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#8196 closed defect (not a bug)

Volume disappears

Reported by:	kristen.browne@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Depiction	Version:
Keywords:		Cc:	Tom Goddard
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.dev202212150508 (2022-12-15 05:08:50 UTC)
Description
loaded attached file and ran through commands as shown in logs.  This was sequence of events when run through NIH 3D.  When get to the Executing: volume #1 region all style surface level 1 limitVoxelCount true voxelLimit 8 everything disappears.  In the NIH 3D logs, when we get to Colored 0 atoms, 1 surfaces, 0 residues, and rings a couple of steps later, it throws an error, probably because there's nothing there.

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.6.dev202212150508 (2022-12-15)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 22.3.1  
[notice] To update, run: C:\Program Files\ChimeraX-Daily\bin\ChimeraX.exe -m
pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Collecting ChimeraX-NIHPresets==1.1.8  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxnihpresets/releases/1.1.8/ChimeraX_NIHPresets-1.1.8-py3-none-
any.whl (7.0 kB)  
Installing collected packages: ChimeraX-NIHPresets  
Attempting uninstall: ChimeraX-NIHPresets  
Found existing installation: ChimeraX-NIHPresets 1.1.7  
Uninstalling ChimeraX-NIHPresets-1.1.7:  
Successfully uninstalled ChimeraX-NIHPresets-1.1.7  
Successfully installed ChimeraX-NIHPresets-1.1.8  
\---  

Successfully installed ChimeraX-NIHPresets-1.1.8  
Installed ChimeraX-NIHPresets (1.1.8)  

> open 2JTN

Summary of feedback from opening 2JTN fetched from pdb  
---  
note | Fetching compressed mmCIF 2jtn from
http://files.rcsb.org/download/2jtn.cif  
  
2jtn title:  
NMR Solution Structure of a ldb1-LID:Lhx3-LIM complex [more info...]  
  
Chain information for 2jtn  
---  
Chain | Description | UniProt  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | LIM domain-binding
protein 1, LIM/homeobox protein Lhx3 | LHX3_MOUSE  
  

> close #1.2-20

> preset nih3d "ribbon by chain (printable)"

Using preset: NIH3D / Ribbon by Chain (Printable)  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
873 atoms, 683 bonds, 182 residues, 1 model selected  
Nothing selected  
Changed 0 pseudobond radii  
Changed 4 atom radii  
728 atoms, 727 bonds, 182 residues, 1 model selected  
35 hydrogen bonds found  
Changed 51 pseudobond radii  
Created 3 struts for @ca | ligand | P, max length 8, max loop length 60  
  
Nothing selected  
Changed 1438 bond radii  
Changed 3 pseudobond dashes  
Preset expands to these ChimeraX commands:

    
    
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    delete H
    preset 'initial styles' cartoon
    nucleotides ladder radius 1.2
    color white target abc
    color helix marine
    color strand firebrick
    color coil goldenrod
    color nucleic-acid forest
    color :A:C:G:U grape
    color byatom
    select (C & ligand) | (C & ligand :< 5 & ~nucleic-acid) | (C & protein) | (C & disulfide)
    color sel carbon_grey atoms
    color ligand | protein & sideonly byhet atoms
    ~select
    rainbow #1.1@ca,c4' chains palette marine:marine target rs
    size min-backbone pseudobondRadius 1.1
    size ions atomRadius +0.8
    select backbone & protein | nucleic-acid & min-backbone | ions | ligand | ligand :< 5 & ~nucleic-acid
    hbonds sel color white restrict both
    size pseudobondRadius 0.6
    wait 1
    struts @ca|ligand|P length 8 loop 60 rad 0.75 color struts_grey
    ~struts @PB,PG resetRibbon false
    ~struts adenine|cytosine|guanine|thymine|uracil resetRibbon false
    color hbonds white pseudobonds
    ~select
    size stickRadius 0.8
    style dashes 0

  

> preset nih3d "ribbon by chain"

