Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#4809 closed defect (fixed)

Volume viewer logs illegal command

Reported by: Tony Schaefer Owned by: Tom Goddard
Priority: normal Milestone:
Component: Command Line Version:
Keywords: Cc: Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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

Change History (5)

comment:1 by pett, 4 years ago

Component: Unassigned → Command Line
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Volume viewer logs illegal command

Reported by Tony Schaefer

comment:2 by Tom Goddard, 4 years ago

Cc: Elaine Meng added
Resolution: → fixed
Status: assigned → closed

Fixed.

Thanks, definitely a bug. Seems unreasonable that the volume command does not allow specifying 2 colors and no levels if there are already two surface levels. So I fixed the command so that is legal.

Elaine, could you fix the volume command "color" option docs? It is always ok to specify one color in which case all levels get that color. If more than one color is specified then it must match the number of levels currently shown or the number of level options given.

in reply to:  3 ; comment:3 by Elaine Meng, 4 years ago 

Sure, will do!  Does this change also apply to the "brightness" and "transparency" options?

in reply to:  4 ; comment:4 by Elaine Meng, 4 years ago 

I guess allowing multiple brightness/transparency is too elaborate, so I've revised the docs assuming what you said applies only to the "color" option.
<https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/commands/volume.html#color>

The only  missing piece of information is how multiple colors are paired to multiple pre-existing levels.  I said it was in ascending order but if that's wrong, let me know.

The explanation is awfully long, but I haven't thought of a way to make it shorter and yet cover all the cases.

in reply to:  5 ; comment:5 by goddard@…, 4 years ago 

A volume has just one brightness and transparency value, not a separate value per surface.  The new explanation of the level and color options looks good.
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