![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 23 months ago
Closed 23 months ago
#10248 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x000000011048a600 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-11-28 13:25:39.00 +0100","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.7 (21G816)","incident_id":"00BE7926-A156-44E4-9FF6-822F50D2FEB1","name":"ChimeraX"}
{
"uptime" : 810000,
"procLaunch" : "2023-11-20 11:33:37.3430 +0100",
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro12,1",
"procStartAbsTime" : 659919973367556,
"coalitionID" : 114577,
"osVersion" : {
"train" : "macOS 12.7",
"build" : "21G816",
"releaseType" : "User"
},
"captureTime" : "2023-11-28 13:23:52.6663 +0100",
"incident" : "00BE7926-A156-44E4-9FF6-822F50D2FEB1",
"bug_type" : "309",
"pid" : 14959,
"procExitAbsTime" : 810501534407151,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"F93C0818-210B-5DA0-BC02-1703ACB91413","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7C72D90F-AD47-C6BD-95F2-72B35F33DB67",
"wakeTime" : 634,
"sleepWakeUUID" : "172C205F-9D7D-4350-8E26-1F217A00E569",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737487241192\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffef0000-7fffffef1000 [ 4K] r-x\/r-x SM=ALI ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"ktriageinfo" : "VM - Fault hit memory shortage\nVM - Fault hit memory shortage\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737487241192\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffef0000-7fffffef1000 [ 4K] r-x\/r-x SM=ALI ",
"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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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7ogt
7ogt title:
Folded elbow of cohesin [more info...]
Chain information for 7ogt #1
---
Chain | Description | UniProt
A | Structural maintenance of chromosomes protein 1 | SMC1_YEAST 1-1225
B | Structural maintenance of chromosomes protein 3 | SMC3_YEAST 1-1230
> close 7ogt
Expected a models specifier or a keyword
> close #1
> open 6qja
Summary of feedback from opening 6qja fetched from pdb
---
note | Fetching compressed mmCIF 6qja from
http://files.rcsb.org/download/6qja.cif
6qja title:
Organizational principles of the NuMA-Dynein interaction interface and
implications for mitotic spindle functions [more info...]
Chain information for 6qja #1
---
Chain | Description | UniProt
A B C D | Nuclear mitotic apparatus protein 1 | NUMA1_HUMAN 1-153
Non-standard residues in 6qja #1
---
CL — chloride ion
MG — magnesium ion
6qja mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
> close #1
> open 6qj4
Summary of feedback from opening 6qj4 fetched from pdb
---
note | Fetching compressed mmCIF 6qj4 from
http://files.rcsb.org/download/6qj4.cif
6qj4 title:
Crystal structure of the C. thermophilum condensin Ycs4-Brn1 subcomplex bound
to the Smc4 ATPase head in complex with the C-terminal domain of Brn1 [more
info...]
Chain information for 6qj4 #1
---
Chain | Description | UniProt
A | Condensin complex subunit 1,Condensin complex subunit 1,Condensin complex
subunit 1 | G0SB82_CHATD 3-1165
B | Condensin complex subunit 2 | G0SBJ6_CHATD 225-418
C | Uncharacterized protein,Uncharacterized protein | G0S2G2_CHATD 263-1359
1366-1542
D | Brn1 |
E | Condensin complex subunit 2 | G0SBJ6_CHATD 764-898
> show cartoons
> style stick
Changed 10778 atom styles
> style stick
Changed 10778 atom styles
> hide atoms
> select /D:1-24
110 atoms, 109 bonds, 22 residues, 1 model selected
> sequence chain #1/C
Alignment identifier is 1/C
> open 4rsi
4rsi title:
Yeast Smc2-Smc4 hinge domain with extended coiled coils [more info...]
