ISOLDE: OpenMM: residue_graph: edges should be a n x 2 array of unsigned ints!

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/anne-xandervanderstel/run_it012_class004.mrc

Opened run_it012_class004.mrc, grid size 232,232,232, pixel 1.65, shown at
level 0.0325, step 1, values float32  

> open /Users/anne-xandervanderstel/run_it012_class003.mrc

Opened run_it012_class003.mrc, grid size 232,232,232, pixel 1.65, shown at
level 0.0329, step 1, values float32  

> open /Users/anne-xandervanderstel/run_it012_class002.mrc

Opened run_it012_class002.mrc, grid size 232,232,232, pixel 1.65, shown at
level 0.0295, step 1, values float32  

> open /Users/anne-xandervanderstel/run_it012_class001.mrc

Opened run_it012_class001.mrc, grid size 232,232,232, pixel 1.65, shown at
level 0.0414, step 1, values float32  

> ui tool show "Fit in Map"

Fit map run_it012_class004.mrc in map run_it012_class001.mrc using 124828
points  
correlation = 0.9718, correlation about mean = 0.6184, overlap = 253.8  
steps = 44, shift = 0.105, angle = 0.141 degrees  
  
Position of run_it012_class004.mrc (#1) relative to run_it012_class001.mrc
(#4) coordinates:  
Matrix rotation and translation  
0.99999967 0.00049023 0.00065028 -0.15843902  
-0.00048873 0.99999720 -0.00231350 0.60177438  
-0.00065142 0.00231318 0.99999711 -0.21388023  
Axis 0.94325912 0.26538257 -0.19958537  
Axis point 0.00000000 88.21100735 253.93552963  
Rotation angle (degrees) 0.14051764  
Shift along axis 0.05293874  
  
Fit map run_it012_class003.mrc in map run_it012_class001.mrc using 124822
points  
correlation = 0.9488, correlation about mean = 0.4319, overlap = 229.4  
steps = 44, shift = 0.0815, angle = 0.0552 degrees  
  
Position of run_it012_class003.mrc (#2) relative to run_it012_class001.mrc
(#4) coordinates:  
Matrix rotation and translation  
0.99999986 -0.00017915 0.00049691 -0.03789797  
0.00017955 0.99999966 -0.00080528 0.17474537  
-0.00049676 0.00080537 0.99999955 0.00020528  
Axis 0.83618189 0.51586871 0.18622383  
Axis point 0.00000000 13.37035044 179.52107253  
Rotation angle (degrees) 0.05518169  
Shift along axis 0.05849430  
  
Fit map run_it012_class002.mrc in map run_it012_class001.mrc using 124849
points  
correlation = 0.942, correlation about mean = 0.4168, overlap = 206.6  
steps = 48, shift = 0.174, angle = 0.123 degrees  
  
Position of run_it012_class002.mrc (#3) relative to run_it012_class001.mrc
(#4) coordinates:  
Matrix rotation and translation  
0.99999915 0.00057194 -0.00117094 0.24702264  
-0.00056995 0.99999839 0.00170427 -0.09846196  
0.00117192 -0.00170360 0.99999786 0.11056476  
Axis -0.79432324 -0.54608666 -0.26615777  
Axis point 0.00000000 37.90665594 112.88246305  
Rotation angle (degrees) 0.12290730  
Shift along axis -0.17187473  
  

> hide #!4 models

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> volume #3 level 0.01851

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> volume #3 level 0.02289

> volume #4 level 0.02675

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> volume #2 level 0.02416

> volume #4 level 0.01183

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> volume #4 level 0.03947

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> volume #1 level 0.01949

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> volume #1 level 0.01334

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> volume #4 level 0.01984

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> volume #1 level 0.01767

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> show #!4 models

> volume #4 level 0.0309

> close #1-4

> open /Users/anne-xandervanderstel/run_it026_class004.mrc

Opened run_it026_class004.mrc, grid size 232,232,232, pixel 1.65, shown at
level 0.0337, step 1, values float32  

> open /Users/anne-xandervanderstel/run_it026_class001.mrc

Opened run_it026_class001.mrc, grid size 232,232,232, pixel 1.65, shown at
level 0.0454, step 1, values float32  

> hide #!2 models

> volume #1 level 0.01566

> show #!2 models

> hide #!1 models

> volume #2 level 0.04228

> set bgColor white

> lighting full

> save /Users/anne-
> xandervanderstel/OneDrive/PUBLICATIONS/TnaC/Figures/S2/ESRF/non-rachted.png
> width 1000 height 634 supersample 3

> hide #!2 models

> show #!1 models

> save /Users/anne-
> xandervanderstel/OneDrive/PUBLICATIONS/TnaC/Figures/S2/ESRF/racheted.png
> width 1000 height 634 supersample 3