Using preset: NIH3D / Ribbon by Chain  
Changed 1413 atom radii, 1438 bond radii, 16 pseudobond radii  
Changed 1 pseudobond dash  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
873 atoms, 683 bonds, 182 residues, 1 model selected  
Nothing selected  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    delete H
    preset 'initial styles' cartoon
    nucleotides ladder radius 1.2
    color white target abc
    color helix marine
    color strand firebrick
    color coil goldenrod
    color nucleic-acid forest
    color :A:C:G:U grape
    color byatom
    select (C & ligand) | (C & ligand :< 5 & ~nucleic-acid) | (C & protein) | (C & disulfide)
    color sel carbon_grey atoms
    color ligand | protein & sideonly byhet atoms
    ~select
    rainbow #1.1@ca,c4' chains palette marine:marine target rs

  

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset nih3d "sticks monochrome"

Using preset: NIH3D / Sticks Monochrome  
Changed 1413 atom radii, 1438 bond radii, 16 pseudobond radii  
Changed 1 pseudobond dash  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Changed 1413 atom styles  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    style stick
    ~nuc
    ~ribbon
    disp
    color nih_blue

  

> preset nih3d "surface by chain"

Using preset: NIH3D / Surface by Chain  
Changed 1413 atom radii, 1438 bond radii, 16 pseudobond radii  
Changed 1 pseudobond dash  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Summary of feedback from adding hydrogens to 2jtn #1.1  
---  
notes | Termini for 2jtn (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A SER 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A GLN 182  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A GLN 182  
62 hydrogen bonds  
1346 hydrogens added  
  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    hide H|ligand|~(protein|nucleic-acid) atoms
    ~nuc
    ~ribbon
    ~display
    addh #1.1
    surface #1.1 enclose #1.1 grid 0.650142 sharp true
    rainbow #1.1@ca,c4' chains palette marine:marine target rsa
    color zone #1.1 near #1.1 & main distance 20

  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 2760 atom radii, 2785 bond radii, 16 pseudobond radii  
Changed 1 pseudobond dash  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Summary of feedback from adding hydrogens to 2jtn #1.1  
---  
notes | Termini for 2jtn (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A SER 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A GLN 182  
Chain-final residues that are not actual C termini:  
58 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for Surface #1.1 #1.1.2: minimum, -16.72, mean -1.23, maximum
28.34  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    hide H|ligand|~(protein|nucleic-acid) atoms
    ~nuc
    ~ribbon
    ~display
    addh #1.1
    surface #1.1 enclose #1.1 grid 0.940909 sharp true
    color white
    coulombic surfaces #* chargeMethod gasteiger

  

> close session

> open "C:/Users/brownekm/Downloads/emd_7037_0 (1).map"

Opened emd_7037_0 (1).map as #1, grid size 320,320,320, pixel 1.06, shown at
level 0.121, step 2, values float32  

> volume #1 level 0.137

> volume #1 level 0.162

> preset nih3d "volume radial"

Using preset: NIH3D / Volume Radial  
Enclosed volume for surface (#1.1) = 1.61e+05  
Enclosed volume for surface (#1.1) = 1.375e+05  
Changed 0 atom radii, 0 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    volume #1 region all style surface step 1 limitVoxelCount false
    wait 1
    surface dust #1.1 size 1 metric 'size rank'
    color radial #1 palette red:yellow:green:cyan:blue center #1

  

> preset nih3d "volume monochrome"

Using preset: NIH3D / Volume Monochrome  
Enclosed volume for surface (#1.1) = 1.61e+05  
Enclosed volume for surface (#1.1) = 1.375e+05  
Changed 0 atom radii, 0 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    volume #1 region all style surface step 1 limitVoxelCount false
    wait 1
    surface dust #1.1 size 1 metric 'size rank'
    color nih_blue

  

> preset nih3d "volume radial"

Using preset: NIH3D / Volume Radial  
Enclosed volume for surface (#1.1) = 1.61e+05  
Enclosed volume for surface (#1.1) = 1.375e+05  
Changed 0 atom radii, 0 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    volume #1 region all style surface step 1 limitVoxelCount false
    wait 1
    surface dust #1.1 size 1 metric 'size rank'
    color radial #1 palette red:yellow:green:cyan:blue center #1

