biological assemblies for 7ao8  

> select

10905 atoms, 11152 bonds, 8 pseudobonds, 1358 residues, 2 models selected  

> surface hidePatches (#!1 & sel)

> cartoon hide (#!1 & sel)

> hide (#!1 & sel) target a

> show (#!1 & sel) target ab

> color sel bypolymer

> color sel bychain

> color sel byhetero

> rainbow sel

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A MET 150  
/A LYS 161  
/A LYS 167  
/A SER 171  
/A LYS 174  
/A ARG 195  
/A LYS 212  
/B LYS 182  
/B GLU 183  
/B GLU 185  
/B ARG 193  
/B HIS 239  
/B ASP 334  
/B ARG 335  
/B GLN 339  
/B LYS 340  
/C LYS 182  
/C GLU 183  
/C GLU 185  
/C ARG 193  
/C HIS 239  
/C ASP 334  
/C ARG 335  
/C GLN 339  
/C LYS 340  
/D LYS 74  
/D ARG 80  
/D LYS 89  
/D GLU 108  
/D ASN 349  
/E LYS 74  
/E ARG 80  
/E LYS 89  
/E GLU 108  
/E ASN 349  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 7ao8 bioassembly 1_A SES surface #1.2: minimum, -8.35,
mean 1.20, maximum 14.50  
Coulombic values for 7ao8 bioassembly 1_B SES surface #1.3: minimum, -19.19,
mean -2.62, maximum 10.83  
Coulombic values for 7ao8 bioassembly 1_C SES surface #1.4: minimum, -19.54,
mean -2.62, maximum 10.95  
Coulombic values for 7ao8 bioassembly 1_D SES surface #1.5: minimum, -21.06,
mean -1.85, maximum 13.50  
Coulombic values for 7ao8 bioassembly 1_E SES surface #1.6: minimum, -21.19,
mean -1.85, maximum 13.91  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp sel

Map values for surface ""7ao8 bioassembly 1_A SES surface"": minimum -29.29,
mean -5.537, maximum 19.02  
Map values for surface ""7ao8 bioassembly 1_B SES surface"": minimum -33.44,
mean -4.484, maximum 23.82  
Map values for surface ""7ao8 bioassembly 1_C SES surface"": minimum -33.16,
mean -4.426, maximum 23.76  
Map values for surface ""7ao8 bioassembly 1_D SES surface"": minimum -31.16,
mean -4.932, maximum 21.93  
Map values for surface ""7ao8 bioassembly 1_E SES surface"": minimum -30.62,
mean -4.957, maximum 21.47  
To also show corresponding color key, enter the above mlp command and add key
true  

> select

10905 atoms, 11152 bonds, 8 pseudobonds, 1358 residues, 2 models selected  

> hide (#!1 & sel) target a

> surface hidePatches (#!1 & sel)

> cartoon (#!1 & sel)

> set bgColor white

> set bgColor #ffffff00

> select clear

> select

10905 atoms, 11152 bonds, 8 pseudobonds, 1358 residues, 2 models selected  

> cartoon style (#!1 & sel) modeHelix tube sides 20

> cartoon style (#!1 & sel & coil) xsection oval

> cartoon style (#!1 & sel) xsection barbell modeHelix default

> cartoon style (#!1 & sel) modeHelix tube sides 20

> select clear

> select /D/E

5928 atoms, 6084 bonds, 738 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel dark salmon

> select /B/C

4412 atoms, 4496 bonds, 8 pseudobonds, 548 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel medium aquamarine

> color sel olive

> color sel lime green

> color sel forest green

> color sel medium sea green

> color sel sea green

> color sel olive drab

> color sel medium aquamarine

> color sel light sea green

> color sel sea green

> select /A

487 atoms, 500 bonds, 64 residues, 1 model selected  

> color sel deep sky blue

> select clear

> select

10905 atoms, 11152 bonds, 8 pseudobonds, 1358 residues, 2 models selected  

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> select clear

> save ""/Users/mahesh/Desktop/7AO8 HDAC1-MTA1-MBD2.cxs""

