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#5478 closed defect (fixed)

All atoms for zone mask must be from a single model

Reported by:	chimerax-bug-report@…	Owned by:	Tristan Croll
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:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
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 /Users/munetakaakatsu/Downloads/temp.looping/composite_map.ccp4

Opened composite_map.ccp4 as #1, grid size 360,360,360, pixel 1.06, shown at
level 4.98, step 2, values float32  

> open
> /Users/munetakaakatsu/Downloads/temp.looping/211025_largetemp_nucleosome.pdb

Chain information for 211025_largetemp_nucleosome.pdb #2  
---  
Chain | Description  
N | No description available  
T | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
  

> open
> /Users/munetakaakatsu/Downloads/temp.looping/211025_largetemp_RNAPIIonly.pdb

Chain information for 211025_largetemp_RNAPIIonly.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
N | No description available  
P | No description available  
T | No description available  
  

> hide cartoons

> hide atoms

> show cartoons

> volume #1 step 1

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for 211025_largetemp_nucleosome.pdb  
---  
Chain | Description  
2.2/N | No description available  
2.2/T | No description available  
2.2/a | No description available  
2.2/b | No description available  
2.2/c | No description available  
2.2/d | No description available  
2.2/e | No description available  
2.2/f | No description available  
2.2/g | No description available  
2.2/h | No description available  
  
Done loading forcefield  
Opened composite_map.ccp4 as #2.1.1.1, grid size 360,360,360, pixel 1.06,
shown at step 1, values float32  

> clipper spotlight radius 30.00

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Not adding hydrogens to 211025_largetemp_RNAPIIonly.pdb #3/N DT -50
P because it is missing heavy-atom bond partners  
Not adding hydrogens to 211025_largetemp_RNAPIIonly.pdb #3/P G -2 P because it
is missing heavy-atom bond partners  
Not adding hydrogens to 211025_largetemp_RNAPIIonly.pdb #3/T DC 21 P because
it is missing heavy-atom bond partners  
Not adding hydrogens to 211025_largetemp_nucleosome.pdb #2.2/N DC -105 P
because it is missing heavy-atom bond partners  
notes | No usable SEQRES records for 211025_largetemp_RNAPIIonly.pdb (#3)
chain A; guessing termini instead  
No usable SEQRES records for 211025_largetemp_RNAPIIonly.pdb (#3) chain B;
guessing termini instead  
No usable SEQRES records for 211025_largetemp_RNAPIIonly.pdb (#3) chain C;
guessing termini instead  
No usable SEQRES records for 211025_largetemp_RNAPIIonly.pdb (#3) chain D;
guessing termini instead  
No usable SEQRES records for 211025_largetemp_RNAPIIonly.pdb (#3) chain E;
guessing termini instead  
10 messages similar to the above omitted  
Chain-initial residues that are actual N termini:
211025_largetemp_RNAPIIonly.pdb #3/A SER 2, 211025_largetemp_RNAPIIonly.pdb
#3/B ASP 9, 211025_largetemp_RNAPIIonly.pdb #3/C GLU 4,
211025_largetemp_RNAPIIonly.pdb #3/D VAL 3, 211025_largetemp_RNAPIIonly.pdb
#3/E GLU 2, 211025_largetemp_RNAPIIonly.pdb #3/F GLU 71,
211025_largetemp_RNAPIIonly.pdb #3/G MET 1, 211025_largetemp_RNAPIIonly.pdb
#3/H SER 3, 211025_largetemp_RNAPIIonly.pdb #3/I SER 3,
211025_largetemp_RNAPIIonly.pdb #3/J MET 1, 211025_largetemp_RNAPIIonly.pdb
#3/K MET 1, 211025_largetemp_RNAPIIonly.pdb #3/L GLY 28,
211025_largetemp_RNAPIIonly.pdb #3/N DT -50, 211025_largetemp_RNAPIIonly.pdb
#3/P G -2, 211025_largetemp_RNAPIIonly.pdb #3/T DC 21  
Chain-initial residues that are not actual N termini:
211025_largetemp_RNAPIIonly.pdb #3/A ARG 165, 211025_largetemp_RNAPIIonly.pdb
#3/A ALA 196, 211025_largetemp_RNAPIIonly.pdb #3/A ASN 1095,
211025_largetemp_RNAPIIonly.pdb #3/A GLN 1190, 211025_largetemp_RNAPIIonly.pdb
#3/A GLU 1258, 211025_largetemp_RNAPIIonly.pdb #3/B GLY 153,
211025_largetemp_RNAPIIonly.pdb #3/B VAL 675, 211025_largetemp_RNAPIIonly.pdb
#3/B LEU 719, 211025_largetemp_RNAPIIonly.pdb #3/B TYR 931,
211025_largetemp_RNAPIIonly.pdb #3/D ILE 84, 211025_largetemp_RNAPIIonly.pdb
#3/D LEU 137, 211025_largetemp_RNAPIIonly.pdb #3/H LYS 76,
211025_largetemp_RNAPIIonly.pdb #3/N DA -31  
Chain-final residues that are actual C termini:
211025_largetemp_RNAPIIonly.pdb #3/L ARG 72, 211025_largetemp_RNAPIIonly.pdb
#3/N DG -21, 211025_largetemp_RNAPIIonly.pdb #3/P U 11,
211025_largetemp_RNAPIIonly.pdb #3/T DA 50  
Chain-final residues that are not actual C termini:
211025_largetemp_RNAPIIonly.pdb #3/A THR 1463, 211025_largetemp_RNAPIIonly.pdb
#3/A ALA 152, 211025_largetemp_RNAPIIonly.pdb #3/A SER 189,
211025_largetemp_RNAPIIonly.pdb #3/A MET 1081, 211025_largetemp_RNAPIIonly.pdb
#3/A SER 1177, 211025_largetemp_RNAPIIonly.pdb #3/A ILE 1245,
211025_largetemp_RNAPIIonly.pdb #3/B GLY 1222, 211025_largetemp_RNAPIIonly.pdb
#3/B ASP 128, 211025_largetemp_RNAPIIonly.pdb #3/B ASP 662,
211025_largetemp_RNAPIIonly.pdb #3/B SER 711, 211025_largetemp_RNAPIIonly.pdb
#3/B PRO 920, 211025_largetemp_RNAPIIonly.pdb #3/C ARG 266,
211025_largetemp_RNAPIIonly.pdb #3/D TYR 185, 211025_largetemp_RNAPIIonly.pdb
#3/D VAL 75, 211025_largetemp_RNAPIIonly.pdb #3/D HIS 129,
211025_largetemp_RNAPIIonly.pdb #3/E LEU 214, 211025_largetemp_RNAPIIonly.pdb
#3/F ASP 154, 211025_largetemp_RNAPIIonly.pdb #3/G ILE 171,
211025_largetemp_RNAPIIonly.pdb #3/H ARG 145, 211025_largetemp_RNAPIIonly.pdb
#3/H LEU 65, 211025_largetemp_RNAPIIonly.pdb #3/I GLU 113,
211025_largetemp_RNAPIIonly.pdb #3/J GLU 66, 211025_largetemp_RNAPIIonly.pdb
#3/K ASN 113, 211025_largetemp_RNAPIIonly.pdb #3/N DG -44  
3393 hydrogen bonds  
Adding 'H' to 211025_largetemp_RNAPIIonly.pdb #3/A ARG 165  
Adding 'H' to 211025_largetemp_RNAPIIonly.pdb #3/A ALA 196  
Adding 'H' to 211025_largetemp_RNAPIIonly.pdb #3/A ASN 1095  
Adding 'H' to 211025_largetemp_RNAPIIonly.pdb #3/A GLN 1190  
Adding 'H' to 211025_largetemp_RNAPIIonly.pdb #3/A GLU 1258  
7 messages similar to the above omitted  
211025_largetemp_RNAPIIonly.pdb #3/A THR 1463 is not terminus, removing H atom
from 'C'  
211025_largetemp_RNAPIIonly.pdb #3/B GLY 1222 is not terminus, removing H atom
from 'C'  
211025_largetemp_RNAPIIonly.pdb #3/C ARG 266 is not terminus, removing H atom
from 'C'  
211025_largetemp_RNAPIIonly.pdb #3/D TYR 185 is not terminus, removing H atom
from 'C'  
211025_largetemp_RNAPIIonly.pdb #3/E LEU 214 is not terminus, removing H atom
from 'C'  
6 messages similar to the above omitted  
No usable SEQRES records for 211025_largetemp_nucleosome.pdb (#2.2) chain N;
guessing termini instead  
No usable SEQRES records for 211025_largetemp_nucleosome.pdb (#2.2) chain T;
guessing termini instead  
No usable SEQRES records for 211025_largetemp_nucleosome.pdb (#2.2) chain a;
guessing termini instead  
No usable SEQRES records for 211025_largetemp_nucleosome.pdb (#2.2) chain b;
guessing termini instead  
No usable SEQRES records for 211025_largetemp_nucleosome.pdb (#2.2) chain c;
guessing termini instead  
5 messages similar to the above omitted  
Chain-initial residues that are actual N termini:
211025_largetemp_nucleosome.pdb #2.2/N DC -105,
211025_largetemp_nucleosome.pdb #2.2/T DA -72, 211025_largetemp_nucleosome.pdb
#2.2/a PRO 38, 211025_largetemp_nucleosome.pdb #2.2/b LYS 20,
211025_largetemp_nucleosome.pdb #2.2/c THR 16, 211025_largetemp_nucleosome.pdb
#2.2/d ARG 28, 211025_largetemp_nucleosome.pdb #2.2/e HIS 39,
211025_largetemp_nucleosome.pdb #2.2/f ASN 25, 211025_largetemp_nucleosome.pdb
#2.2/g ALA 14, 211025_largetemp_nucleosome.pdb #2.2/h SER 29  
Chain-initial residues that are not actual N termini:
211025_largetemp_nucleosome.pdb #2.2/N DC -20, 211025_largetemp_nucleosome.pdb
#2.2/T DC 51  
Chain-final residues that are actual C termini:
211025_largetemp_nucleosome.pdb #2.2/N DT 72, 211025_largetemp_nucleosome.pdb
#2.2/T DG 105, 211025_largetemp_nucleosome.pdb #2.2/b GLY 102,
211025_largetemp_nucleosome.pdb #2.2/d LYS 122,
211025_largetemp_nucleosome.pdb #2.2/e ALA 135,
211025_largetemp_nucleosome.pdb #2.2/f GLY 102  
Chain-final residues that are not actual C termini:
211025_largetemp_nucleosome.pdb #2.2/N DG -51, 211025_largetemp_nucleosome.pdb
#2.2/T DG 20, 211025_largetemp_nucleosome.pdb #2.2/a ARG 134,
211025_largetemp_nucleosome.pdb #2.2/c LYS 118,
211025_largetemp_nucleosome.pdb #2.2/g LYS 118,
211025_largetemp_nucleosome.pdb #2.2/h ALA 121  
1124 hydrogen bonds  
211025_largetemp_nucleosome.pdb #2.2/a ARG 134 is not terminus, removing H
atom from 'C'  
211025_largetemp_nucleosome.pdb #2.2/c LYS 118 is not terminus, removing H
atom from 'C'  
211025_largetemp_nucleosome.pdb #2.2/g LYS 118 is not terminus, removing H
atom from 'C'  
211025_largetemp_nucleosome.pdb #2.2/h ALA 121 is not terminus, removing H
atom from 'C'  
41675 hydrogens added  
  