Chain information for 4rsi #2
---
Chain | Description | UniProt
A | Structural maintenance of chromosomes protein 2 | SMC2_YEAST 396-792
B | Structural maintenance of chromosomes protein 4 | SMC4_YEAST 555-951
Non-standard residues in 4rsi #2
---
PO4 — phosphate ion
> close #1
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A LYS 453
/A CYS 455
/A LYS 461
/A ARG 463
/A GLU 468
/A ASP 478
/A GLN 481
/A ARG 482
/A GLN 561
/A GLU 636
/A GLU 674
/A SER 675
/A LYS 713
/A ASP 720
/A LYS 732
/A ARG 733
/A LEU 735
/A ASP 736
/A ASN 738
/B GLU 557
/B GLU 559
/B LYS 568
/B LYS 588
/B LYS 735
/B ASN 760
/B LYS 771
/B GLN 794
/B ASN 796
/B LYS 802
/B ASN 826
/B HIS 827
/B LYS 830
/B LEU 835
/B LYS 842
/B ASP 844
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-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/c2/l6rjqpc95g91z6fc7868svyc0000gp/T/tmpl2ko0186/ante.in.mol2 -fi
mol2 -o
/var/folders/c2/l6rjqpc95g91z6fc7868svyc0000gp/T/tmpl2ko0186/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/c2/l6rjqpc95g91z6fc7868svyc0000gp/T/tmpl2ko0186/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-1.6.1.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-1.6.1.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-1.6.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 29
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 49
| QMMM: diag iterations used for timing = 20
| QMMM:
| QMMM: Internal diag routine = 0.006508 seconds
| QMMM: Dspev diag routine = 0.008240 seconds
| QMMM: Dspevd diag routine = 0.007440 seconds
| QMMM: Dspevx diag routine = 0.026270 seconds
| QMMM: Dsyev diag routine = 0.008981 seconds
| QMMM: Dsyevd diag routine = 0.009691 seconds
| QMMM: Dsyevr diag routine = 0.008926 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.002045 seconds
| QMMM:
| QMMM: Using internal diagonalization routine (diag_routine=1).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 N 38.8440 -17.8230 -0.5060
QMMM: 2 2 C 37.9530 -18.8950 -0.9680
QMMM: 3 3 C 37.7120 -18.7060 -2.4510
QMMM: 4 4 O 37.5100 -17.5750 -2.9100
QMMM: 5 5 C 36.6200 -18.8830 -0.2130
QMMM: 6 6 H 38.6920 -16.8790 -0.8300
QMMM: 7 7 H 38.4420 -19.8560 -0.8080
QMMM: 8 8 C 39.8470 -18.0710 0.3300
QMMM: 9 9 C 40.8160 -16.9220 0.6170
QMMM: 10 10 H 40.3020 -15.9610 0.4650
QMMM: 11 11 H 41.1660 -16.9890 1.6580
QMMM: 12 12 H 41.6770 -16.9890 -0.0650
QMMM: 13 13 N 37.7660 -19.7930 -3.2120
QMMM: 14 14 C 37.2870 -19.7340 -4.5900
QMMM: 15 15 H 37.1800 -18.6830 -4.8970
QMMM: 16 16 H 36.3110 -20.2370 -4.6610
QMMM: 17 17 H 38.0080 -20.2380 -5.2510
QMMM: 18 18 H 38.1360 -20.6560 -2.8400
QMMM: 19 19 O 39.9980 -19.1730 0.8750
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1977E+06 DeltaE = -0.3242E-07 DeltaP = 0.4091E-05
QMMM: Smallest DeltaE = -0.7072E-08 DeltaP = 0.6205E-05 Step = 998
Failure running ANTECHAMBER for residue HIS Check reply log for details
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A LYS 453
/A CYS 455
/A LYS 461
/A ARG 463
/A GLU 468
/A ASP 478
/A GLN 481
/A ARG 482
/A GLN 561
/A GLU 636
/A GLU 674
/A SER 675
/A LYS 713