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

> open 11837 fromDatabase emdb format ccp4

Summary of feedback from opening 11837 fetched from emdb  
---  
notes | Fetching compressed map 11837 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11837/map/emd_11837.map.gz  
Fetching map header 11837 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11837/header/emd-11837.xml  
  
Opened emdb 11837 as #2, grid size 300,300,300, pixel 1.09, shown at level
0.01, step 2, values float32, fit PDB 7ao8  

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting soft

> transparency 50

> surface dust #2 size 10.9

> fitmap #1 inMap #2

Fit molecule 7ao8 bioassembly 1 (#1) to map emdb 11837 (#2) using 10905 atoms  
average map value = 0.01372, steps = 40  
shifted from previous position = 0.108  
rotated from previous position = 0.433 degrees  
atoms outside contour = 2740, contour level = 0.01  
  
Position of 7ao8 bioassembly 1 (#1) relative to emdb 11837 (#2) coordinates:  
Matrix rotation and translation  
0.99999838 -0.00040214 0.00175640 -0.22730647  
0.00041502 0.99997301 -0.00733480 1.04537688  
-0.00175340 0.00733552 0.99997156 -0.81881106  
Axis 0.97112974 0.23233792 0.05409358  
Axis point 0.00000000 112.01316108 142.81256742  
Rotation angle (degrees) 0.43277190  
Shift along axis -0.02215581  
  

> vop gaussian #2 sdev 3.27

Opened emdb 11837 gaussian as #3, grid size 300,300,300, pixel 1.09, shown at
step 1, values float32  

> undo

> vop gaussian #3 sdev 3.27

Opened emdb 11837 gaussian as #4, grid size 300,300,300, pixel 1.09, shown at
step 1, values float32  

> fitmap #1 inMap #4

Fit molecule 7ao8 bioassembly 1 (#1) to map emdb 11837 gaussian (#4) using
10905 atoms  
average map value = 0.01102, steps = 56  
shifted from previous position = 0.178  
rotated from previous position = 2.33 degrees  
atoms outside contour = 327, contour level = 0.0057979  
  
Position of 7ao8 bioassembly 1 (#1) relative to emdb 11837 gaussian (#4)
coordinates:  
Matrix rotation and translation  
0.99991161 0.01092539 -0.00757739 -0.45477356  
-0.01068805 0.99947198 0.03068439 -3.24350914  
0.00790863 -0.03060069 0.99950040 3.92324664  
Axis -0.91738182 -0.23181168 -0.32353353  
Axis point -0.00000000 125.37484276 108.62010700  
Rotation angle (degrees) 1.91415905  
Shift along axis -0.10021753  
  

> hide #!4 models

> show #!2 models

> hide #!3 target m

> lighting flat

> lighting full

> lighting soft

> select clear

> graphics silhouettes false

> surface dust #2 size 10.9

> volume zone #2 nearAtoms #1 range 6.54

> volume #!2 region all imageMode ""full region""

> volume unzone #!2

> mousemode rightMode ""crop volume""

> volume #2 orthoplanes xyz positionPlanes 150,150,150 style image region all

> mousemode rightMode ""move planes""

> volume #2 style image region all imageMode ""tilted slab"" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 163.5 tiltedSlabSpacing 1.09 tiltedSlabPlaneCount 10

> mousemode rightMode ""rotate slab""

> volume #!2 planes z style image imageMode ""full region""

> mousemode rightMode ""move planes""

> volume #!2 step 2

> volume #!2 step 1

> volume #!2 showOutlineBox false

> volume #!2 showOutlineBox true

> transparency #1.2-6 0

> volume #!2 style image

> volume #!2 style mesh

> volume #!2 style surface

> fitmap #1 inMap #2

Fit molecule 7ao8 bioassembly 1 (#1) to map emdb 11837 (#2) using 10905 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 10905, contour level = 0.01  
  