> volume #2.1.1.1 level 5.377

> volume #2.1.1.1 level 11.43

> isolde restrain distances #2.2/N:-70--51/T:51-70

> isolde adjust distances #2.2/N:-70--51/T:51-70 kappa 100

Traceback (most recent call last):  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2599, in _xtal_mask_to_selection  
self._xtal_mask_to_atoms(sel, focus)  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2607, in _xtal_mask_to_atoms  
sh.isolate_and_cover_selection(  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/symmetry.py", line 987, in
isolate_and_cover_selection  
self.map_mgr.cover_atoms(atoms, transforms=transforms,
transform_indices=indices,  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  

> isolde adjust distances #2.2/N:-70--51/T:51-70 kappa 100

Traceback (most recent call last):  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2599, in _xtal_mask_to_selection  
self._xtal_mask_to_atoms(sel, focus)  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2607, in _xtal_mask_to_atoms  
sh.isolate_and_cover_selection(  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/symmetry.py", line 987, in
isolate_and_cover_selection  
self.map_mgr.cover_atoms(atoms, transforms=transforms,
transform_indices=indices,  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  

> volume #2.1.1.1 level 3.009

Traceback (most recent call last):  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2599, in _xtal_mask_to_selection  
self._xtal_mask_to_atoms(sel, focus)  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2607, in _xtal_mask_to_atoms  
sh.isolate_and_cover_selection(  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/symmetry.py", line 987, in
isolate_and_cover_selection  
self.map_mgr.cover_atoms(atoms, transforms=transforms,
transform_indices=indices,  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/Users/munetakaakatsu/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.5.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)

Software:

    System Software Overview:

      System Version: macOS 11.6 (20G165)
      Kernel Version: Darwin 20.6.0
      Time since boot: 2 days 27 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    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-Clipper: 0.16.1
    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-ISOLDE: 1.2.2
    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-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
    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
    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
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    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
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    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
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    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
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 4 years ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → All atoms for zone mask must be from a single model

Somehow arrange to throw LimitationError or UserError instead of TypeError?

comment:2 by Tristan Croll, 4 years ago

Resolution:	→ fixed
Status:	assigned → closed

I've already reworked this to throw a UserError here (and also to throw one earlier when starting a simulation, if the mobile selection contains no atoms - which would also otherwise end up here). That being said, I think I have to add some more verbose logging elsewhere, because I can't tell from the log exactly how the user ended up here in this case.

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