/A ASP 720
/A LYS 732
/A ARG 733
/A LEU 735
/A ASP 736
/A ASN 738
/B GLU 557
/B GLU 559
/B LYS 568
/B LYS 588
/B LYS 735
/B ASN 760
/B LYS 771
/B GLN 794
/B ASN 796
/B LYS 802
/B ASN 826
/B HIS 827
/B LYS 830
/B LEU 835
/B LYS 842
/B ASP 844
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-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/c2/l6rjqpc95g91z6fc7868svyc0000gp/T/tmpkdsi88k8/ante.in.mol2 -fi
mol2 -o
/var/folders/c2/l6rjqpc95g91z6fc7868svyc0000gp/T/tmpkdsi88k8/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/c2/l6rjqpc95g91z6fc7868svyc0000gp/T/tmpkdsi88k8/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-1.6.1.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-1.6.1.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-1.6.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 29
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 49
| QMMM: diag iterations used for timing = 20
| QMMM:
| QMMM: Internal diag routine = 0.007706 seconds
| QMMM: Dspev diag routine = 0.008894 seconds
| QMMM: Dspevd diag routine = 0.008195 seconds
| QMMM: Dspevx diag routine = 0.027486 seconds
| QMMM: Dsyev diag routine = 0.009930 seconds
| QMMM: Dsyevd diag routine = 0.015255 seconds
| QMMM: Dsyevr diag routine = 0.016710 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.004647 seconds
| QMMM:
| QMMM: Using internal diagonalization routine (diag_routine=1).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 N 38.8440 -17.8230 -0.5060
QMMM: 2 2 C 37.9530 -18.8950 -0.9680
QMMM: 3 3 C 37.7120 -18.7060 -2.4510
QMMM: 4 4 O 37.5100 -17.5750 -2.9100
QMMM: 5 5 C 36.6200 -18.8830 -0.2130
QMMM: 6 6 H 38.6920 -16.8790 -0.8300
QMMM: 7 7 H 38.4420 -19.8560 -0.8080
QMMM: 8 8 C 39.8470 -18.0710 0.3300
QMMM: 9 9 C 40.8160 -16.9220 0.6170
QMMM: 10 10 H 40.3020 -15.9610 0.4650
QMMM: 11 11 H 41.1660 -16.9890 1.6580
QMMM: 12 12 H 41.6770 -16.9890 -0.0650
QMMM: 13 13 O 39.9980 -19.1730 0.8750
QMMM: 14 14 N 37.7660 -19.7930 -3.2120
QMMM: 15 15 C 37.2870 -19.7340 -4.5900
QMMM: 16 16 H 37.1800 -18.6830 -4.8970
QMMM: 17 17 H 36.3110 -20.2370 -4.6610
QMMM: 18 18 H 38.0080 -20.2380 -5.2510
QMMM: 19 19 H 38.1360 -20.6560 -2.8400
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1977E+06 DeltaE = -0.3233E-07 DeltaP = 0.4091E-05
QMMM: Smallest DeltaE = -0.7130E-08 DeltaP = 0.5405E-05 Step = 995
Failure running ANTECHAMBER for residue HIS Check reply log for details
> mlp
Map values for surface "4rsi_A SES surface": minimum -28.69, mean -4.761,
maximum 23.53
Map values for surface "4rsi_B SES surface": minimum -27.89, mean -4.469,
maximum 22.8
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A LYS 453
/A CYS 455
/A LYS 461
/A ARG 463
/A GLU 468
/A ASP 478
/A GLN 481
/A ARG 482
/A GLN 561
/A GLU 636
/A GLU 674
/A SER 675
/A LYS 713
/A ASP 720
/A LYS 732
/A ARG 733
/A LEU 735
/A ASP 736
/A ASN 738
/B GLU 557
/B GLU 559
/B LYS 568
/B LYS 588
/B LYS 735
/B ASN 760
/B LYS 771
/B GLN 794
/B ASN 796
/B LYS 802
/B ASN 826
/B HIS 827
/B LYS 830
/B LEU 835
/B LYS 842
/B ASP 844