Position of 7ao8 bioassembly 1 (#1) relative to emdb 11837 (#2) coordinates:  
Matrix rotation and translation  
0.99991161 0.01092539 -0.00757739 -0.45477356  
-0.01068805 0.99947198 0.03068439 -3.24350914  
0.00790863 -0.03060069 0.99950040 3.92324664  
Axis -0.91738182 -0.23181168 -0.32353353  
Axis point -0.00000000 125.37484276 108.62010700  
Rotation angle (degrees) 1.91415905  
Shift along axis -0.10021753  
  

> volume zone #2 nearAtoms #1 range 6.54

> fitmap #1 inMap #2

Fit molecule 7ao8 bioassembly 1 (#1) to map emdb 11837 (#2) using 10905 atoms  
average map value = 0.01372, steps = 84  
shifted from previous position = 0.17  
rotated from previous position = 2.35 degrees  
atoms outside contour = 3538, contour level = 0.01  
  
Position of 7ao8 bioassembly 1 (#1) relative to emdb 11837 (#2) coordinates:  
Matrix rotation and translation  
0.99999837 -0.00041146 0.00175879 -0.21424317  
0.00042479 0.99997111 -0.00758967 1.08464848  
-0.00175562 0.00759040 0.99996965 -0.85893578  
Axis 0.97283184 0.22522462 0.05359187  
Axis point 0.00000000 113.65990138 142.78019786  
Rotation angle (degrees) 0.44702617  
Shift along axis -0.01016501  
  

> vop gaussian #2 sdev 3.27

Opened emdb 11837 gaussian as #5, grid size 300,300,300, pixel 1.09, shown at
step 1, values float32  

> hide #!5 models

> close session

> open 21382 fromDatabase emdb format ccp4

Summary of feedback from opening 21382 fetched from emdb  
---  
notes | Fetching compressed map 21382 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-21382/map/emd_21382.map.gz  
Fetching map header 21382 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-21382/header/emd-21382.xml  
  
Opened emdb 21382 as #1, grid size 148,148,148, pixel 2.79, shown at level
0.12, step 1, values float32  

> transparency 50

> volume hide

> volume show

> volume style surface

> volume style mesh

> cartoon

> select

2 models selected  
No visible atoms or bonds selected  

> close session

> open 22906 fromDatabase emdb format ccp4

Summary of feedback from opening 22906 fetched from emdb  
---  
notes | Fetching compressed map 22906 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22906/map/emd_22906.map.gz  
Fetching map header 22906 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22906/header/emd-22906.xml  
  
Opened emdb 22906 as #1, grid size 256,256,256, pixel 2.4, shown at level
0.309, step 1, values float32  

> open 22895 fromDatabase emdb format ccp4

Opened emdb 22895 as #2, grid size 300,300,300, pixel 2.17, shown at level
0.05, step 2, values float32  

> transparency 50

> transparency 0

> volume showOutlineBox true

> volume region all imageMode ""full region""

> volume unzone

> mousemode rightMode ""crop volume""

> volume region all imageMode ""full region""

> volume unzone

> mousemode rightMode ""crop volume""

Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 2 maps.  

Hide dust shortcut requires a displayed map surface  

> fitmap #1 inMap #2

Fit map emdb 22906 in map emdb 22895 using 129614 points  
correlation = 0.8164, correlation about mean = 0.2136, overlap = 2.192e+05  
steps = 316, shift = 31.3, angle = 19.5 degrees  
  
Position of emdb 22906 (#1) relative to emdb 22895 (#2) coordinates:  
Matrix rotation and translation  
0.98705471 0.14422045 0.07016744 -42.95438264  
-0.11713550 0.94708340 -0.29885164 167.00769044  
-0.10955494 0.28676382 0.95171646 -52.66959165  
Axis 0.87930593 0.26985448 -0.39242789  
Axis point 0.00000000 228.42765842 493.13138733  
Rotation angle (degrees) 19.45088577  
Shift along axis 27.96674605  
  

> vop subtract #1 #2 minrms True

Opened volume difference as #3, grid size 256,256,256, pixel 2.4, shown at
step 1, values float32  
Minimum RMS scale factor for ""emdb 22895 #2"" above level 0.05 is 0.32815  
  

