SEQCROW: various errors reading possible ORCA output

[chimerax-bug-report@…]

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
Replace this text with list of actions that caused this problem to occur

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  

> open "D:\computation\POLYDBM\TDDFT NROOT_50\POLYDBM.out" format out

Summary of feedback from opening D:\computation\POLYDBM\TDDFT
NROOT_50\POLYDBM.out  
---  
error | unable to open POLYDBM.out as a ORCA output file  
  
Opened POLYDBM.out as an ORCA output file  

> open "D:/computation/POLYDBM/TDDFT NROOT_50/POLYDBM_crash.out"

Summary of feedback from opening D:/computation/POLYDBM/TDDFT
NROOT_50/POLYDBM_crash.out  
---  
error | unable to open POLYDBM_crash.out as a ORCA output file  
  
Summary of feedback from opening D:/computation/POLYDBM/TDDFT
NROOT_50/POLYDBM_crash.out  
---  
error | unable to open POLYDBM_crash.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: 100 100 ( 0.00 , 0.00 ) ( 0.00 ,  
-0.06 ) ( -0.00 , 0.50 )  
  
  
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: 100 100 ( 0.00 , 0.00 ) ( 0.00 ,  
-0.06 ) ( -0.00 , 0.50 )  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, multiplicity, opt_steps,  
basis_set_by_ele, charge, 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  
  
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: 100 100 ( 0.00 , 0.00 ) ( 0.00 ,  
-0.06 ) ( -0.00 , 0.50 )  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, multiplicity, opt_steps,  
basis_set_by_ele, charge, 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  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
  
================================================================================  
NAME = POLYDBM.inp  
| 1> ! CAM-B3LYP D3 def2-TZVP def2/J RIJCOSX SMD(ethanol) opt tightSCF  
printbasis printMOs  
  
| 2> %tddft  
  
| 3> nroots 100  
  
| 4> iroot 1  
  
| 5> dosoc true  
  
| 6> tda false  
  
| 7> printlevel 3  
  
| 8> end  
  
| 9> %maxcore 5000  
  
| 10> %pal nprocs 12 end  
  
| 11> * xyz 0 1  
  
| 12> O -12.20787922590418 -6.46515741779967  
0.04062429430907  
  
| 13> C -12.29682566978128 -5.21127101666438  
-0.07570005250366  
  
| 14> C -11.12617745595900 -4.39065112727619  
-0.09093693639878  
  
| 15> C -9.87127969938667 -4.94549102809647  
0.00079214391171  
  
| 16> O -9.71855577568144 -6.26009931919365  
0.11501449595511  
  
| 17> C -8.62206688775856 -4.17438128839971  
-0.00670644200286  
  
| 18> C -8.59338300533348 -2.81857555884147  
-0.35704609727825  
  
| 19> C -7.40358311461631 -2.11436026225189  
-0.35829057667378  
  
| 20> C -6.19488057894049 -2.73445889060029  
-0.01339843137149  
  
| 21> C -4.92636672005321 -1.98037677039240  
-0.02565366040436  
  
| 22> C -4.89349506956165 -0.62086739313111  
0.31302495509973  
  
| 23> C -3.70685654307699 0.08878593176247  
0.28885332812567  
  
| 24> C -2.50515664566147 -0.53339620912887  
-0.06688387993574  
  
| 25> C -1.25931965696598 0.27389337583165  
-0.09336869484089  
  
| 26> C 0.01598728554126 -0.36893155334736  
-0.12863036214987  
  
| 27> C 1.17783975168085 0.36767123358320  
-0.15442815457437  
  
| 28> O 1.13710256825403 1.69494610901478  
-0.14218894294758  
  
| 29> C 2.52617229759806 -0.21182461606648  
-0.18179298665229  
  
| 30> C 2.73969642548592 -1.57524562034338  
-0.42146734616609  
  
| 31> C 4.01978267116919 -2.09771397773763  
-0.43505053931822  
  
| 32> C 5.13750724309369 -1.28146919221182  
-0.21413572530978  
  
| 33> C 6.50257887003180 -1.84248667508282  
-0.22504241673997  
  
| 34> C 6.75164250699229 -3.14176445769285  
0.23734533544886  
  
| 35> C 8.03203918007758 -3.66457548852436  
0.23005262718017  
  
| 36> C 9.11432781632049 -2.90792072764295  
-0.23257401420663  
  
| 37> C 10.46980216916434 -3.51395855519080  
-0.22311969651824  
  
| 38> C 11.62918221258586 -2.68958859223886  
-0.35948612615373  
  
| 39> C 12.89052628865924 -3.23762255605352  
-0.34997857183327  
  
| 40> O 13.05968149735025 -4.54683580374394  
-0.20765778089706  
  
| 41> C 14.12991258880952 -2.46083370998269  
-0.47424387479789  
  
| 42> C 14.12273947298159 -1.12255224104666  
-0.88682453359408  
  
| 43> C 15.30318620355309 -0.40984148178124  
-0.99046502052513  
  
| 44> C 16.53596928890007 -1.00492627359114  
-0.68982586557447  
  
| 45> C 17.79436467645308 -0.24127780620818  
-0.79782203472044  
  
| 46> C 17.82877723816682 1.13181282093457  
-0.51381023411755  
  
| 47> C 19.00800583973736 1.84556564639141  
-0.60796639040702  
  
| 48> C 20.19677243441973 1.21358452204104  
-0.99114470714641  
  
| 49> C 21.43985609478156 2.01509961552675  
-1.07336919564626  
  
| 50> C 22.72584163562281 1.30167316186526  
-1.46498357170270  
  
| 51> C 23.88033771541129 2.26341944125500  
-1.48841961627061  
  
| 52> O 24.42937807684527 2.42845412056570  
-0.27868283926041  
  
| 53> O 24.27356316119185 2.84019451208903  
-2.47765257357225  
  
| 54> O 21.44839440880518 3.21314072395971  
-0.83661278345783  
  
| 55> C 20.16788583233035 -0.15459041749624  
-1.27888602243730  
  
| 56> C 18.98545275508962 -0.86874764056486  
-1.18261109160551  
  
| 57> C 16.53943052203563 -2.34472498467573  
-0.28418918562554  
  
| 58> C 15.35985738557162 -3.06064617430233  
-0.17875587407406  
  
| 59> O 10.57294786764021 -4.76318425527946  
-0.07756888943967  
  
| 60> C 8.86958445363902 -1.61126603189342  
-0.69719423277487  
  
| 61> C 7.58630746064549 -1.09072839590429  
-0.69547050252475  
  
| 62> C 4.92050926719076 0.08183696926301  
0.01842280310622  
  
| 63> C 3.64055464715605 0.60791356677978  
0.03429975813524  
  
| 64> O -1.35440136225254 1.53217154512993  
-0.06678055805162  
  
| 65> C -2.53275142906092 -1.89162418540749  
-0.40097507124590  
  
| 66> C -3.72265445961653 -2.60013583083919  
-0.38321495954018  
  
| 67> C -6.22709648529619 -4.09005929034147  
0.33456382659621  
  
| 68> C -7.41647839780628 -4.79787612275523  
0.33728209695241  
  
| 69> C -13.64415525174667 -4.59926904182888  
-0.18996711723582  
  
| 70> C -14.77138337957588 -5.39149134522961  
0.05630742770748  
  
| 71> C -16.04647857631302 -4.86553916645201  
-0.04585169083957  
  
| 72> C -13.84090345263787 -3.26103891689188  
-0.54900688743026  
  
| 73> C -15.11851607950840 -2.73839400778694  
-0.66049414696127  
  
| 74> C -16.24777626122304 -3.52715607805602  
-0.40938764582929  
  
| 75> C -17.61024432764490 -2.96661734236372  
-0.52764804003507  
  
| 76> C -17.90713313316270 -2.00289710959917  
-1.49931136312172  
  
| 77> C -19.18796265010909 -1.47805713791448  
-1.61278831865659  
  
| 78> C -20.19787097963300 -1.90184357498445  
-0.75450481217462  
  
| 79> C -19.91588921240355 -2.85755833383123  
0.21671837371162  
  
| 80> C -18.63649082895214 -3.38664787164683  
0.32763580679672  
  
| 81> H -11.22154557329437 -3.32167722459648  
-0.14929343398946  
  
| 82> H -10.65880932089156 -6.64084105629114  
0.12206775331012  
  
| 83> H -9.49941493016464 -2.30943187384739  
-0.65419309726595  
  
| 84> H -7.40905180260717 -1.07509161023129  
-0.65853401592733  
  
| 85> H -5.80304918276883 -0.11993012769582  
0.61716964413082  
  
| 86> H -3.70057230463416 1.13560624366226  
0.55970529488337  
  
| 87> H 0.07625661798989 -1.44199660517208  
-0.10284909330338  
  
| 88> H 0.15206748715042 1.93549574370938  
-0.10227008669725  
  
| 89> H 1.90668353086726 -2.23513987352097  
-0.61898423068993  
  
| 90> H 4.15479481699178 -3.15036229898386  
-0.64499114055111  
  
| 91> H 5.93889898221452 -3.73946567359347  
0.62837347165230  
  
| 92> H 8.20666153258100 -4.66527156944682  
0.60084176279011  
  
| 93> H 11.52406239008094 -1.62231253916773  
-0.43612099470341  
  
| 94> H 12.12567916890583 -4.93142865730589  
-0.11502028222761  
  
| 95> H 13.19461912679995 -0.63528812397041  
-1.15082313383712  
  
| 96> H 15.26907699169217 0.61516517478335  
-1.33460712453279  
  
| 97> H 16.92796337470848 1.63840980712245  
-0.19404499765632  
  
| 98> H 19.02035800582704 2.90179423345283  
-0.37584928175335  
  
| 99> H 22.60578834865466 0.86644946058997  
-2.45769485872705  
  
|100> H 22.91680552309021 0.49236413658762  
-0.75835209794176  
  
|101> H 25.14744977422678 3.08367205989256  
-0.33978028609470  
  
|102> H 21.06486982778196 -0.67331838371222  
-1.58716279250441  
  
|103> H 18.98478326349799 -1.92200224447582  
-1.42870730994659  
  
|104> H 17.47245875242838 -2.82709538343549  
-0.02506020412488  
  
|105> H 15.38905975153684 -4.08958701777031  
0.15020808844218  
  
|106> H 9.67379900210902 -1.00485065158674  
-1.08926003169904  
  
|107> H 7.42167486492549 -0.09553721363685  
-1.08643108281386  
  
|108> H 5.76010228193497 0.73561974270874  
0.21337747982566  
  
|109> H 3.50094152588252 1.66139882272133  
0.23060120932536  
  
|110> H -1.63003957451196 -2.40230946838380  
-0.70539420781843  
  
|111> H -3.71929172482992 -3.64158691990903  
-0.67615047488615  
  
|112> H -5.31478592408456 -4.59288988030023  
0.62691204722532  
  
|113> H -7.41458399261592 -5.84060920809717  
0.62110654656139  
  
|114> H -14.63823773829917 -6.42972781818801  
0.32776152004513  
  
|115> H -16.89905700777672 -5.50617283390740  
0.13753445321361  
  
|116> H -12.99968833395016 -2.61425584829094  
-0.75380540035637  
  
|117> H -15.23874854194911 -1.69719708778173  
-0.92929648011944  
  
|118> H -17.13548237708736 -1.67764600087080  
-2.18506553927995  
  
|119> H -19.39883583127719 -0.74054283855087  
-2.37749045328110  
  
|120> H -21.19608340421124 -1.49115955746049  
-0.84199809248670  
  
|121> H -20.69315490295414 -3.18900981467183  
0.89432166449378  
  
|122> H -18.42774867632995 -4.11678865306258  
1.09905479455384  
  
  
  
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: 100 100 ( 0.00 , 0.00 ) ( 0.00 ,  
-0.06 ) ( -0.00 , 0.50 )  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, multiplicity, opt_steps,  
basis_set_by_ele, charge, 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  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
  
================================================================================  
NAME = POLYDBM.inp  
| 1> ! CAM-B3LYP D3 def2-TZVP def2/J RIJCOSX SMD(ethanol) opt tightSCF  
printbasis printMOs  
  
| 2> %tddft  
  
| 3> nroots 100  
  
| 4> iroot 1  
  
| 5> dosoc true  
  
| 6> tda false  
  
| 7> printlevel 3  
  
| 8> end  
  
| 9> %maxcore 5000  
  
| 10> %pal nprocs 12 end  
  
| 11> * xyz 0 1  
  
| 12> O -12.20787922590418 -6.46515741779967  
0.04062429430907  
  
| 13> C -12.29682566978128 -5.21127101666438  
-0.07570005250366  
  
| 14> C -11.12617745595900 -4.39065112727619  
-0.09093693639878  
  
| 15> C -9.87127969938667 -4.94549102809647  
0.00079214391171  
  
| 16> O -9.71855577568144 -6.26009931919365  
0.11501449595511  
  
| 17> C -8.62206688775856 -4.17438128839971  
-0.00670644200286  
  
| 18> C -8.59338300533348 -2.81857555884147  
-0.35704609727825  
  
| 19> C -7.40358311461631 -2.11436026225189  
-0.35829057667378  
  
| 20> C -6.19488057894049 -2.73445889060029  
-0.01339843137149  
  
| 21> C -4.92636672005321 -1.98037677039240  
-0.02565366040436  
  
| 22> C -4.89349506956165 -0.62086739313111  
0.31302495509973  
  
| 23> C -3.70685654307699 0.08878593176247  
0.28885332812567  
  
| 24> C -2.50515664566147 -0.53339620912887  
-0.06688387993574  
  
| 25> C -1.25931965696598 0.27389337583165  
-0.09336869484089  
  
| 26> C 0.01598728554126 -0.36893155334736  
-0.12863036214987  
  
| 27> C 1.17783975168085 0.36767123358320  
-0.15442815457437  
  
| 28> O 1.13710256825403 1.69494610901478  
-0.14218894294758  
  
| 29> C 2.52617229759806 -0.21182461606648  
-0.18179298665229  
  
| 30> C 2.73969642548592 -1.57524562034338  
-0.42146734616609  
  
| 31> C 4.01978267116919 -2.09771397773763  
-0.43505053931822  
  
| 32> C 5.13750724309369 -1.28146919221182  
-0.21413572530978  
  
| 33> C 6.50257887003180 -1.84248667508282  
-0.22504241673997  
  
| 34> C 6.75164250699229 -3.14176445769285  
0.23734533544886  
  
| 35> C 8.03203918007758 -3.66457548852436  
0.23005262718017  
  
| 36> C 9.11432781632049 -2.90792072764295  
-0.23257401420663  
  
| 37> C 10.46980216916434 -3.51395855519080  
-0.22311969651824  
  
| 38> C 11.62918221258586 -2.68958859223886  
-0.35948612615373  
  
| 39> C 12.89052628865924 -3.23762255605352  
-0.34997857183327  
  
| 40> O 13.05968149735025 -4.54683580374394  
-0.20765778089706  
  
| 41> C 14.12991258880952 -2.46083370998269  
-0.47424387479789  
  
| 42> C 14.12273947298159 -1.12255224104666  
-0.88682453359408  
  
| 43> C 15.30318620355309 -0.40984148178124  
-0.99046502052513  
  
| 44> C 16.53596928890007 -1.00492627359114  
-0.68982586557447  
  
| 45> C 17.79436467645308 -0.24127780620818  
-0.79782203472044  
  
| 46> C 17.82877723816682 1.13181282093457  
-0.51381023411755  
  
| 47> C 19.00800583973736 1.84556564639141  
-0.60796639040702  
  
| 48> C 20.19677243441973 1.21358452204104  
-0.99114470714641  
  
| 49> C 21.43985609478156 2.01509961552675  
-1.07336919564626  
  
| 50> C 22.72584163562281 1.30167316186526  
-1.46498357170270  
  
| 51> C 23.88033771541129 2.26341944125500  
-1.48841961627061  
  
| 52> O 24.42937807684527 2.42845412056570  
-0.27868283926041  
  
| 53> O 24.27356316119185 2.84019451208903  
-2.47765257357225  
  
| 54> O 21.44839440880518 3.21314072395971  
-0.83661278345783  
  
| 55> C 20.16788583233035 -0.15459041749624  
-1.27888602243730  
  
| 56> C 18.98545275508962 -0.86874764056486  
-1.18261109160551  
  