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-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/c2/l6rjqpc95g91z6fc7868svyc0000gp/T/tmp97pjnhwg/ante.in.mol2 -fi
mol2 -o
/var/folders/c2/l6rjqpc95g91z6fc7868svyc0000gp/T/tmp97pjnhwg/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/c2/l6rjqpc95g91z6fc7868svyc0000gp/T/tmp97pjnhwg/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-1.6.1.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-1.6.1.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-1.6.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 29
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 49
| QMMM: diag iterations used for timing = 20
| QMMM:
| QMMM: Internal diag routine = 0.007202 seconds
| QMMM: Dspev diag routine = 0.008899 seconds
| QMMM: Dspevd diag routine = 0.007962 seconds
| QMMM: Dspevx diag routine = 0.028778 seconds
| QMMM: Dsyev diag routine = 0.010690 seconds
| QMMM: Dsyevd diag routine = 0.009436 seconds
| QMMM: Dsyevr diag routine = 0.009307 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.002033 seconds
| QMMM:
| QMMM: Using internal diagonalization routine (diag_routine=1).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 N 38.8440 -17.8230 -0.5060
QMMM: 2 2 C 37.9530 -18.8950 -0.9680
QMMM: 3 3 C 37.7120 -18.7060 -2.4510
QMMM: 4 4 O 37.5100 -17.5750 -2.9100
QMMM: 5 5 C 36.6200 -18.8830 -0.2130
QMMM: 6 6 H 38.6920 -16.8790 -0.8300
QMMM: 7 7 H 38.4420 -19.8560 -0.8080
QMMM: 8 8 C 39.8470 -18.0710 0.3300
QMMM: 9 9 C 40.8160 -16.9220 0.6170
QMMM: 10 10 H 40.3020 -15.9610 0.4650
QMMM: 11 11 H 41.1660 -16.9890 1.6580
QMMM: 12 12 H 41.6770 -16.9890 -0.0650
QMMM: 13 13 O 39.9980 -19.1730 0.8750
QMMM: 14 14 N 37.7660 -19.7930 -3.2120
QMMM: 15 15 C 37.2870 -19.7340 -4.5900
QMMM: 16 16 H 37.1800 -18.6830 -4.8970
QMMM: 17 17 H 36.3110 -20.2370 -4.6610
QMMM: 18 18 H 38.0080 -20.2380 -5.2510
QMMM: 19 19 H 38.1360 -20.6560 -2.8400
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1977E+06 DeltaE = -0.3233E-07 DeltaP = 0.4091E-05
QMMM: Smallest DeltaE = -0.7130E-08 DeltaP = 0.5405E-05 Step = 995
Failure running ANTECHAMBER for residue HIS Check reply log for details
> open 6wge
Summary of feedback from opening 6wge fetched from pdb
---
notes | Fetching compressed mmCIF 6wge from
http://files.rcsb.org/download/6wge.cif
Fetching CCD ANP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ANP/ANP.cif
6wge title:
Cryo-EM structure of human Cohesin-NIPBL-DNA complex without STAG1 [more
info...]
Chain information for 6wge #1
---
Chain | Description | UniProt
A | Structural maintenance of chromosomes protein 1A | SMC1A_HUMAN 1-1233
B | Structural maintenance of chromosomes protein 3 | SMC3_HUMAN 1-1217
C | Double-strand-break repair protein rad21 homolog | RAD21_HUMAN 1-631
E | Nipped-B-like protein | NIPBL_HUMAN 1163-2804
F | DNA (43-MER) |
G | DNA (43-MER) |
Non-standard residues in 6wge #1
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
> cloise #1
Unknown command: cloise #1
> close #1
> close #2
> open 6wge
6wge title:
Cryo-EM structure of human Cohesin-NIPBL-DNA complex without STAG1 [more
info...]
