id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17232 ORCA output: could not convert string to float kst61@… Tony Schaefer "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.26100 ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Attempted to open a S1 optimization run of an ORCA output file. Windows 11. ORCA version 5.0.3 Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show QWindowsWindow::setGeometry: Unable to set geometry 1058x1096+671+166 (frame: 1076x1143+662+128) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1056x1088+672+173 (frame: 1074x1135+663+135) margins: 9, 38, 9, 9 minimum size: 840x877 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=1068, y=1143))) > toolshed show QWindowsWindow::setGeometry: Unable to set geometry 1058x1096+671+166 (frame: 1076x1143+662+128) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1056x1088+672+173 (frame: 1074x1135+663+135) margins: 9, 38, 9, 9 minimum size: 840x877 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=1068, y=1143))) Downloading bundle SEQCROW-1.8.18-py3-none-any.whl Installed SEQCROW (1.8.18) > ui tool show ""Build QM Input"" settings migrated from version 2 QWindowsWindow::setGeometry: Unable to set geometry 1330x633+535+398 (frame: 1348x680+526+360) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1328x625+536+405 (frame: 1346x672+527+367) margins: 9, 38, 9, 9 minimum size: 417x375 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=539, y=516))) > ui mousemode right distance [Repeated 1 time(s)] > ui mousemode right select > open ""H:/My Drive/Crespo/Rhodanines/1/ACN/1_gs_opt_freq/1-acn-opt-freq.out"" Summary of feedback from opening H:/My Drive/Crespo/Rhodanines/1/ACN/1_gs_opt_freq/1-acn-opt-freq.out --- note | 1-acn-opt-freq.out has 0 imaginary harmonic vibrational modes Opened 1-acn-opt-freq.out as an ORCA output file QWindowsWindow::setGeometry: Unable to set geometry 553x411+924+509 (frame: 571x458+915+471) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 551x403+925+516 (frame: 569x450+916+478) margins: 9, 38, 9, 9 minimum size: 442x329 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=571, y=458))) > open ""H:/My > Drive/Crespo/Rhodanines/GS_reaction_pathways_Z_E/5/8_vac_optts_wb97M-V/8_vac_optts_wB97M-V.out"" Summary of feedback from opening H:/My Drive/Crespo/Rhodanines/GS_reaction_pathways_Z_E/5/8_vac_optts_wb97M-V/8_vac_optts_wB97M-V.out --- notes | 8_vac_optts_wB97M-V.out has 2 imaginary harmonic vibrational modes 889.99i 41.66i Opened 8_vac_optts_wB97M-V.out as an ORCA output file QWindowsWindow::setGeometry: Unable to set geometry 553x411+924+509 (frame: 571x458+915+471) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 551x403+925+516 (frame: 569x450+916+478) margins: 9, 38, 9, 9 minimum size: 442x329 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=571, y=458))) > close #1 > close > open ""H:/My > Drive/Crespo/Rhodanines/GS_reaction_pathways_Z_E/5/2-vacuum_xtb/1-nebts_xtb/output/1-nebts_xtb.out"" Opened 1-nebts_xtb.out as an ORCA output file QWindowsWindow::setGeometry: Unable to set geometry 553x411+924+509 (frame: 571x458+915+471) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 551x403+925+516 (frame: 569x450+916+478) margins: 9, 38, 9, 9 minimum size: 442x329 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=571, y=458))) > select clear > close > open ""H:/My > Drive/Crespo/Rhodanines/GS_reaction_pathways_Z_E/5/2-vacuum_xtb/1-nebts_xtb/output/1-nebts_xtb_MEP_trj.xyz"" opened 1-nebts_xtb_MEP_trj.xyz as an XYZ coordinate file movie QWindowsWindow::setGeometry: Unable to set geometry 553x449+924+490 (frame: 571x496+915+452) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 551x441+925+497 (frame: 569x488+916+459) margins: 9, 38, 9, 9 minimum size: 442x359 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=571, y=496))) > open ""H:/My > Drive/Crespo/Rhodanines/5S/Water/6_S1_opt_freq/5S_water_S1_opt_freq_soc.out"" Summary of feedback from opening H:/My Drive/Crespo/Rhodanines/5S/Water/6_S1_opt_freq/5S_water_S1_opt_freq_soc.out --- error | unable to open 5S_water_S1_opt_freq_soc.out as a ORCA output file warnings | WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR *** WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR *** WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR *** WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out INPUT FILE ================================================================================ NAME = S1_opt_freq_soc.inp | 1> # Excite to get 8 singlet excited states and optimize S1 | 2> | 