id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10248 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ 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. 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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) Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG HDR 4K: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 24-Bit Color (ARGB8888) Display Serial Number: 207NTZN5F837 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 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 }}} " defect closed normal Window Toolkit duplicate Tom Goddard all ChimeraX