Chain information for 6wge #1
---
Chain | Description | UniProt
A | Structural maintenance of chromosomes protein 1A | SMC1A_HUMAN 1-1233
B | Structural maintenance of chromosomes protein 3 | SMC3_HUMAN 1-1217
C | Double-strand-break repair protein rad21 homolog | RAD21_HUMAN 1-631
E | Nipped-B-like protein | NIPBL_HUMAN 1163-2804
F | DNA (43-MER) |
G | DNA (43-MER) |
Non-standard residues in 6wge #1
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
> show cartoons
> hide atoms
> style stick
Changed 20194 atom styles
> show atoms
> hide atoms
> select :ANP
62 atoms, 66 bonds, 2 residues, 1 model selected
> style sel stick
Changed 62 atom styles
> show sel atoms
> close #1
> open 6wg3
Summary of feedback from opening 6wg3 fetched from pdb
---
note | Fetching compressed mmCIF 6wg3 from
http://files.rcsb.org/download/6wg3.cif
6wg3 title:
Cryo-EM structure of human Cohesin-NIPBL-DNA complex [more info...]
Chain information for 6wg3 #1
---
Chain | Description | UniProt
A | Structural maintenance of chromosomes protein 1A | SMC1A_HUMAN 1-1233
B | Structural maintenance of chromosomes protein 3 | SMC3_HUMAN 1-1217
C | Double-strand-break repair protein rad21 homolog | RAD21_HUMAN 1-631
D | Cohesin subunit SA-1 | STAG1_HUMAN 1-1258
E | Nipped-B-like protein | NIPBL_HUMAN 1163-2804
F | DNA (51-MER) |
G | DNA (51-MER) |
Non-standard residues in 6wg3 #1
---
ANP — phosphoaminophosphonic acid-adenylate ester
> \
Unknown command: \
> hide atoms
> show cartoons
> sequence chain #1/E
Alignment identifier is 1/E
> select #1D
Expected an objects specifier or a keyword
> select #1/E
9865 atoms, 10021 bonds, 11 pseudobonds, 1226 residues, 2 models selected
> unselect #1/E
Unknown command: unselect #1/E
> deselect #1/E
Unknown command: deselect #1/E
> select all
31683 atoms, 32431 bonds, 124 pseudobonds, 3764 residues, 3 models selected
> clear selection
Unknown command: clear selection
> select none
Expected an objects specifier or a keyword
> select
31683 atoms, 32431 bonds, 124 pseudobonds, 3764 residues, 3 models selected
> cs
Unknown command: cs
> clear
Unknown command: clear
> clear
Unknown command: clear
> close
> open 6wg3
6wg3 title:
Cryo-EM structure of human Cohesin-NIPBL-DNA complex [more info...]
Chain information for 6wg3 #1
---
Chain | Description | UniProt
A | Structural maintenance of chromosomes protein 1A | SMC1A_HUMAN 1-1233
B | Structural maintenance of chromosomes protein 3 | SMC3_HUMAN 1-1217
C | Double-strand-break repair protein rad21 homolog | RAD21_HUMAN 1-631
D | Cohesin subunit SA-1 | STAG1_HUMAN 1-1258
E | Nipped-B-like protein | NIPBL_HUMAN 1163-2804
F | DNA (51-MER) |
G | DNA (51-MER) |
Non-standard residues in 6wg3 #1
---
ANP — phosphoaminophosphonic acid-adenylate ester
> hide atoms
> show cartoons
> show atoms
> hide atoms
> close all
> open 6yuf]
'6yuf]' has no suffix
> open 6yuf
Summary of feedback from opening 6yuf fetched from pdb
---
notes | Fetching compressed mmCIF 6yuf from
http://files.rcsb.org/download/6yuf.cif
Fetching CCD BEF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/BEF/BEF.cif
Fetching CCD ADP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ADP/ADP.cif
6yuf title:
Cohesin complex with loader gripping DNA [more info...]
Chain information for 6yuf #1
---
Chain | Description | UniProt
A | Structural maintenance of chromosomes protein 1 | SMC1_SCHPO 1-1228
B | Cohesin subunit rad21 | RAD21_SCHPO 1-628
C | Structural maintenance of chromosomes protein 3 | SMC3_SCHPO 1-1194
D | Sister chromatid cohesion protein mis4 | MIS4_SCHPO 1-1587
X | DNA (32-MER) |
Y | DNA (32-MER) |
Non-standard residues in 6yuf #1
---
ADP — adenosine-5'-diphosphate
BEF — beryllium trifluoride ion
> show cartoons
> hide atoms
> close
> open 7w1m
Summary of feedback from opening 7w1m fetched from pdb
---
notes | Fetching compressed mmCIF 7w1m from
http://files.rcsb.org/download/7w1m.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
7w1m title:
Cryo-EM structure of human cohesin-CTCF-DNA complex [more info...]
