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Opened 4 months ago
Closed 4 months ago
#18259 closed defect (fixed)
NIH preset fails on structure with no chains
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\Users\luis_\Desktop\PRE-MAESTRIA\PRUEBA CASCARA DE MANGO\DPP
> IV\RESULTADO mangiferin prueba ddpiv PRUEBA2.pdb" format pdb
Summary of feedback from opening C:\Users\luis_\Desktop\PRE-MAESTRIA\PRUEBA
CASCARA DE MANGO\DPP IV\RESULTADO mangiferin prueba ddpiv PRUEBA2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU B 45 LYS B 50 1 6
Start residue of secondary structure not found: HELIX 2 2 TRP B 201 PHE B 208
1 8
Start residue of secondary structure not found: HELIX 3 3 THR B 273 SER B 275
1 3
Start residue of secondary structure not found: HELIX 4 4 ALA B 291 LEU B 294
1 4
Start residue of secondary structure not found: HELIX 5 5 VAL B 341 ARG B 343
1 3
52 messages similar to the above omitted
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for RESULTADO mangiferin prueba ddpiv PRUEBA2.pdb
---
Chain | Description
1.1/B | No description available
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select #1.1/B
7274 atoms, 7442 bonds, 9 pseudobonds, 727 residues, 2 models selected
> select ::name="UNL"
38 atoms, 41 bonds, 1 residue, 1 model selected
> graphics silhouettes false
> undo
> select clear
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select #1.1/B
7274 atoms, 7442 bonds, 9 pseudobonds, 727 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark cyan
> color sel cornflower blue
> color sel light sea green
> color sel medium turquoise
> color sel turquoise
> color sel dodger blue
> color sel medium spring green
> color sel dark turquoise
> color sel olive
> color sel lime
> color sel orange
[Repeated 1 time(s)]
> color sel dark orange
> color sel green yellow
> color sel goldenrod
> color sel sandy brown
> select ::name="UNL"
38 atoms, 41 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel maroon
[Repeated 1 time(s)]
> color sel dark red
> color sel orange red
> color sel crimson
> color sel dark red
> color sel maroon
> color sel fire brick
> color sel brown
> color sel tomato
> color sel chocolate
> color sel light pink
> color sel dark slate gray
> color sel chartreuse
> color sel lawn green
> color sel indian red
> color sel yellow
> color sel coral
> color sel chocolate
> color sel brown
> color sel fire brick
> color sel maroon
> color sel dark red
> color sel maroon
> color sel dark red
> color sel crimson
> color sel fire brick
> color sel brown
> color sel orange red
> color sel red
> color sel crimson
> color sel dark red
> color sel byhetero
> color sel maroon
> color sel byhetero
> color sel red
> color sel byhetero
> color sel crimson
> color sel byhetero
> color sel fire brick
> color sel byhetero
> color sel tomato
> color sel byhetero
> color sel saddle brown
> color sel sienna
> color sel indian red
> color sel yellow
> color sel gold
> color sel orange
> color sel dark orange
> color sel green yellow
> select #1.1/B
7274 atoms, 7442 bonds, 9 pseudobonds, 727 residues, 2 models selected
> color sel orange red
> color sel dark orange
> color sel goldenrod
> color sel peru
> color sel crimson
> color sel orange red
> color sel orange
> color sel royal blue
> color sel olive drab
> color sel cyan
> color sel sandy brown
> color sel goldenrod
> color sel green yellow
> color sel lime green
> color sel lawn green
> color sel spring green
> color sel dark salmon
> color sel salmon
> color sel indian red
> color sel sienna
> color sel coral
> color sel sandy brown
> color sel dark khaki
> color sel salmon
> color sel dark salmon
> color sel salmon
> select ::name="UNL"
38 atoms, 41 bonds, 1 residue, 1 model selected
> color sel coral
> color sel dark khaki
> color sel byhetero
> color sel light salmon
> color sel yellow green
> color sel dark red
> color sel maroon
> color sel fire brick
> color sel tomato
> color sel medium blue
> color sel slate gray
> color sel light slate gray
> color sel cadet blue
> color sel orchid
> color sel medium orchid
> color sel slate blue
> color sel rosy brown
> color sel light coral
> color sel wheat
> color sel white smoke
> color sel gray
> color sel dim gray
> color sel green yellow
> color sel yellow
> color sel gold
> color sel orange
> color sel dark orange
> color sel orange red
> color sel crimson
> color sel dark red
> color sel fire brick
> color sel brown
> color sel chocolate
> color sel saddle brown
> color sel indian red
> color sel sandy brown
> color sel green yellow
> color sel dark orange
> color sel chartreuse
> color sel lawn green
> color sel spring green
> color sel forest green
> color sel medium sea green
> color sel sea green
> color sel cyan
> color sel gold
> color sel yellow
> color sel sienna
> color sel coral
> color sel saddle brown