> vop gaussian #3 sdev 7.2

Opened volume difference gaussian as #4, grid size 256,256,256, pixel 2.4,
shown at step 1, values float32  

> volume show

> volume style surface

> volume style mesh

> volume style image

> volume showOutlineBox false

> volume step 1

> volume step 2

> volume planes z style image imageMode ""full region""

> mousemode rightMode ""move planes""

> volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 307.2 tiltedSlabSpacing 2.4 tiltedSlabPlaneCount 10

> mousemode rightMode ""rotate slab""

> volume #2 style image region all imageMode ""tilted slab"" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 325.5 tiltedSlabSpacing 2.17 tiltedSlabPlaneCount 10

> mousemode rightMode ""rotate slab""

> volume #3 style image region all imageMode ""tilted slab"" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 307.2 tiltedSlabSpacing 2.4 tiltedSlabPlaneCount 10

> mousemode rightMode ""rotate slab""

> volume #4 style image region all imageMode ""tilted slab"" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 307.2 tiltedSlabSpacing 2.4 tiltedSlabPlaneCount 10

> mousemode rightMode ""rotate slab""

> volume #1 orthoplanes xyz positionPlanes 128,128,128 style image region all

> mousemode rightMode ""move planes""

> volume #2 orthoplanes xyz positionPlanes 150,150,150 style image region all

> mousemode rightMode ""move planes""

> volume #3 orthoplanes xyz positionPlanes 128,128,128 style image region all

> mousemode rightMode ""move planes""

> volume #4 orthoplanes xyz positionPlanes 128,128,128 style image region all

> mousemode rightMode ""move planes""

> volume region all imageMode ""full region""

> volume unzone

> mousemode rightMode ""crop volume""

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 4 maps.  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 4 maps.  

Hide dust shortcut requires a displayed map surface  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 4 maps.  

> lighting full

> lighting soft

> lighting simple

> volume #1 level -0.127,0 level 0.1448,0.8 level 3.236,1

> volume #1 level -0.127,0 level 0.6492,0.7846 level 3.236,1

> volume #2 level -0.09525,0 level 0.2742,0.8 level 4.668,1

> volume #2 level -0.09525,0 level 0.4796,0.6769 level 4.668,1

> volume #3 level -0.127,0 level -0.0887,0.7538 level 3.236,1

> close session

> open 22906 format ccp4 fromDatabase emdb

Opened emdb 22906 as #1, grid size 256,256,256, pixel 2.4, shown at level
0.309, step 1, values float32  

> graphics silhouettes true

> lighting flat

> graphics silhouettes false

> lighting full

> open 22895 fromDatabase emdb format ccp4

Opened emdb 22895 as #2, grid size 300,300,300, pixel 2.17, shown at level
0.05, step 2, values float32  

> lighting full

> transparency 40

> surface

No atomic models open.  

> lighting full

> lighting simple

> lighting soft

> lighting simple

> view

> ui tool show ""Side View""

> volume #1 level 0.309

> volume #1 level 0.3328

> color magenta

> undo

> volume #1 color #4f8f00

> volume #2 color #ff85ff

> volume #1 style mesh

> volume #2 style mesh

> volume #1 step 4

> volume #1 step 1

> volume #2 step 1

> volume #1 style image

> volume #1 style mesh

> volume #1 style image maximumIntensityProjection true

> volume #1 style mesh maximumIntensityProjection false

> volume #2 style image colorMode opaque8 showOutlineBox true imageMode ""box
> faces""

> volume #2 style mesh

> save /Users/mahesh/Desktop/22906_22895.cxs

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

> save ""/Users/mahesh/Desktop/NURD grant/22906_22895.cxs""

> close session

> open 4pzs fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 4pzs fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
notes | Fetching compressed 4pzs bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/4pzs-assembly-1.cif.gz  
Fetching CCD ACO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/ACO/ACO.cif  
Fetching CCD DMS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/DMS/DMS.cif  
  
4pzs bioassembly 1 title:  
Crystal structure of p300 histone acetyltransferase domain in complex with
Acetyl-Coenzyme A [more info...]  
  