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2 CPCM(water) | 4> | 5> %maxcore 6000 | 6> | 7> %base ""5S_S1_opt_freq_1"" #WATER!!!! | 8> | 9> %cpcm | 10> num_leb 302 | 11> end | 12> | 13> %scf | 14> maxiter 300 | 15> end | 16> | 17> %geom | 18> maxiter 300 | 19> end | 20> | 21> %pal | 22> nprocs 16 | 23> end | 24> | 25> %tddft | 26> NROOTS 8 | 27> | 28> # Optimize S1 | 29> IROOT 1 | 30> | 31> # Which type of states for IROOT? singlet. WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR *** WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out INPUT FILE ================================================================================ NAME = S1_opt_freq_soc.inp | 1> # Excite to get 8 singlet excited states and optimize S1 | 2> | 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2 CPCM(water) | 4> | 5> %maxcore 6000 | 6> | 7> %base ""5S_S1_opt_freq_1"" #WATER!!!! | 8> | 9> %cpcm | 10> num_leb 302 | 11> end | 12> | 13> %scf | 14> maxiter 300 | 15> end | 16> | 17> %geom | 18> maxiter 300 | 19> end | 20> | 21> %pal | 22> nprocs 16 | 23> end | 24> | 25> %tddft | 26> NROOTS 8 | 27> | 28> # Optimize S1 | 29> IROOT 1 | 30> | 31> # Which type of states for IROOT? singlet. WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\ui\graphics.py"", line 54, in event if self.handle_drag_and_drop(event): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\ui\graphics.py"", line 124, in handle_drag_and_drop mw.dropEvent(event) File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py"", line 731, in dropEvent _open_dropped_file(self.session, p) File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py"", line 2117, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\open_command\cmd.py"", line 132, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\open_command\cmd.py"", line 215, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\open_command\cmd.py"", line 526, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\open_command\cmd.py"", line 497, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\SEQCROW\\__init__.py"", line 596, in open return open_aarontools( ^^^^^^^^^^^^^^^^ File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\SEQCROW\io.py"", line 46, in open_aarontools raise e File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\SEQCROW\io.py"", line 33, in open_aarontools fr = FileReader( ^^^^^^^^^^^ File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\fileIO.py"", line 1630, in __init__ self.read_orca_out(f, get_all, just_geom, log=None) File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\fileIO.py"", line 3189, in read_orca_out raise e File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\fileIO.py"", line 3031, in read_orca_out self.other[""uv_vis""] = ValenceExcitations(s, orca_version=orca_version, style=""orca"") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\spectra.py"", line 1429, in __init__ super().__init__(*args, **kwargs) File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\spectra.py"", line 84, in __init__ self.parse_orca_lines(lines, *args, **kwargs) File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\spectra.py"", line 1755, in parse_orca_lines soc_oscillator_str.append(float(info[6])) ^^^^^^^^^^^^^^ ValueError: could not convert string to float: '(' ValueError: could not convert string to float: '(' File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\spectra.py"", line 1755, in parse_orca_lines soc_oscillator_str.append(float(info[6])) ^^^^^^^^^^^^^^ See log for complete Python traceback. > close > open ""H:/My > Drive/Crespo/Rhodanines/5S/Water/6_S1_opt_freq/5S_water_S1_opt_freq_soc.out"" Summary of feedback from opening H:/My Drive/Crespo/Rhodanines/5S/Water/6_S1_opt_freq/5S_water_S1_opt_freq_soc.out --- error | unable to open 5S_water_S1_opt_freq_soc.out as a ORCA output file warnings | WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR *** WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out INPUT FILE ================================================================================ NAME = S1_opt_freq_soc.inp | 1> # Excite to get 8 singlet excited states and optimize S1 | 2> | 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2 CPCM(water) | 4> | 5> %maxcore 6000 | 6> | 7> %base ""5S_S1_opt_freq_1"" #WATER!!!! | 8> | 9> %cpcm | 10> num_leb 302 | 11> end | 12> | 13> %scf | 14> maxiter 300 | 15> end | 16> | 17> %geom | 18> maxiter 300 | 19> end | 20> | 21> %pal | 22> nprocs 16 | 23> end | 24> | 25> %tddft | 26> NROOTS 8 | 27> | 28> # Optimize S1 | 29> IROOT 1 | 30> | 31> # Which type of