> color sel chocolate
> color sel brown
> color sel tomato
> color sel fire brick
> color sel maroon
> color sel byhetero
> select clear
> ui tool show "Find Cavities"
No structures chosen
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> lighting flat
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> save C:/Users/luis_/Desktop/renderizado1.jpg width 955 height 587
> supersample 3
> lighting flat
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting full
> graphics silhouettes false
> lighting full
> lighting flat
> lighting soft
> lighting simple
> help help:user/preferences.html#startup
Downloading bundle ChimeraX_Clipper-0.24.0-cp311-cp311-win_amd64.whl
[Repeated 1 time(s)]
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> save "C:/Users/luis_/Desktop/Prueba chimerax/prueba2.jpg" width 955 height
> 587 supersample 3
> set bgColor white
> set bgColor gray
> set bgColor black
> set bgColor white
> set bgColor #ffffff00
> graphics silhouettes true
> toolshed show
Downloading bundle ChimeraX_NIHPresets-1.2.7-py3-none-any.whl
Installed ChimeraX-NIHPresets (1.2.7)
> preset nih3d "surface monochrome (printable)"
Using preset: NIH3D / Surface Monochrome (Printable)
Changed 7312 atom radii, 7483 bond radii, 9 pseudobond radii
Changed 1 pseudobond dash
Computing secondary structure
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 RESULTADO mangiferin prueba ddpiv
PRUEBA2.pdb #1.1
---
warnings | Not adding hydrogens to RESULTADO mangiferin prueba ddpiv PRUEBA2.pdb #1.1/B ARG 40 CA because it is missing heavy-atom bond partners
Not adding hydrogens to RESULTADO mangiferin prueba ddpiv PRUEBA2.pdb #1.1/B
ARG 40 NE because it is missing heavy-atom bond partners
Not adding hydrogens to RESULTADO mangiferin prueba ddpiv PRUEBA2.pdb #1.1/B
ARG 40 CZ because it is missing heavy-atom bond partners
Not adding hydrogens to RESULTADO mangiferin prueba ddpiv PRUEBA2.pdb #1.1/B
ARG 40 NH1 because it is missing heavy-atom bond partners
Not adding hydrogens to RESULTADO mangiferin prueba ddpiv PRUEBA2.pdb #1.1/B
ARG 40 NH2 because it is missing heavy-atom bond partners
12 messages similar to the above omitted
Unknown hybridization for atom (O) of residue type ARG; not adding hydrogens
to it
notes | No usable SEQRES records for RESULTADO mangiferin prueba ddpiv PRUEBA2.pdb (#1.1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: RESULTADO mangiferin prueba
ddpiv PRUEBA2.pdb #1.1/B ARG 40
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: RESULTADO mangiferin prueba
ddpiv PRUEBA2.pdb #1.1/B PRO 766
Chain-final residues that are not actual C termini:
4374 hydrogens added
Summary of feedback from adding hydrogens to RESULTADO mangiferin prueba ddpiv
PRUEBA2.pdb #1.2
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
10 hydrogens added
Changed 11696 atom radii
Preset expands to these ChimeraX commands:
~struts
~hbonds
close ##name='3D-printable missing structure'
show ##name='missing structure' models
size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
style dashes 7
graphics quality bondSides default
graphics quality pseudobondSides 10
cartoon style sides 12
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 hb f
addh #1.2 hb f
size atomRadius default
surface #1.1 enclose #1.1 grid 0.875839 sharp false
surface #1.2 enclose #1.2 grid 0.3 sharp false
color nih_blue
> select ::name="UNL"
48 atoms, 51 bonds, 1 residue, 1 model selected
> show sel target ab
> preset nih3d "surface by chain"
Using preset: NIH3D / Surface by Chain
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py",
line 1341, in <lambda>
run(ses, "preset %s%s" % (cat, StringArg.unparse(name.lower()))))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\preset_mgr\cmd.py", line 61, in preset_cmd
run_preset(session, cat, matches[0])
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\preset_mgr\cmd.py", line 82, in run_preset
session.presets.preset_function(category, preset)()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\preset_mgr\manager.py", line 71, in cb
bi.run_provider(self.session, name, self)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\luis_\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\nih_presets\\__init__.py", line 33, in run_provider
run_preset(session, name, mgr, **kw)
File "C:\Users\luis_\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\nih_presets\presets.py", line 489, in run_preset
printable) + by_chain_cmds(session, rainbow=True, target_atoms=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\luis_\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\nih_presets\presets.py", line 128, in by_chain_cmds
cmds.append(rainbow_cmd(s, target_atoms=target_atoms))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\luis_\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\nih_presets\presets.py", line 391, in rainbow_cmd