Chain information for 4pzs bioassembly 1 #1  
---  
Chain | Description  
A | Histone acetyltransferase p300  
  
Non-standard residues in 4pzs bioassembly 1 #1  
---  
ACO — (ACO)  
DMS — (DMS)  
  
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Opened 1 biological assemblies for 4pzs  

> ui tool show ""Show Sequence Viewer""

> close session

> open 4bhw fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 4bhw fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
notes | Fetching compressed 4bhw bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/4bhw-assembly-1.cif.gz  
Fetching CCD 01K from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/01K/01K.cif  
  
4bhw bioassembly 1 title:  
Structural basis for autoinhibition of the acetyltransferase activity of p300
[more info...]  
  
Chain information for 4bhw bioassembly 1 #1  
---  
Chain | Description  
A B | HISTONE ACETYLTRANSFERASE P300  
  
Non-standard residues in 4bhw bioassembly 1 #1  
---  
01K — (01K)  
ZN — (ZN)  
  
Opened 1 biological assemblies for 4bhw  

> save ""/Users/mahesh/Desktop/NURD grant/p300 4bhw.cxs""

> close session

> open 4pzs format mmcif fromDatabase pdbe_bio

Summary of feedback from opening 4pzs fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
4pzs bioassembly 1 title:  
Crystal structure of p300 histone acetyltransferase domain in complex with
Acetyl-Coenzyme A [more info...]  
  
Chain information for 4pzs bioassembly 1 #1  
---  
Chain | Description  
A | Histone acetyltransferase p300  
  
Non-standard residues in 4pzs bioassembly 1 #1  
---  
ACO — (ACO)  
DMS — (DMS)  
  
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Opened 1 biological assemblies for 4pzs  

> save ""/Users/mahesh/Desktop/NURD grant/p300 4pzs.cxs""

> close session

> open 5u7g fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 5u7g fetched from pdbe_bio  
---  
warnings | Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
notes | Fetching compressed 5u7g bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/5u7g-assembly-1.cif.gz  
Fetching compressed 5u7g bioassembly 2 from
https://www.ebi.ac.uk/pdbe/static/entry/download/5u7g-assembly-2.cif.gz  
  
5u7g bioassembly 1 title:  
Crystal Structure of the Catalytic Core of CBP [more info...]  
  
Chain information for 5u7g bioassembly 1 #1.1  
---  
Chain | Description  
A | CREB-binding protein  
  
Non-standard residues in 5u7g bioassembly 1 #1.1  
---  
ZN — (ZN)  
  
5u7g bioassembly 1 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
5u7g bioassembly 2 title:  
Crystal Structure of the Catalytic Core of CBP [more info...]  
  
Chain information for 5u7g bioassembly 2 #1.2  
---  
Chain | Description  
B | CREB-binding protein  
  
Non-standard residues in 5u7g bioassembly 2 #1.2  
---  
ZN — (ZN)  
  
5u7g bioassembly 2 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
Opened 2 biological assemblies for 5u7g  

> select #1.1/A

4426 atoms, 4554 bonds, 3 pseudobonds, 547 residues, 2 models selected  

> hide (#!1.1 & sel) target a

> cartoon hide (#!1.1 & sel)

> hide (#!1.1 & sel) target a

> select #1.1/A

4426 atoms, 4554 bonds, 3 pseudobonds, 547 residues, 2 models selected  

> hide (#!1.1 & sel) target a

> ui tool show ""Show Sequence Viewer""

> sequence chain #1.1/A #1.2/B

Alignment identifier is 1  


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 570X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 96 GB
      System Firmware Version: 2022.100.22.0.0
      OS Loader Version: 580.140.1~8
      SMC Version (system): 2.46f12

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 44 days, 13 hours, 56 minutes

Graphics/Displays:

    Radeon Pro 570X:

      Chipset Model: Radeon Pro 570X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c5
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A14GL-003
      EFI Driver Version: 01.B1.042
      Metal Support: Metal 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG FULL HD:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 005NTBKDQ053
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 0.00


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX