id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14435 Charge failure otrunsch@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Uploaded the ""NTG.mol2"" file. Selected ""Tools, Structure editing, Dock Prep"" Selected Pubchem:89909564 #1.1 and clicked ""OK"" for all the following windows. (Describe the actions that caused this problem to occur here) Log: 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 ""C:/Users/olive/Desktop/Wyoming/Information/Molegro/Compund Model > files/Focus compounds/NTG.mol2"" Opened NTG.mol2 containing 2 structures (140 atoms, 146 bonds) > ui tool show ""Dock Prep"" > hide #1.2 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.2 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.2 models > ui tool show ""Dock Prep"" Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs Summary of feedback from adding hydrogens to pubchem:89909564 #1.1 --- notes | Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds 0 hydrogens added Closest equivalent command: addcharge #1.1 standardizeResidues none Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue UNL (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\olive\AppData\Local\Temp\tmppi32dmig\ante.in.mol2 -fi mol2 -o C:\Users\olive\AppData\Local\Temp\tmppi32dmig\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (UNL) `` (UNL) `Welcome to antechamber 20.0: molecular input file processor.` (UNL) `` (UNL) `Info: Finished reading file (C:\Users\olive\AppData\Local\Temp\tmppi32dmig\ante.in.mol2); atoms read (70), bonds read (73).` (UNL) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (UNL) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/bondtype"" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `` (UNL) `` (UNL) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `Info: Total number of electrons: 284; net charge: 0` (UNL) `` (UNL) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm"" -O -i sqm.in -o sqm.out` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `/usr/bin/antechamber: Fatal Error!` (UNL) `Cannot properly run """"C:/Program Files/ChimeraX/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 =104 | QMMM: *** Selected Hamiltonian *** | QMMM: AM1 | QMMM: *** Parameter sets in use *** | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: C : 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 = 184 | QMMM: diag iterations used for timing = 5 | QMMM: | QMMM: Internal diag routine = 0.081402 seconds | QMMM: Dspev diag routine = 0.071848 seconds | QMMM: Dspevd diag routine = 0.055359 seconds | QMMM: Dspevx diag routine = 0.238989 seconds | QMMM: Dsyev diag routine = 0.078126 seconds | QMMM: Dsyevd diag routine = 0.058881 seconds | QMMM: Dsyevr diag routine = 0.060725 seconds | QMMM: | QMMM: Pseudo diag routine = 0.035736 seconds | QMMM: | QMMM: Using dspevd routine (diag_routine=3). QMMM: QM Region Cartesian Coordinates (*=link atom) QMMM: QM_NO. MM_NO. ATOM X Y Z QMMM: 1 1 O 6.8670 -1.5870 0.0000 QMMM: 2 2 O 5.5580 0.3640 0.0000 QMMM: 3 3 O 5.1350 -1.5870 0.0000 QMMM: 4 4 O 6.8670 -3.5870 0.0000 QMMM: 5 5 O 5.1350 -4.5870 0.0000 QMMM: 6 6 O 3.4030 -3.5870 0.0000 QMMM: 7 7 O 4.8720 -0.4830 0.0000 QMMM: 8 8 O 2.5370 -2.0870 0.0000 QMMM: 9 9 O 10.1360 -3.4700 0.0000 QMMM: 10 10 O 10.4450 3.2470 0.0000 QMMM: 11 11 O 8.6500 -4.8090 0.0000 QMMM: 12 12 O 8.9590 4.5850 0.0000 QMMM: 13 13 C 6.8670 -0.5870 0.0000 QMMM: 14 14 C 7.1760 0.3640 0.0000 QMMM: 15 15 C 6.0010 -2.0870 0.0000 QMMM: 16 16 C 7.8180 -0.8960 0.0000 QMMM: 17 17 C 6.3670 0.9520 0.0000 QMMM: 18 18 C 8.1270 0.6730 0.0000 QMMM: 19 19 C 6.0010 -3.0870 0.0000 QMMM: 20 20 C 5.8670 -0.5870 0.0000 QMMM: 21 21 C 5.1350 -3.5870 0.0000 QMMM: 22 22 C 4.2690 -3.0870 0.0000 QMMM: 23 23 C 4.2690 -2.0870 0.0000 QMMM: 24 24 C 8.0260 -1.8740 0.0000 QMMM: 25 25 C 8.3350 1.6510 0.0000 QMMM: 26 26 C 3.4030 -1.5870 0.0000 QMMM: 27 27 C 8.9770 -2.1830 0.0000 QMMM: 28 28 C 7.2830 -2.5430 0.0000 QMMM: 29 29 C 9.2860 1.9600 0.0000 QMMM: 30 30 C 7.5920 2.3200 0.0000 QMMM: 31 31 C 9.1850 -3.1620 0.0000 QMMM: 32 32 C 7.4910 -3.5220 0.0000 QMMM: 33 33 C 9.4940 2.9380 0.0000 QMMM: 34 34 C 7.8000 3.2980 0.0000 QMMM: 35 35 C 8.4420 -3.8310 0.0000 QMMM: 36 36 C 8.7510 3.6070 0.0000 QMMM: 37 37 C 10.8790 -2.8010 0.0000 QMMM: 38 38 C 10.6530 4.2250 0.0000 QMMM: 39 39 H 7.2730 0.9760 0.0000 QMMM: 40 40 H 6.0010 -1.4670 0.0000 QMMM: 41 41 H 8.4380 -0.8750 0.0000 QMMM: 42 42 H 7.9040 -0.2820 0.0000 QMMM: 43 43 H 6.7820 1.4120 0.0000 QMMM: 44 44 H 5.9520 1.4120 0.0000 QMMM: 45 45 H 8.2130 0.0590 0.0000 QMMM: 46 46 H 8.7470 0.6510 0.0000 QMMM: 47 47 H 6.0010 -3.7070 0.0000 QMMM: 48 48 H 4.5980 -3.8970 0.0000 QMMM: 49 49 H 4.2690 -3.7070 0.0000 QMMM: 50 50 H 4.2690 -1.4670 0.0000 QMMM: 51 51 H 3.8010 -1.1120 0.0000 QMMM: 52 52 H 3.0040 -1.1120 0.0000 QMMM: 53 53 H 6.8670 -4.2070 0.0000 QMMM: 54 54 H 4.5980 -4.8970 0.0000 QMMM: 55 55 H 3.4030 -4.2070 0.0000 QMMM: 56 56 H 9.4380 -1.7680 0.0000 QMMM: 57 57 H 6.6930 -2.3520 0.0000 QMMM: 58 58 H 9.7470 1.5450 0.0000 QMMM: 59 59 H 7.0020 2.1290 0.0000 QMMM: 60 60 H 7.0300 -3.9370 0.0000 QMMM: 61 61 H 2.0000 -1.7770 0.0000 QMMM: 62 62 H 7.3390 3.7130 0.0000 QMMM: 63 63 H 9.2390 -5.0000 0.0000 QMMM: 64 64 H 8.4980 5.0000 0.0000 QMMM: 65 65 H 11.2940 -3.2620 0.0000 QMMM: 66 66 H 11.3400 -2.3860 0.0000 QMMM: 67 67 H 10.4640 -2.3410 0.0000 QMMM: 68 68 H 11.2590 4.0960 0.0000 QMMM: 69 69 H 10.7820 4.8320 0.0000 QMMM: 70 70 H 10.0460 4.3540 0.0000 -------------------------------------------------------------------------------- RESULTS -------------------------------------------------------------------------------- QMMM: ERROR! QMMM: Unable to achieve self consistency to the tolerances specified QMMM: No convergence in SCF after 1000 steps. QMMM: E = -0.1974E+07 DeltaE = 0.2157E+01 DeltaP = 0.4873E-01 QMMM: Smallest DeltaE = -0.3257E-02 DeltaP = 0.1499E-01 Step = 26 Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\tool.py"", line 263, in add_charges add_nonstandard_res_charges(self.session, residues, charge, method=method) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\charge.py"", line 319, in add_nonstandard_res_charges nonstd_charge(session, tautomer_residues, net_charge, method, status=status) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\charge.py"", line 602, in nonstd_charge raise ChargeError(ante_failure_msg) chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for residue UNL Check reply log for details chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for residue UNL Check reply log for details File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\charge.py"", line 602, in nonstd_charge raise ChargeError(ante_failure_msg) See log for complete Python traceback. > ui tool show ""Dock Prep"" Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs Summary of feedback from adding hydrogens to pubchem:89909564 #1.1 --- notes | Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds 0 hydrogens added Closest equivalent command: addcharge #1.1 standardizeResidues none Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue UNL (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\olive\AppData\Local\Temp\tmp7f9n415z\ante.in.mol2 -fi mol2 -o C:\Users\olive\AppData\Local\Temp\tmp7f9n415z\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (UNL) `` (UNL) `Welcome to antechamber 20.0: molecular input file processor.