id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4809 Volume viewer logs illegal command Tony Schaefer Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description Not necessarily a bug, but there's a difference between the color command the volume viewer prints to the log when you change the color of a threshold and a command I can type out to change the color of a threshold. The last command I executed was `volume #1 color #5500ff color blue`. Two commands above that, I set there to be two levels. I understand the documentation says I need to specify the levels when I set more than one color, but the commands the volume viewer seems to execute don't have this limitation (I know it's not actually executing a command). The `volume color...` ""commands"" that don't specify levels and don't result in an error are from the volume viewer. I copy-pasted those and got errors. According to the documentation, I should get errors. I think it's kind of strange that the tool makes it look like it's running a command that I cannot. Log: UI Theme > cd C:\Users\normn/Desktop Current working directory is: C:\Users\normn\Desktop > graphics selection width 2 UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:\Users\normn\Downloads\rotatedxyz\FORM_ROT_new.47 format nbo Summary of feedback from opening C:\Users\normn\Downloads\rotatedxyz\FORM_ROT_new.47 --- notes | FORM_ROT_new.47 C:\Users\normn\Downloads\rotatedxyz C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.32 Opened FORM_ROT_new.47 as an NBO file > ui tool show ""Orbital Viewer"" Opened MO alpha 1 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 2 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 3 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 4 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > volume style mesh > close #1.1 Opened MO alpha 5 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 6 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 7 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 8 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 9 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 10 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 11 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 12 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 13 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 14 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close > open C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.47 Summary of feedback from opening C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.47 --- notes | FORM_ROT_new.47 C:/Users/normn/Downloads/rotatedxyz C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.37 Opened FORM_ROT_new.47 as an NBO file Opened MO alpha 1 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 2 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close > open C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.36 Unrecognized file suffix '.36' > open C:\Users\normn\Downloads\rotatedxyz\FORM_ROT_new.47 format nbo Summary of feedback from opening C:\Users\normn\Downloads\rotatedxyz\FORM_ROT_new.47 --- notes | FORM_ROT_new.47 C:\Users\normn\Downloads\rotatedxyz C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.36 Opened FORM_ROT_new.47 as an NBO file Opened MO alpha 11 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 12 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 1 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 2 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 3 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 4 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 5 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 6 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 7 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 8 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 9 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 10 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 11 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 12 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > open C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.47 Summary of feedback from opening C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.47 --- notes | FORM_ROT_new.47 C:/Users/normn/Downloads/rotatedxyz C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.40 Opened FORM_ROT_new.47 as an NBO file Opened MO alpha 1 as #2.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > hide #!1 models > close #2.1 Opened MO alpha 2 as #2.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 3 as #2.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 4 as #2.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 5 as #2.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 6 as #2.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 7 as #2.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 8 as #2.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 9 as #2.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 10 as #2.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 11 as #2.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 12 as #2.