  

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> close session

> open "C:\Users\brownekm\Downloads\emd_7037_0 (1).map" format ccp4

Opened emd_7037_0 (1).map as #1, grid size 320,320,320, pixel 1.06, shown at
level 0.121, step 2, values float32  

> volume #1 level 0.162

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> volume #1 region all style surface level 1 limitVoxelCount true voxelLimit 8

> close session

> open "C:\Users\brownekm\Downloads\emd_7037_0 (1).map" format ccp4

Opened emd_7037_0 (1).map as #1, grid size 320,320,320, pixel 1.06, shown at
level 0.121, step 2, values float32  

> ~struts

> ~hbonds

> size atomRadius default stickRadius 0.2 pseudobondRadius 0.2

Changed 0 atom radii, 0 bond radii, 0 pseudobond radii  

> style dashes 7

Changed 0 pseudobond dashes  

> graphics bgColor white

> color name marine 0,50,100

Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  

> color name forest 13.3,54.5,13.3

Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  

> color name tangerine 95.3,51.8,0

Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  

> color name grape 64.3,0,86.7

Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  

> color name nih_blue 12.5,33.3,54.1

Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  

> color name jmol_carbon 56.5,56.5,56.5

Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  

> color name bond_purple 57.6,43.9,85.9

Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  

> color name struts_grey 48,48,48

Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  

> color name carbon_grey 22.2,22.2,22.2

Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  

> surface close

> preset "initial styles" 'original look'

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> volume #1 region all style surface level 1 limitVoxelCount true voxelLimit 8

> wait 1

> surface dust #1.1 size 1 metric "size rank"

> close session

> open "C:\Users\brownekm\Downloads\emd_7037_0 (1).map" format ccp4

Opened emd_7037_0 (1).map as #1, grid size 320,320,320, pixel 1.06, shown at
level 0.121, step 2, values float32  

> volume #1.1 region all style surface level 1 limitVoxelCount true voxelLimit
> 8

No volumes specified  




OpenGL version: 3.3.0 NVIDIA 466.47
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.0, Qt 6.4.0
Qt runtime version: 6.4.1
Qt platform: windows

Manufacturer: HP
Model: HP Z4 G4 Workstation
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 137,220,087,808
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) i9-10900X CPU @ 3.70GHz
OSLanguage: en-US

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.5.7
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    ChimeraX-AlignmentMatrices: 2.1
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    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
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    ChimeraX-AtomicLibrary: 9.0
    ChimeraX-AtomSearch: 2.0.1
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    ChimeraX-DockPrep: 1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.3
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    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.11
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.10
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.8
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    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NIHPresets: 1.1.8
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.3
    ChimeraX-PDB: 2.6.9
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.4
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.25.2
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.6
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comm: 0.1.2
    comtypes: 1.1.10
    contourpy: 1.0.6
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.19.2
    ipython: 8.7.0
    ipython-genutils: 0.2.0
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 7.4.8
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.6.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.8
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 22.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.6.0
    prompt-toolkit: 3.0.36
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.4.0
    PyQt6-Qt6: 6.4.1
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.1
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
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    RandomWords: 0.4.0
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    setuptools: 65.1.1
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File attachment: emd_7037_0 (1).map

emd_7037_0 (1).map

Attachments (1)

emd_7037_0 (1).map (125.0 MB ) - added by kristen.browne@… 3 years ago.: Added by email2trac

Change History (11)

by kristen.browne@…, 3 years ago

Attachment:	emd_7037_0 (1).map added

Added by email2trac

comment:1 by Eric Pettersen, 3 years ago

Component:	Unassigned → Depiction
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Volume disappears

comment:2 by Eric Pettersen, 3 years ago

Status:	accepted → feedback

When I run this file through cx_unified.py, it works fine and produces visible surfaces. But it doesn't use the "volume" command you report. It uses:

volume #1 region all style surface step 1 limitVoxelCount false

Looking at the script, the difference means that when you run it, the script believes that there is a specified contour level (either as a script argument or fetched from the EMDB database), and when I run it there is no specified contour level. When you run the pipeline, is the --level argument being given to the script?

in reply to: 4 comment:3 by kristen.browne@…, 3 years ago

Yes, the user provides a contour level and that is used by ChimeraX.

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Monday, December 19, 2022 5:05 PM
Cc: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu
Subject: [EXTERNAL] Re: [ChimeraX] #8196: Volume disappears

#8196: Volume disappears
---------------------------------------+----------------------
          Reporter:  kristen.browne@...  |      Owner:  pett
              Type:  defect            |     Status:  feedback
          Priority:  normal            |  Milestone:
         Component:  Depiction         |    Version:
        Resolution:                    |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback


Comment:

 When I run this file through cx_unified.py, it works fine and produces  visible surfaces.  But it doesn't use the "volume" command you report.  It
 uses:

 volume #1 region all style surface step 1 limitVoxelCount false

 Looking at the script, the difference means that when you run it, the  script believes that there is a specified contour level (either as a  script argument or fetched from the EMDB database), and when I run it  there is no specified contour level.  When you run the pipeline, is the  --level argument being given to the script?

--
Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F8196%23comment%3A2&data=05%7C01%7Ckristen.browne%40nih.gov%7C03a69d9abaac4dec083608dae20d2d47%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638070843469701189%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=sHlSDR2HfBijdaCfGWS3sipV6sR6QzynODpt35zQNJY%3D&reserved=0>
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follow-up: 3 comment:4 by Eric Pettersen, 3 years ago

Cc:	Tom Goddard added
Resolution:	→ not a bug
Status:	feedback → closed

I would imagine it would be best if specifying the contour level were optional -- the ChimeraX computed default or EMDB-fetched value will typically be good and frequently the naive user will have no idea what a good contour level is. In the case of this map, all values are < 1 and so a contour level of 1 shows nothing, hence the volume "disappearing".

in reply to: 6 comment:5 by kristen.browne@…, 3 years ago

Ahh.  I should’ve caught that one.  There was a very specific requirement to use a provided contour level if one was there.  We might need to do a subsequent check… something like “is there <20 polygons” and if so return an error for the user that their contour level was likely wrong and suggest they run again without one and let ChimeraX guess.  Right now in NIH3D  we have contour level as a required field, but this could easily be changed.
I’ll talk to Phil about this.  Thanks for the suggestions and info.  We’ll take this one from here.

K
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________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, December 19, 2022 5:42:18 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [ChimeraX] #8196: Volume disappears

#8196: Volume disappears
---------------------------------------+--------------------
          Reporter:  kristen.browne@…  |      Owner:  pett
              Type:  defect            |     Status:  closed
          Priority:  normal            |  Milestone:
         Component:  Depiction         |    Version:
        Resolution:  not a bug         |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+--------------------
Changes (by pett):

 * cc: Tom Goddard (added)
 * status:  feedback => closed
 * resolution:   => not a bug


Comment:

 I would imagine it would be best if specifying the contour level were
 optional -- the ChimeraX computed default or EMDB-fetched value will
 typically be good and frequently the naive user will have no idea what a
 good contour level is.  In the case of this map, all values are < 1 and so
 a contour level of 1 shows nothing, hence the volume "disappearing".

--
Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F8196%23comment%3A4&data=05%7C01%7Ckristen.browne%40nih.gov%7Cc7cdec8fc0fc4bed539308dae21258f5%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638070865686544066%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2B8TZLSrPtjNpZc0V%2FN4Szabs9b5MpWHYtitHR9Vzzm8%3D&reserved=0>
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follow-up: 5 comment:6 by Tom Goddard, 3 years ago

The command that gives the warning "No volumes specified" will never work no matter what the threshold level is because #1.1 is not a volume model. The volume model is #1, and #1.1 might be a volume surface if one was shown (even an empty one), but the volume command does not accept surfaces as its first argument even if they are the surface for a volume model.

"volume #1.1 region all style surface level 1 limitVoxelCount true voxelLimit 8"

comment:7 by Eric Pettersen, 3 years ago

I believe that command was typed by hand as a test, but that's just a guess. The script-generated commands aren't using #1.1, they use #1.

in reply to: 9 comment:8 by kristen.browne@…, 3 years ago

That reminds me, I did notice that when I was running.  That makes sense as it was the only map file that failed.  All other user provided contours were fine.    Is it something to do with this file that it was built that the contour was applied to the wrong object?