| 57> C 16.53943052203563 -2.34472498467573  
-0.28418918562554  
  
| 58> C 15.35985738557162 -3.06064617430233  
-0.17875587407406  
  
| 59> O 10.57294786764021 -4.76318425527946  
-0.07756888943967  
  
| 60> C 8.86958445363902 -1.61126603189342  
-0.69719423277487  
  
| 61> C 7.58630746064549 -1.09072839590429  
-0.69547050252475  
  
| 62> C 4.92050926719076 0.08183696926301  
0.01842280310622  
  
| 63> C 3.64055464715605 0.60791356677978  
0.03429975813524  
  
| 64> O -1.35440136225254 1.53217154512993  
-0.06678055805162  
  
| 65> C -2.53275142906092 -1.89162418540749  
-0.40097507124590  
  
| 66> C -3.72265445961653 -2.60013583083919  
-0.38321495954018  
  
| 67> C -6.22709648529619 -4.09005929034147  
0.33456382659621  
  
| 68> C -7.41647839780628 -4.79787612275523  
0.33728209695241  
  
| 69> C -13.64415525174667 -4.59926904182888  
-0.18996711723582  
  
| 70> C -14.77138337957588 -5.39149134522961  
0.05630742770748  
  
| 71> C -16.04647857631302 -4.86553916645201  
-0.04585169083957  
  
| 72> C -13.84090345263787 -3.26103891689188  
-0.54900688743026  
  
| 73> C -15.11851607950840 -2.73839400778694  
-0.66049414696127  
  
| 74> C -16.24777626122304 -3.52715607805602  
-0.40938764582929  
  
| 75> C -17.61024432764490 -2.96661734236372  
-0.52764804003507  
  
| 76> C -17.90713313316270 -2.00289710959917  
-1.49931136312172  
  
| 77> C -19.18796265010909 -1.47805713791448  
-1.61278831865659  
  
| 78> C -20.19787097963300 -1.90184357498445  
-0.75450481217462  
  
| 79> C -19.91588921240355 -2.85755833383123  
0.21671837371162  
  
| 80> C -18.63649082895214 -3.38664787164683  
0.32763580679672  
  
| 81> H -11.22154557329437 -3.32167722459648  
-0.14929343398946  
  
| 82> H -10.65880932089156 -6.64084105629114  
0.12206775331012  
  
| 83> H -9.49941493016464 -2.30943187384739  
-0.65419309726595  
  
| 84> H -7.40905180260717 -1.07509161023129  
-0.65853401592733  
  
| 85> H -5.80304918276883 -0.11993012769582  
0.61716964413082  
  
| 86> H -3.70057230463416 1.13560624366226  
0.55970529488337  
  
| 87> H 0.07625661798989 -1.44199660517208  
-0.10284909330338  
  
| 88> H 0.15206748715042 1.93549574370938  
-0.10227008669725  
  
| 89> H 1.90668353086726 -2.23513987352097  
-0.61898423068993  
  
| 90> H 4.15479481699178 -3.15036229898386  
-0.64499114055111  
  
| 91> H 5.93889898221452 -3.73946567359347  
0.62837347165230  
  
| 92> H 8.20666153258100 -4.66527156944682  
0.60084176279011  
  
| 93> H 11.52406239008094 -1.62231253916773  
-0.43612099470341  
  
| 94> H 12.12567916890583 -4.93142865730589  
-0.11502028222761  
  
| 95> H 13.19461912679995 -0.63528812397041  
-1.15082313383712  
  
| 96> H 15.26907699169217 0.61516517478335  
-1.33460712453279  
  
| 97> H 16.92796337470848 1.63840980712245  
-0.19404499765632  
  
| 98> H 19.02035800582704 2.90179423345283  
-0.37584928175335  
  
| 99> H 22.60578834865466 0.86644946058997  
-2.45769485872705  
  
|100> H 22.91680552309021 0.49236413658762  
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|101> H 25.14744977422678 3.08367205989256  
-0.33978028609470  
  
|102> H 21.06486982778196 -0.67331838371222  
-1.58716279250441  
  
|103> H 18.98478326349799 -1.92200224447582  
-1.42870730994659  
  
|104> H 17.47245875242838 -2.82709538343549  
-0.02506020412488  
  
|105> H 15.38905975153684 -4.08958701777031  
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|106> H 9.67379900210902 -1.00485065158674  
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|107> H 7.42167486492549 -0.09553721363685  
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|108> H 5.76010228193497 0.73561974270874  
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|109> H 3.50094152588252 1.66139882272133  
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|110> H -1.63003957451196 -2.40230946838380  