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close > open C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.47 Summary of feedback from opening C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.47 --- notes | FORM_ROT_new.47 C:/Users/normn/Downloads/rotatedxyz C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.41 Opened FORM_ROT_new.47 as an NBO file Opened MO alpha 1 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 2 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 3 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 4 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 5 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 6 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 7 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 8 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 9 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 10 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 11 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 12 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close > open C:\Users\normn\Downloads\rotatedxyz\FORM_ROT_new.47 format nbo Summary of feedback from opening C:\Users\normn\Downloads\rotatedxyz\FORM_ROT_new.47 --- notes | FORM_ROT_new.47 C:\Users\normn\Downloads\rotatedxyz C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.39 Opened FORM_ROT_new.47 as an NBO file Opened MO alpha 1 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 2 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 3 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 4 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 5 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 6 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 7 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 8 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 9 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 10 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 11 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 12 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close > open C:\Users\normn\Downloads\rotatedxyz\FORM_ROT_new.47 format nbo Summary of feedback from opening C:\Users\normn\Downloads\rotatedxyz\FORM_ROT_new.47 --- notes | FORM_ROT_new.47 C:\Users\normn\Downloads\rotatedxyz C:/Users/normn/Downloads/rotatedxyz/FORM_ROT_new.37 Opened FORM_ROT_new.47 as an NBO file Opened MO alpha 10 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 11 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 4 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 1 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 2 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 3 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 4 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 5 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 6 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 7 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 8 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 9 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 10 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 11 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 12 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 11 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 4 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 4 as #1.1, grid size 175,162,120, pixel 0.05,0.0501,0.0504, shown at level -0.02,0.02, step 1, values float32 > volume style mesh > volume style surface > volume style mesh > close #1.1 Opened MO alpha 4 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > volume style mesh > close #1.1 Opened MO alpha 4 as #1.1, grid size 175,162,120, pixel 0.05,0.0501,0.0504, shown at level -0.02,0.02, step 1, values float32 > lighting soft > preset seqcrow ball-stick-endcap Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > lighting soft > lighting full > lighting soft > preset seqcrow ball-stick-endcap Preset implemented in Python; no expansion to individual ChimeraX commands available. > close #1.1 Opened MO alpha 5 as #1.1, grid size 175,162,120, pixel 0.05,0.0501,0.0504, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 6 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 7 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 8 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > ui tool show Linter > linter C:/Users/normn/Documents/GitHub/SEQCROW/src/__init__.py linter > pyflakes linting C:/Users/normn/Documents/GitHub/SEQCROW/src/__init__.py D:\ChimeraX 1.2.5\bin\ChimeraX.exe -m pyflakes C:/Users/normn/Documents/GitHub/SEQCROW/src/__init__.py C:/Users/normn/Documents/GitHub/SEQCROW/src/__init__.py:20:37 undefined name 'settings' C:/Users/normn/Documents/GitHub/SEQCROW/src/__init__.py:31:44 undefined name 'settings' > linter C:/Users/normn/Documents/GitHub/SEQCROW/src/io.py linter pyflakes linting C:/Users/normn/Documents/GitHub/SEQCROW/src/io.py D:\ChimeraX 1.2.5\bin\ChimeraX.exe -m pyflakes C:/Users/normn/Documents/GitHub/SEQCROW/src/io.py > linter C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py linter pyflakes linting C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py D:\ChimeraX 1.2.5\bin\ChimeraX.exe -m pyflakes C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:14:1 'from AaronTools.theory import *' used; unable to detect undefined names C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:341:13 local variable 'monomers' is assigned to but never used C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:494:17 local variable 'x1' is assigned to but never used C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:495:17 local variable 'x2' is assigned to but never used C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:496:17 local variable 'x3' is assigned to but never used C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:1746:21 local variable 'header' is assigned to but never used C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:1915:33 'GAUSSIAN_ROUTE' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:1957:37 'OptimizationJob' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:1961:42 'GAUSSIAN_ROUTE' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:1967:50 'GAUSSIAN_ROUTE' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:1972:33 