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________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, December 19, 2022 5:56:38 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [ChimeraX] #8196: Volume disappears

#8196: Volume disappears
---------------------------------------+--------------------
          Reporter:  kristen.browne@…  |      Owner:  pett
              Type:  defect            |     Status:  closed
          Priority:  normal            |  Milestone:
         Component:  Depiction         |    Version:
        Resolution:  not a bug         |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+--------------------

Comment (by Tom Goddard):

 The command that gives the warning "No volumes specified" will never work
 no matter what the threshold level is because #1.1 is not a volume model.
 The volume model is #1, and #1.1 might be a volume surface if one was
 shown (even an empty one), but the volume command does not accept surfaces
 as its first argument even if they are the surface for a volume model.

 {{{
 "volume #1.1 region all style surface level 1 limitVoxelCount true
 voxelLimit 8"
 }}}

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in reply to: 10 ; follow-up: 8 comment:9 by kristen.browne@…, 3 years ago

I copied that command out of the NIH3D logs.  My command line ChimeraX isn’t that good :p

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________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, December 19, 2022 6:02:13 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [ChimeraX] #8196: Volume disappears

#8196: Volume disappears
---------------------------------------+--------------------
          Reporter:  kristen.browne@…  |      Owner:  pett
              Type:  defect            |     Status:  closed
          Priority:  normal            |  Milestone:
         Component:  Depiction         |    Version:
        Resolution:  not a bug         |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+--------------------

Comment (by pett):

 I believe that command was typed by hand as a test, but that's just a
 guess.  The script-generated commands aren't using #1.1, they use #1.

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in reply to: 11 ; follow-up: 9 comment:10 by kristen.browne@…, 3 years ago

The workflows are rerunning as we speak, it will likely come up again and can revisit then :)

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________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, December 19, 2022 6:04:10 PM
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [ChimeraX] #8196: Volume disappears

#8196: Volume disappears
---------------------------------------+--------------------
          Reporter:  kristen.browne@…  |      Owner:  pett
              Type:  defect            |     Status:  closed
          Priority:  normal            |  Milestone:
         Component:  Depiction         |    Version:
        Resolution:  not a bug         |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+--------------------

Comment (by kristen.browne@…):

 {{{
 I copied that command out of the NIH3D logs.  My command line ChimeraX
 isn’t that good :p

 Get Outlook for iOS<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fo0ukef&data=05%7C01%7Ckristen.browne%40nih.gov%7C034b6c3d069d41a134d308dae21558be%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638070878569499998%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=pgw54ZAL3u1upQhIAV6PcX4ExxMWG86zud4LqY0Agb8%3D&reserved=0>
 ________________________________
 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 Sent: Monday, December 19, 2022 6:02:13 PM
 Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Browne, Kristen
 (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu
 <pett@cgl.ucsf.edu>
 Subject: [EXTERNAL] Re: [ChimeraX] #8196: Volume disappears

 #8196: Volume disappears
 ---------------------------------------+--------------------
           Reporter:  kristen.browne@…  |      Owner:  pett
               Type:  defect            |     Status:  closed
           Priority:  normal            |  Milestone:
          Component:  Depiction         |    Version:
         Resolution:  not a bug         |   Keywords:
         Blocked By:                    |   Blocking:
 Notify when closed:                    |   Platform:  all
            Project:  ChimeraX          |
 ---------------------------------------+--------------------

 Comment (by pett):

  I believe that command was typed by hand as a test, but that's just a
  guess.  The script-generated commands aren't using #1.1, they use #1.

 --
 Ticket URL:
 <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F8196%23comment%3A7&data=05%7C01%7Ckristen.browne%40nih.gov%7C034b6c3d069d41a134d308dae21558be%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638070878569499998%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=h%2Bu04Oemia3uOp3xfMrHVjHDYcuHQ2apMo%2FzToxPS0M%3D&reserved=0>
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