states for IROOT? singlet. WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR *** WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out INPUT FILE ================================================================================ NAME = S1_opt_freq_soc.inp | 1> # Excite to get 8 singlet excited states and optimize S1 | 2> | 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2 CPCM(water) | 4> | 5> %maxcore 6000 | 6> | 7> %base ""5S_S1_opt_freq_1"" #WATER!!!! | 8> | 9> %cpcm | 10> num_leb 302 | 11> end | 12> | 13> %scf | 14> maxiter 300 | 15> end | 16> | 17> %geom | 18> maxiter 300 | 19> end | 20> | 21> %pal | 22> nprocs 16 | 23> end | 24> | 25> %tddft | 26> NROOTS 8 | 27> | 28> # Optimize S1 | 29> IROOT 1 | 30> | 31> # Which type of states for IROOT? singlet. WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR *** WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR *** WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out INPUT FILE ================================================================================ NAME = S1_opt_freq_soc.inp | 1> # Excite to get 8 singlet excited states and optimize S1 | 2> | 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2 CPCM(water) | 4> | 5> %maxcore 6000 | 6> | 7> %base ""5S_S1_opt_freq_1"" #WATER!!!! | 8> | 9> %cpcm | 10> num_leb 302 | 11> end | 12> | 13> %scf | 14> maxiter 300 | 15> end | 16> | 17> %geom | 18> maxiter 300 | 19> end | 20> | 21> %pal | 22> nprocs 16 | 23> end | 24> | 25> %tddft | 26> NROOTS 8 | 27> | 28> # Optimize S1 | 29> IROOT 1 | 30> | 31> # Which type of states for IROOT? singlet. WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR *** WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR *** WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out INPUT FILE ================================================================================ NAME = S1_opt_freq_soc.inp | 1> # Excite to get 8 singlet excited states and optimize S1 | 2> | 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2 CPCM(water) | 4> | 5> %maxcore 6000 | 6> | 7> %base ""5S_S1_opt_freq_1"" #WATER!!!! | 8> | 9> %cpcm | 10> num_leb 302 | 11> end | 12> | 13> %scf | 14> maxiter 300 | 15> end | 16> | 17> %geom | 18> maxiter 300 | 19> end | 20> | 21> %pal | 22> nprocs 16 | 23> end | 24> | 25> %tddft | 26> NROOTS 8 | 27> | 28> # Optimize S1 | 29> IROOT 1 | 30> | 31> # Which type of states for IROOT? singlet. WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR *** WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out INPUT FILE ================================================================================ NAME = S1_opt_freq_soc.inp | 1> # Excite to get 8 singlet excited states and optimize S1 | 2> | 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2 CPCM(water) | 4> | 5> %maxcore 6000 | 6> | 7> %base ""5S_S1_opt_freq_1"" #WATER!!!! | 8> | 9> %cpcm | 10> num_leb 302 | 11> end | 12> | 13> %scf | 14> maxiter 300 | 15> end | 16> | 17> %geom | 18> maxiter 300 | 19> end | 20> | 21> %pal | 22> nprocs 16 | 23> end | 24> | 25> %tddft | 26> NROOTS 8 | 27> | 28> # Optimize S1 | 29> IROOT 1 | 30> | 31> # Which type of states for IROOT? singlet. WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR *** WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out INPUT FILE ================================================================================ NAME = S1_opt_freq_soc.inp | 1> # Excite to get 8 singlet excited states and optimize S1 | 2> | 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2 CPCM(water) | 4> | 5> %maxcore 6000 | 6> | 7> %base ""5S_S1_opt_freq_1"" #WATER!!!! | 8> | 9> %cpcm | 10> num_leb 302 | 11> end | 12> | 13> %scf | 14> maxiter 300 | 15> end | 16> | 17> %geom | 18> maxiter 300 | 19> end | 20> | 21> %pal | 22> nprocs 16 | 23> end | 24> | 25> %tddft | 26> NROOTS 8 | 27> | 28> # Optimize S1 | 29> IROOT 1 | 30> | 31> # Which type of states for IROOT? singlet. WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out an error occured while reading the ORCA output file WARNING AaronTools.fileIO.FileReader.read_orca_out last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR *** WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy WARNING AaronTools.fileIO.FileReader.read_orca_out INPUT FILE ================================================================================ NAME = S1_opt_freq_soc.inp | 1> # Excite to get 8 singlet excited states and optimize S1 | 2> | 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2 CPCM(water) | 4> | 5> %maxcore 6000 | 6> | 7> %base ""5S_S1_opt_freq_1"" #WATER!!!! | 8> | 