![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#16055 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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.
{"app_name":"ChimeraX","timestamp":"2024-10-02 10:42:15.00 -0600","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"4EB002F5-1525-4D9A-887D-371BF802B21D"}
{
"uptime" : 1000000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "iMac19,1",
"coalitionID" : 107904,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-10-02 10:42:06.0312 -0600",
"codeSigningMonitor" : 0,
"incident" : "4EB002F5-1525-4D9A-887D-371BF802B21D",
"pid" : 11719,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-01 15:39:39.9533 -0600",
"procStartAbsTime" : 969320950236179,
"procExitAbsTime" : 1004751359983197,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"225424A9-C9E6-5B82-AFD7-C573F2E77FB5","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E7D81971-9911-088E-6B51-0EF6CC3630EC",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 3482,
"sleepWakeUUID" : "6FABD13A-6AC5-4C5F-B5AA-1075C01808D0",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000002, 0x0000000000000000","rawCodes":[2,0],"type":"EXC_BREAKPOINT","signal":"SIGTRAP"},
"termination" : {"flags":0,"code":5,"namespace":"SIGNAL","indicator":"Trace\/BPT trap: 5","byProc":"exc handler","byPid":11719},
"os_fault" : {"process":"ChimeraX"},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"name" : "Python",
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"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21172216,
"uuid" : "d0e19a37-f677-32b5-b3d2-005e60b90f7f",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=3.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 880K 53 \nColorSync 252K 31 \nCoreAnimation 2944K 193 \nCoreGraphics 32K 5 \nCoreImage 24K 2 \nCoreServices 820K 3 \nCoreUI image data 5528K 48 \nFoundation 32K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 2.4G 109 \nMALLOC guard page 48K 12 \nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.2M 49 \nStack 329.9M 49 \nVM_ALLOCATE 341.8M 360 \nVM_ALLOCATE (reserved) 192.0M 3 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 46.0M 836 \n__DATA_CONST 60.3M 434 \n__DATA_DIRTY 1691K 221 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 219.5M 223 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2201K 2 \n__TEXT 1.1G 833 \ndyld private memory 40K 2 \nmapped file 261.6M 81 \nshared memory 3508K 28 \n=========== ======= ======= \nTOTAL 5.0G 3597 \nTOTAL, minus reserved VM space 4.8G 3597 \n",
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"logWritingSignature" : "39f331149a618a3d25e804068401d33d0c5777c2",
"trialInfo" : {
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{
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{
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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
Change History (2)
comment:1 by , 13 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Qt crash in _NSViewHierarchyDidChangeBackingProperties.