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|111> H -3.71929172482992 -3.64158691990903  
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|112> H -5.31478592408456 -4.59288988030023  
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|113> H -7.41458399261592 -5.84060920809717  
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|114> H -14.63823773829917 -6.42972781818801  
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|115> H -16.89905700777672 -5.50617283390740  
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|116> H -12.99968833395016 -2.61425584829094  
-0.75380540035637  
  
|117> H -15.23874854194911 -1.69719708778173  
-0.92929648011944  
  
|118> H -17.13548237708736 -1.67764600087080  
-2.18506553927995  
  
|119> H -19.39883583127719 -0.74054283855087  
-2.37749045328110  
  
|120> H -21.19608340421124 -1.49115955746049  
-0.84199809248670  
  
|121> H -20.69315490295414 -3.18900981467183  
0.89432166449378  
  
|122> H -18.42774867632995 -4.11678865306258  
1.09905479455384  
  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, multiplicity, opt_steps,  
basis_set_by_ele, charge, 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  
  
Traceback (most recent call last):  
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\ASUS\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\\__init__.py", line 596, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "C:\Users\ASUS\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\io.py", line 42, in open_aarontools  
raise e  
File "C:\Users\ASUS\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\io.py", line 33, in open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "C:\Users\ASUS\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\ASUS\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\fileIO.py", line 2411, in read_orca_out  
line = f.readline()  
^^^^^^^^^^^^  
File "<frozen codecs>", line 322, in decode  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0:
invalid start byte  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
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 225, in provider_open  
models, status = collated_open(session, None, [data], data_format,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
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\ASUS\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\\__init__.py", line 596, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "C:\Users\ASUS\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\io.py", line 46, in open_aarontools  
raise e  
File "C:\Users\ASUS\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\io.py", line 33, in open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "C:\Users\ASUS\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\ASUS\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\fileIO.py", line 3189, in read_orca_out  
raise e  
File "C:\Users\ASUS\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\fileIO.py", line 2994, in read_orca_out  
re_z = float(line[23:30])  
^^^^^^^^^^^^^^^^^^  
ValueError: could not convert string to float: '( 0.0'  
  
ValueError: could not convert string to float: '( 0.0'  
  
File "C:\Users\ASUS\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\fileIO.py", line 2994, in read_orca_out  
re_z = float(line[23:30])  
^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 572.16
OpenGL renderer: NVIDIA GeForce RTX 4070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG Flow X16 GV601VI_GV601VI
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 68,325,638,144
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i9-13900H
OSLanguage: zh-CN

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
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