` (UNL) `` (UNL) `Info: Finished reading file (C:\Users\olive\AppData\Local\Temp\tmp7f9n415z\ante.in.mol2); atoms read (70), bonds read (73).` (UNL) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (UNL) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/bondtype"" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `` (UNL) `` (UNL) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `Info: Total number of electrons: 284; net charge: 0` (UNL) `` (UNL) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm"" -O -i sqm.in -o sqm.out` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `/usr/bin/antechamber: Fatal Error!` (UNL) `Cannot properly run """"C:/Program Files/ChimeraX/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 =104 | QMMM: *** Selected Hamiltonian *** | QMMM: AM1 | QMMM: *** Parameter sets in use *** | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: C : 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 = 184 | QMMM: diag iterations used for timing = 5 | QMMM: | QMMM: Internal diag routine = 0.079216 seconds | QMMM: Dspev diag routine = 0.071098 seconds | QMMM: Dspevd diag routine = 0.054125 seconds | QMMM: Dspevx diag routine = 0.236499 seconds | QMMM: Dsyev diag routine = 0.075961 seconds | QMMM: Dsyevd diag routine = 0.058941 seconds | QMMM: Dsyevr diag routine = 0.062282 seconds | QMMM: | QMMM: Pseudo diag routine = 0.036449 seconds | QMMM: | QMMM: Using dspevd routine (diag_routine=3). QMMM: QM Region Cartesian Coordinates (*=link atom) QMMM: QM_NO. MM_NO. ATOM X Y Z QMMM: 1 1 O 6.8670 -1.5870 0.0000 QMMM: 2 2 O 5.5580 0.3640 0.0000 QMMM: 3 3 O 5.1350 -1.5870 0.0000 QMMM: 4 4 O 6.8670 -3.5870 0.0000 QMMM: 5 5 O 5.1350 -4.5870 0.0000 QMMM: 6 6 O 3.4030 -3.5870 0.0000 QMMM: 7 7 O 4.8720 -0.4830 0.0000 QMMM: 8 8 O 2.5370 -2.0870 0.0000 QMMM: 9 9 O 10.1360 -3.4700 0.0000 QMMM: 10 10 O 10.4450 3.2470 0.0000 QMMM: 11 11 O 8.6500 -4.8090 0.0000 QMMM: 12 12 O 8.9590 4.5850 0.0000 QMMM: 13 13 C 6.8670 -0.5870 0.0000 QMMM: 14 14 C 7.1760 0.3640 0.0000 QMMM: 15 15 C 6.0010 -2.0870 0.0000 QMMM: 16 16 C 7.8180 -0.8960 0.0000 QMMM: 17 17 C 6.3670 0.9520 0.0000 QMMM: 18 18 C 8.1270 0.6730 0.0000 QMMM: 19 19 C 6.0010 -3.0870 0.0000 QMMM: 20 20 C 5.8670 -0.5870 0.0000 QMMM: 21 21 C 5.1350 -3.5870 0.0000 QMMM: 22 22 C 4.2690 -3.0870 0.0000 QMMM: 23 23 C 4.2690 -2.0870 0.0000 QMMM: 24 24 C 8.0260 -1.8740 0.0000 QMMM: 25 25 C 8.3350 1.6510 0.0000 QMMM: 26 26 C 3.4030 -1.5870 0.0000 QMMM: 27 27 C 8.9770 -2.1830 0.0000 QMMM: 28 28 C 7.2830 -2.5430 0.0000 QMMM: 29 29 C 9.2860 1.9600 0.0000 QMMM: 30 30 C 7.5920 2.3200 0.0000 QMMM: 31 31 C 9.1850 -3.1620 0.0000 QMMM: 32 32 C 7.4910 -3.5220 0.0000 QMMM: 33 33 C 9.4940 2.9380 0.0000 QMMM: 34 34 C 7.8000 3.2980 0.0000 QMMM: 35 35 C 8.4420 -3.8310 0.0000 QMMM: 36 36 C 8.7510 3.6070 0.0000 QMMM: 37 37 C 10.8790 -2.8010 0.0000 QMMM: 38 38 C 10.6530 4.2250 0.0000 QMMM: 39 39 H 7.2730 0.9760 0.0000 QMMM: 40 40 H 6.0010 -1.4670 0.0000 QMMM: 41 41 H 8.4380 -0.8750 0.0000 QMMM: 42 42 