'OptimizationJob' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:1986:49 'FrequencyJob' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:1989:42 'GAUSSIAN_ROUTE' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:1995:50 'GAUSSIAN_ROUTE' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:1999:45 'FrequencyJob' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2002:45 'SinglePointJob' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2011:49 'FrequencyJob' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2017:44 'IntegrationGrid' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2021:61 'GAUSSIAN_ROUTE' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2023:54 'GAUSSIAN_ROUTE' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2026:50 'GAUSSIAN_ROUTE' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2036:46 'GAUSSIAN_ROUTE' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2040:46 'GAUSSIAN_ROUTE' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2044:46 'GAUSSIAN_ROUTE' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2049:34 'Theory' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2207:18 'Theory' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2221:40 'SinglePointJob' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2223:37 'OptimizationJob' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2225:40 'OptimizationJob' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2227:40 'ForceJob' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2229:40 'FrequencyJob' may be undefined, or defined from star imports: AaronTools.theory C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2240:13 local variable 'char_match' is assigned to but never used C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2559:25 local variable 'bohr' is assigned to but never used C:/Users/normn/Documents/GitHub/AaronTools/fileIO.py:2728:53 'nmodes' may be undefined, or defined from star imports: AaronTools.theory > close #1.1 Opened MO alpha 4 as #1.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > open C:\Users\normn\Desktop\Form_rot.fchk format fchk Opened Form_rot.fchk as an FCHK file Opened MO alpha 12 as #2.1, grid size 88,81,60, pixel 0.1,0.101,0.102, shown at level -0.02,0.02, step 1, values float32 > close #2.1 > close #1.1 Opened MO alpha 12 as #2.1, grid size 175,162,120, pixel 0.05,0.0501,0.0504, shown at level -0.02,0.02, step 1, values float32 > hide #!2 models Opened MO alpha 4 as #1.1, grid size 175,162,120, pixel 0.05,0.0501,0.0504, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 4 as #1.1, grid size 175,162,120, pixel 0.05,0.0501,0.0504, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 12 as #2.1, grid size 175,162,120, pixel 0.05,0.0501,0.0504, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 4 as #1.1, grid size 175,162,120, pixel 0.05,0.0501,0.0504, shown at level -0.02,0.02, step 1, values float32 > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > close #1.1 Opened MO alpha 1 as #1.1, grid size 175,162,120, pixel 0.05,0.0501,0.0504, shown at level -0.02,0.02, step 1, values float32 > show #!1 models > close #1.1 Opened MO alpha 1 as #1.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 2 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > close #2.1 > close #1.1 > tile 2 models tiled > tile columns 2 spacingFactor 2 2 models tiled Opened MO alpha 2 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 Opened MO alpha 1 as #1.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 2 as #1.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 3 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 3 as #1.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 1 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 4 as #1.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 12 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 5 as #1.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 6 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 6 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 11 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 6 as #1.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 7 as #1.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 5 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 8 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 8 as #1.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 9 as #1.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 7 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 10 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 10 as #1.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 11 as #1.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 3 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 4 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #2.1 Opened MO alpha 9 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > close #1.1 Opened MO alpha 12 as #1.