9> %cpcm | 10> num_leb 302 | 11> end | 12> | 13> %scf | 14> maxiter 300 | 15> end | 16> | 17> %geom | 18> maxiter 300 | 19> end | 20> | 21> %pal | 22> nprocs 16 | 23> end | 24> | 25> %tddft | 26> NROOTS 8 | 27> | 28> # Optimize S1 | 29> IROOT 1 | 30> | 31> # Which type of states for IROOT? singlet. WARNING AaronTools.fileIO.FileReader.read_orca_out the following data has been read: error, opt_steps, basis_set_by_ele, charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta, alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion correction energy, energy, forces, gradient, rotational_temperature, frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group, rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1), SOC GS stabilization energy Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py"", line 731, in dropEvent _open_dropped_file(self.session, p) File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py"", line 2117, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\open_command\cmd.py"", line 132, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\open_command\cmd.py"", line 215, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\open_command\cmd.py"", line 526, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\open_command\cmd.py"", line 497, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\SEQCROW\\__init__.py"", line 596, in open return open_aarontools( ^^^^^^^^^^^^^^^^ File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\SEQCROW\io.py"", line 46, in open_aarontools raise e File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\SEQCROW\io.py"", line 33, in open_aarontools fr = FileReader( ^^^^^^^^^^^ File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\fileIO.py"", line 1630, in __init__ self.read_orca_out(f, get_all, just_geom, log=None) File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\fileIO.py"", line 3189, in read_orca_out raise e File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\fileIO.py"", line 3031, in read_orca_out self.other[""uv_vis""] = ValenceExcitations(s, orca_version=orca_version, style=""orca"") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\spectra.py"", line 1429, in __init__ super().__init__(*args, **kwargs) File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\spectra.py"", line 84, in __init__ self.parse_orca_lines(lines, *args, **kwargs) File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\spectra.py"", line 1755, in parse_orca_lines soc_oscillator_str.append(float(info[6])) ^^^^^^^^^^^^^^ ValueError: could not convert string to float: '(' ValueError: could not convert string to float: '(' File ""C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\AaronTools\spectra.py"", line 1755, in parse_orca_lines soc_oscillator_str.append(float(info[6])) ^^^^^^^^^^^^^^ See log for complete Python traceback. QWindowsWindow::setGeometry: Unable to set geometry 750x599+825+415 (frame: 768x646+816+377) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 748x591+826+422 (frame: 766x638+817+384) margins: 9, 38, 9, 9 minimum size: 600x325 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=768, y=453))) OpenGL version: 3.3.0 - Build 32.0.101.5763 OpenGL renderer: Intel(R) UHD Graphics OpenGL vendor: Intel Python: 3.11.4 Locale: en_US.cp1252 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: windows Manufacturer: LENOVO Model: 82X7 OS: Microsoft Windows 11 Home Single Language (Build 26100) Memory: 8,267,882,496 MaxProcessMemory: 137,438,953,344 CPU: 6 13th Gen Intel(R) Core(TM) i3-1305U OSLanguage: en-US Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2024.8.30 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 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: 2.3 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: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 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-MutationScores: 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: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 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: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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 comtypes: 1.4.5 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pywin32: 306 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 Send2Trash: 1.8.3 SEQCROW: 1.8.18 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 WMI: 1.5.1 File attachment: 5S_water_S1_opt_freq_soc.out }}} [attachment:""5S_water_S1_opt_freq_soc.out""] " defect assigned normal Third Party all ChimeraX