H 7.9040 -0.2820 0.0000 QMMM: 43 43 H 6.7820 1.4120 0.0000 QMMM: 44 44 H 5.9520 1.4120 0.0000 QMMM: 45 45 H 8.2130 0.0590 0.0000 QMMM: 46 46 H 8.7470 0.6510 0.0000 QMMM: 47 47 H 6.0010 -3.7070 0.0000 QMMM: 48 48 H 4.5980 -3.8970 0.0000 QMMM: 49 49 H 4.2690 -3.7070 0.0000 QMMM: 50 50 H 4.2690 -1.4670 0.0000 QMMM: 51 51 H 3.8010 -1.1120 0.0000 QMMM: 52 52 H 3.0040 -1.1120 0.0000 QMMM: 53 53 H 6.8670 -4.2070 0.0000 QMMM: 54 54 H 4.5980 -4.8970 0.0000 QMMM: 55 55 H 3.4030 -4.2070 0.0000 QMMM: 56 56 H 9.4380 -1.7680 0.0000 QMMM: 57 57 H 6.6930 -2.3520 0.0000 QMMM: 58 58 H 9.7470 1.5450 0.0000 QMMM: 59 59 H 7.0020 2.1290 0.0000 QMMM: 60 60 H 7.0300 -3.9370 0.0000 QMMM: 61 61 H 2.0000 -1.7770 0.0000 QMMM: 62 62 H 7.3390 3.7130 0.0000 QMMM: 63 63 H 9.2390 -5.0000 0.0000 QMMM: 64 64 H 8.4980 5.0000 0.0000 QMMM: 65 65 H 11.2940 -3.2620 0.0000 QMMM: 66 66 H 11.3400 -2.3860 0.0000 QMMM: 67 67 H 10.4640 -2.3410 0.0000 QMMM: 68 68 H 11.2590 4.0960 0.0000 QMMM: 69 69 H 10.7820 4.8320 0.0000 QMMM: 70 70 H 10.0460 4.3540 0.0000 -------------------------------------------------------------------------------- RESULTS -------------------------------------------------------------------------------- QMMM: ERROR! QMMM: Unable to achieve self consistency to the tolerances specified QMMM: No convergence in SCF after 1000 steps. QMMM: E = -0.1974E+07 DeltaE = 0.2157E+01 DeltaP = 0.4873E-01 QMMM: Smallest DeltaE = -0.3257E-02 DeltaP = 0.1499E-01 Step = 26 Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\tool.py"", line 263, in add_charges add_nonstandard_res_charges(self.session, residues, charge, method=method) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\charge.py"", line 319, in add_nonstandard_res_charges nonstd_charge(session, tautomer_residues, net_charge, method, status=status) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\charge.py"", line 602, in nonstd_charge raise ChargeError(ante_failure_msg) chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for residue UNL Check reply log for details chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for residue UNL Check reply log for details File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\charge.py"", line 602, in nonstd_charge raise ChargeError(ante_failure_msg) See log for complete Python traceback. > ui tool show ""Dock Prep"" OpenGL version: 3.3.0 - Build 27.20.100.8729 OpenGL renderer: Intel(R) UHD Graphics 620 OpenGL vendor: Intel Python: 3.9.11 Locale: en_US.cp1252 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: windows Manufacturer: LENOVO Model: 81EK OS: Microsoft Windows 11 Home (Build 22621) Memory: 8,458,571,776 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz OSLanguage: de-DE Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 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: 2023.5.7 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 comtypes: 1.1.14 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: 2022.9.26 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: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 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 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 pywin32: 305 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 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 WMI: 1.5.1 zipp: 3.15.0 File attachment: NTG.mol2 }}} [attachment:""NTG.mol2""] " defect closed normal Structure Editing not a bug all ChimeraX