if max([len(chain.chain_id) for chain in structure.chains]) > 1:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: max() arg is an empty sequence
ValueError: max() arg is an empty sequence
File "C:\Users\luis_\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\nih_presets\presets.py", line 391, in rainbow_cmd
if max([len(chain.chain_id) for chain in structure.chains]) > 1:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> preset nih3d cpk
Using preset: NIH3D / CPK
Changed 11696 atom radii, 11867 bond radii, 9 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 11696 atom styles
Changed 5712 atom radii
Changed 0 atom radii
Changed 11867 bond radii
Changed 1 pseudobond dash
Changed 9 pseudobond radii
Changed 0 atom radii
Preset expands to these ChimeraX commands:
~struts
~hbonds
close ##name='3D-printable missing structure'
show ##name='missing structure' models
size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
style dashes 7
graphics quality bondSides default
graphics quality pseudobondSides 10
cartoon style sides 12
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'
color jmol_carbon
color byhet
style sphere
~nuc
~ribbon
disp
size H atomRadius 1.1
size ions atomRadius +0.35
size stickRadius 0.8
style dashes 0
graphics quality bondSides default
graphics quality pseudobondSides 16
size pseudobondRadius 0.4
size ions atomRadius +0.35
> preset nih3d "surface alphafold/pae domains [all residues]"
Using preset: NIH3D / Surface AlphaFold/PAE Domains [All Residues]
No structures have PAE information!
> preset nih3d "volume monochrome"
Using preset: NIH3D / Volume Monochrome
Changed 11696 atom radii, 11867 bond radii, 9 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.
Preset expands to these ChimeraX commands:
~struts
~hbonds
close ##name='3D-printable missing structure'
show ##name='missing structure' models
size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
style dashes 7
graphics quality bondSides default
graphics quality pseudobondSides 10
cartoon style sides 12
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'
color nih_blue
> select clear
> preset nih3d "ribbon alphafold/plddt [high confidence]"
Using preset: NIH3D / Ribbon AlphaFold/pLDDT [High Confidence]
No structures have pLDDT scores assigned!
> preset nih3d "surface by chain"
Using preset: NIH3D / Surface by Chain
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py",
line 1341, in <lambda>
run(ses, "preset %s%s" % (cat, StringArg.unparse(name.lower()))))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\preset_mgr\cmd.py", line 61, in preset_cmd
run_preset(session, cat, matches[0])
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\preset_mgr\cmd.py", line 82, in run_preset
session.presets.preset_function(category, preset)()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\preset_mgr\manager.py", line 71, in cb
bi.run_provider(self.session, name, self)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\luis_\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\nih_presets\\__init__.py", line 33, in run_provider
run_preset(session, name, mgr, **kw)
File "C:\Users\luis_\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\nih_presets\presets.py", line 489, in run_preset
printable) + by_chain_cmds(session, rainbow=True, target_atoms=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\luis_\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\nih_presets\presets.py", line 128, in by_chain_cmds
cmds.append(rainbow_cmd(s, target_atoms=target_atoms))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\luis_\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\nih_presets\presets.py", line 391, in rainbow_cmd
if max([len(chain.chain_id) for chain in structure.chains]) > 1:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: max() arg is an empty sequence
ValueError: max() arg is an empty sequence
File "C:\Users\luis_\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\nih_presets\presets.py", line 391, in rainbow_cmd
if max([len(chain.chain_id) for chain in structure.chains]) > 1:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 Core Profile Context 25.5.1.250226
OpenGL renderer: AMD Radeon (TM) Graphics
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: es_MX.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: LENOVO
Model: 82RN
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 14,870,306,816
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5625U with Radeon Graphics
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NIHPresets: 1.2.7
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (2)
comment:1 by , 4 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → NIH preset fails on structure with no chains |
comment:2 by , 4 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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