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > volume style mesh > volume style surface > volume style image > set bgColor black > style ball Changed 12 atom styles > preset seqcrow ball-stick-endcap Preset implemented in Python; no expansion to individual ChimeraX commands available. > set bgColor white > set bgColor black > set bgColor gray > close #1 > close #2.1 Opened MO alpha 12 as #2.1, grid size 59,54,40, pixel 0.15,0.152,0.154, shown at level -0.02,0.02, step 1, values float32 > volume style image > ui tool show ""Volume Viewer"" > volume #2.1 level -0.5421,1 level -0.04202,0.8 level 0,0 level 0,0 level > 0.04202,0.8 level 0.5421,1 > volume #2.1 level -0.5421,1 level -0.04202,0.8 level 0,0 level 0,0 level > 0.04202,0.8 level 0.5421,1 > volume #2.1 level -0.5421,1 level -0.02,0.8 level 0,0 level 0,0 level > 0.04202,0.8 level 0.5421,1 > volume #2.1 color black color blue color black color white color white color > white > volume #2.1 level -0.5421,1 level -0.02,0.8 level 0,0 level 0,0 level > 0.04202,0.8 level 0.5421,1 > volume #2.1 level -0.5421,1 level -0.02,0.8 level 0,0 level 0,0 level > 0.02,0.8 level 0.5421,1 > volume #2.1 color black color blue color black color white color red color > white > volume #2.1 level -0.5421,1 level -0.02,0.8 level 0,0 level 5.551e-17,0 > level 0.02,0.8 level 0.5421,1 > volume #2.1 level -0.5421,1 level -0.02,0.8 level 0,0 level 0.002,0 level > 0.02,0.8 level 0.5421,1 > volume #2.1 color black color blue color black color black color red color > white > volume #2.1 level -0.5421,1 level -0.02,0.8 level 0,0 level 0.002,0 level > 0.02,0.8 level 0.5421,1 > volume #2.1 level -0.5421,1 level -0.02,0.8 level 0,0 level 0.002,0 level > 0.02,0.8 level 0.5421,1 > volume #2.1 level -0.5421,1 level -0.02,0.8 level -0.002,0 level 0.002,0 > level 0.02,0.8 level 0.5421,1 > volume #2.1 level -0.5421,1 level -0.02,0.8 level -0.002,0 level 0.002,0 > level 0.02,0.8 level 0.5421,1 > volume #2.1 level -0.2,1 level -0.02,0.8 level -0.002,0 level 0.002,0 level > 0.02,0.8 level 0.5421,1 > volume #2.1 level -0.2,1 level -0.02,0.8 level -0.002,0 level 0.002,0 level > 0.02,0.8 level 0.5421,1 > volume #2.1 level -0.2,1 level -0.02,0.8 level -0.002,0 level 0.002,0 level > 0.02,0.8 level 0.2,1 > volume #2.1 level -0.2,1 level -0.02,0.8 level -0.002,0 level 0.002,0 level > 0.02,0.8 level 0.2,1 > volume #2.1 level -0.2,1 level -0.02,0.8 level -0.002,0 level 0.002,0 level > 0.02,0.8 level 0.2,1 > volume #2.1 color black color blue color black color white color red color > white > volume #2.1 level -0.2,1 level -0.02,0.8 level -0.002,0 level 0.002,0 level > 0.02,0.8 level 0.2,1 > volume #2.1 level -0.2,1 level -0.02,0.8 level -0.002,0 level 0.002,0 level > 0.02,0.8 level 0.2,1 > volume #2.1 color black color blue color white color white color red color > white > volume #2.1 level -0.2,1 level -0.02,0.8 level -0.002,0 level 0.002,0 level > 0.02,0.8 level 0.2,1 > volume #2.1 color black color blue color white color white color red color > black > volume #2.1 color black color blue color white color white color red color > #aa0000 > volume #2.1 color black color blue color white color white color red color > red > volume #2.1 level -0.2,1 level -0.02,0.8 level -0.002,0 level 0.002,0 level > 0.02,0.8 level 0.4,1 > volume #2.1 level -0.2,1 level -0.02,0.8 level -0.002,0 level 0.002,0 level > 0.02,0.8 level 0.4,1 > volume #2.1 level -0.4,1 level -0.02,0.8 level -0.002,0 level 0.002,0 level > 0.02,0.8 level 0.4,1 > volume #2.1 color blue color blue color white color white color red color > red > volume style surface > volume style image > volume #2.1 color red color red color white color white color blue color > blue Number of colors (6) does not match number of levels (0) > help volume > volume #2.1 color #5500ff color blue color white color white color red color > red > volume #2.1 color #5500ff color blue color white color white color red color > red Number of colors (6) does not match number of levels (0) > volume #2.1 color blue color blue color white color white color red color > red > open C:/Users/normn/Desktop/test.cube Opened test.cube as #1, grid size 41,62,65, pixel 0.2,0.202,0.203, shown at level -0.032,0.032, step 1, values float32 > volume #1 level -0.02 level 0.02 color red color blue > transparency #1 50 > hide #!2 models > volume #!1 style image > volume #1 color #5500ff color black color black color white color white > color white > volume #1 color #5500ff color black color black color white color white > color white Number of colors (6) does not match number of levels (0) > volume #1 color #5500ff color black color black color white color white > color white level -0.2,1 level -0.02,0.8 level -0.002,0 level 0.002,0 level > 0.02,0.8 level 0.4,1 > help volume > volume #!1 style surface > volume #1 color #5500ff color black color black color white color white > color white level -0.2,1 level -0.02,0.8 level -0.002,0 level 0.002,0 level > 0.02,0.8 level 0.4,1 Surface level must be a single value > volume #1 color red color blue level -0.02 level 0.02 > volume #1 color #5500ff color blue > volume #1 color #5500ff color blue Number of colors (2) does not match number of levels (0) OpenGL version: 3.3.0 NVIDIA 471.11 OpenGL renderer: NVIDIA GeForce RTX 2070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: To Be Filled By O.E.M. Model: To Be Filled By O.E.M. OS: Microsoft Windows 10 Home (Build 19042) Memory: 17,107,529,728 MaxProcessMemory: 137,438,953,344 CPU: 16 AMD Ryzen 7 2700X Eight-Core Processor OSLanguage: en-US Locale: ('en_US', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 astroid: 1.3.8 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-TestManager: 0.3 ChimeraX-themes: 0.3.1 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 flake8: 3.9.2 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 isort: 5.8.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 logilab-common: 1.8.1 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 mccabe: 0.6.1 msgpack: 1.0.0 mypy: 0.812 mypy-extensions: 0.4.3 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 pycodestyle: 2.7.0 pycollada: 0.7.1 pydicom: 2.0.0 pydocstyle: 6.1.1 pyflakes: 2.3.1 Pygments: 2.7.1 pylint: 1.8.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pywin32: 228 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 Send2Trash: 1.5.0 SEQCROW: 1.0.3b1 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 typed-ast: 1.4.3 typing-extensions: 3.10.0.0 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Command Line fixed Elaine Meng all ChimeraX