Chain information for 7w1m #1
---
Chain | Description | UniProt
A | Structural maintenance of chromosomes protein 1A | SMC1A_HUMAN 1-1233
B | Structural maintenance of chromosomes protein 3 | SMC3_HUMAN 1-1217
C | Double-strand-break repair protein rad21 homolog | RAD21_HUMAN 1-631
D | Cohesin subunit SA-1 | STAG1_HUMAN 1-1258
E | Nipped-B-like protein | NIPBL_HUMAN 1164-2630
F | DNA (118-MER) |
G | DNA (118-MER) |
H | Transcriptional repressor CTCF | CTCF_HUMAN 1-727
Non-standard residues in 7w1m #1
---
ADP — adenosine-5'-diphosphate
BEF — beryllium trifluoride ion
ZN — zinc ion
> show cartoons
> hide atoms
> close all
> open 2q1r
Summary of feedback from opening 2q1r fetched from pdb
---
note | Fetching compressed mmCIF 2q1r from
http://files.rcsb.org/download/2q1r.cif
2q1r title:
Crystal Structure Analysis of the RNA Dodecamer CGCGAAUUAGCG, with a G-A
mismatch. [more info...]
Chain information for 2q1r #1
---
Chain | Description
A | RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*AP*GP*CP*G)-3')
Non-standard residues in 2q1r #1
---
MG — magnesium ion
2q1r mmCIF Assemblies
---
1| author_defined_assembly
> hide cartoons
> hide atoms
> show atoms
> nucleotides ladder
> nucleotides atoms
> style nucleic stick
Changed 255 atom styles
> close
> open 6wg3
6wg3 title:
Cryo-EM structure of human Cohesin-NIPBL-DNA complex [more info...]
Chain information for 6wg3 #1
---
Chain | Description | UniProt
A | Structural maintenance of chromosomes protein 1A | SMC1A_HUMAN 1-1233
B | Structural maintenance of chromosomes protein 3 | SMC3_HUMAN 1-1217
C | Double-strand-break repair protein rad21 homolog | RAD21_HUMAN 1-631
D | Cohesin subunit SA-1 | STAG1_HUMAN 1-1258
E | Nipped-B-like protein | NIPBL_HUMAN 1163-2804
F | DNA (51-MER) |
G | DNA (51-MER) |
Non-standard residues in 6wg3 #1
---
ANP — phosphoaminophosphonic acid-adenylate ester
> show atoms
> hide atoms
> show cartoons
> show atoms
> hide atoms
> select #1/D
7580 atoms, 7715 bonds, 3 pseudobonds, 932 residues, 2 models selected
> style sel stick
Changed 7580 atom styles
> show sel atoms
> select #1/G
1020 atoms, 1121 bonds, 51 residues, 1 model selected
> show sel atoms
> select #1/F
1071 atoms, 1223 bonds, 51 residues, 1 model selected
> show sel atoms
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.8.6
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro12,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2,7 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 481.0.0.0.0
OS Loader Version: 540.120.3~37
SMC Version (system): 2.28f7
Software:
System Software Overview:
System Version: macOS 12.7 (21G816)
Kernel Version: Darwin 21.6.0
Time since boot: 58 days 2:15
Graphics/Displays:
Intel Iris Graphics 6100:
Chipset Model: Intel Iris Graphics 6100
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x162b
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
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Online: Yes
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LG HDR 4K:
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UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
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parso: 0.8.3
pep517: 0.13.0
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pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
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PyQt6-sip: 13.4.1
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qtconsole: 5.4.0
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scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 23 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 23 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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