> volume #1 level 0.01205

> volume #2 step 2

> volume #1 step 2

> volume #1 step 1

> volume #1 step 2

> show #!2 models

> hide #!2 models

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> volume #2 level 0.02011

> volume #2 step 1

> volume #1 step 1

> hide #!2 models

> vop gaussian #1 sdev 4.96

> volume #3 level 0.00732

> close #3

> show #!1 models

> toolshed show

> ui tool show "Show Volume Menu"

> ui tool show "Map Coordinates"

> ui mousemode right windowing

> toolshed show

> volume #!1 step 2

> volume #2 step 2

> volume #1 level 0.01205

> save /Users/anne-
> xandervanderstel/OneDrive/PUBLICATIONS/TnaC/Figures/S2/ESRF/racheted.png
> width 1000 height 634 supersample 3

> hide #!1 models

> show #!2 models

> volume #2 level 0.01561

> save /Users/anne-
> xandervanderstel/OneDrive/PUBLICATIONS/TnaC/Figures/S2/ESRF/non-rachted.png
> width 1000 height 634 supersample 3

> close #1

> close #2

> open /Volumes/SSD-
> partition/temp/R23F_polished_WM031120_afterISOLDE_real_space_refined.pdb

Summary of feedback from opening /Volumes/SSD-
partition/temp/R23F_polished_WM031120_afterISOLDE_real_space_refined.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL E 56
ARG E 68 1 13  
Start residue of secondary structure not found: HELIX 2 2 MET E 111 ALA E 118
1 8  
Start residue of secondary structure not found: HELIX 3 3 PRO E 133 GLU E 145
1 13  
Start residue of secondary structure not found: HELIX 4 4 PRO E 150 LYS E 156
1 7  
Start residue of secondary structure not found: SHEET 1 A 4 MET E 71 ASN E 73
0  
6 messages similar to the above omitted  
Cannot find LINK/SSBOND residue U (566561)  
Cannot find LINK/SSBOND residue U (566561)  
Cannot find LINK/SSBOND residue G (566562)  
Cannot find LINK/SSBOND residue G (566562)  
Cannot find LINK/SSBOND residue G (566562)  
4232 messages similar to the above omitted  
  
Chain information for
R23F_polished_WM031120_afterISOLDE_real_space_refined.pdb #1  
---  
Chain | Description  
AA | No description available  
AB | No description available  
AC | No description available  
AD | No description available  
AE | No description available  
AF | No description available  
AG | No description available  
AH | No description available  
AI | No description available  
AJ | No description available  
AK | No description available  
AL | No description available  
AM | No description available  
AN | No description available  
AO | No description available  
AP | No description available  
AQ | No description available  
AR | No description available  
AS | No description available  
AT | No description available  
AU | No description available  
B0 | No description available  
B1 | No description available  
B2 | No description available  
B3 | No description available  
B4 | No description available  
B5 | No description available  
B7 | No description available  
B8 | No description available  
BA | No description available  
BB | No description available  
BC | No description available  
BD | No description available  
BE | No description available  
BF | No description available  
BG | No description available  
BH | No description available  
BI | No description available  
BJ | No description available  
BK | No description available  
BL | No description available  
BM | No description available  
BN | No description available  
BO | No description available  
BP | No description available  
BQ | No description available  
BR | No description available  
BS | No description available  
BT | No description available  
BU | No description available  
BV | No description available  
BW | No description available  
BX | No description available  
BY | No description available  
BZ | No description available  
l | No description available  
m | No description available  
  

> open /Volumes/SSD-partition/temp/PE_polished_907A_sharpened28.ccp4

Opened PE_polished_907A_sharpened28.ccp4, grid size 408,408,408, pixel 0.907,
shown at level 4.78, step 2, values float32  

> volume #2 level 3.942

> volume #2 level 3.9

> style stick

Changed 146753 atom styles  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for
R23F_polished_WM031120_afterISOLDE_real_space_refined.pdb  
---  
Chain | Description  
1.2/AA | No description available  
1.2/AB | No description available  
1.2/AC | No description available  
1.2/AD | No description available  
1.2/AE | No description available  
1.2/AF | No description available  
1.2/AG | No description available  
1.2/AH | No description available  
1.2/AI | No description available  
1.2/AJ | No description available  
1.2/AK | No description available  
1.2/AL | No description available  
1.2/AM | No description available  
1.2/AN | No description available  
1.2/AO | No description available  
1.2/AP | No description available  
1.2/AQ | No description available  
1.2/AR | No description available  
1.2/AS | No description available  
1.2/AT | No description available  
1.2/AU | No description available  
1.2/B0 | No description available  
1.2/B1 | No description available  
1.2/B2 | No description available  
1.2/B3 | No description available  
1.2/B4 | No description available  
1.2/B5 | No description available  
1.2/B7 | No description available  
1.2/B8 | No description available  
1.2/BA | No description available  
1.2/BB | No description available  
1.2/BC | No description available  
1.2/BD | No description available  
1.2/BE | No description available  
1.2/BF | No description available  
1.2/BG | No description available  
1.2/BH | No description available  
1.2/BI | No description available  
1.2/BJ | No description available  
1.2/BK | No description available  
1.2/BL | No description available  
1.2/BM | No description available  
1.2/BN | No description available  
1.2/BO | No description available  
1.2/BP | No description available  
1.2/BQ | No description available  
1.2/BR | No description available  
1.2/BS | No description available  
1.2/BT | No description available  
1.2/BU | No description available  
1.2/BV | No description available  
1.2/BW | No description available  
1.2/BX | No description available  
1.2/BY | No description available  
1.2/BZ | No description available  
1.2/l | No description available  
1.2/m | No description available  
  
Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to
R23F_polished_WM031120_afterISOLDE_real_space_refined.pdb #1.2  
---  
warnings | Not adding hydrogens to /AA A 1 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /AN SER 37 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /AN ASP 38 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /AN GLU 39 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /AN ASP 40 CB because it is missing heavy-atom bond
partners  
275 messages similar to the above omitted  
Unknown hybridization for atoms (O5, O4, O2, O3, O6, O1) of residue type MO6C;
not adding hydrogens to them  
Skipped 8 atom(s) with bad connectivities; see log for details  
notes | No usable SEQRES records for
R23F_polished_WM031120_afterISOLDE_real_space_refined.pdb (#1.2) chain AA;
guessing termini instead  
No usable SEQRES records for
R23F_polished_WM031120_afterISOLDE_real_space_refined.pdb (#1.2) chain AB;
guessing termini instead  
No usable SEQRES records for
R23F_polished_WM031120_afterISOLDE_real_space_refined.pdb (#1.2) chain AC;
guessing termini instead  
No usable SEQRES records for
R23F_polished_WM031120_afterISOLDE_real_space_refined.pdb (#1.2) chain AD;
guessing termini instead  
No usable SEQRES records for
R23F_polished_WM031120_afterISOLDE_real_space_refined.pdb (#1.2) chain AE;
guessing termini instead  
52 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /AA A 1, /AB VAL 4, /AC GLY
2, /AD ALA 2, /AE GLU 10, /AF MET 1, /AG PRO 2, /AH SER 2, /AI ASN 4, /AJ GLN
4, /AK ARG 13, /AL ALA 2, /AM ALA 2, /AN ALA 1, /AO SER 2, /AP MET 1, /AQ LYS
4, /AR GLU 20, /AS ARG 3, /AT ALA 2, /AU PRO 2, /B0 ALA 2, /B1 GLY 4, /B2 MET
1, /B3 PRO 2, /B4 MET 1, /B5 VAL 8, /B7 C 1, /B8 C 1, /BA G 1, /BB U 1, /BC
ALA 2, /BD MET 1, /BE MET 1, /BF ALA 2, /BG SER 2, /BH MET 1, /BI MET 1, /BJ
MET 1, /BK MET 1, /BL MET 1, /BM MET 1, /BN MET 1, /BO MET 1, /BP SER 2, /BQ
ALA 2, /BR MET 1, /BS MET 1, /BT MET 1, /BU ALA 2, /BV MET 1, /BW THR 10, /BX
SER 2, /BY LYS 2, /BZ ALA 2, /l UNK 4, /m UNK 1  
Chain-initial residues that are not actual N termini: /BA A 892  
Chain-final residues that are actual C termini: /AA A 1534, /AC ILE 207, /AD
LYS 206, /AG ALA 152, /AH ALA 130, /AI ARG 130, /AJ LEU 102, /AK VAL 129, /AL
ALA 124, /AM PRO 115, /AN TRP 101, /AO ARG 89, /AP ALA 82, /AQ VAL 83, /AR HIS
74, /AT ALA 87, /B0 LYS 57, /B2 LYS 46, /B3 ALA 65, /B4 GLY 38, /B7 A 9, /B8 A
76, /BA U 2903, /BB U 120, /BC SER 272, /BD ALA 209, /BE ALA 201, /BF ARG 178,
/BG LYS 177, /BJ ILE 142, /BL GLU 144, /BM MET 136, /BO PHE 117, /BP ASN 115,
/BQ ALA 118, /BR ALA 103, /BS ARG 110, /BT LEU 93, /BU ILE 103, /BV ALA 94,
/BW GLU 85, /BX TYR 78, /BY ALA 63, /BZ GLU 59, /l UNK 133, /m UNK 140  
Chain-final residues that are not actual C termini: /AB GLN 227, /AE ILE 164,
/AF LYS 106, /AS ALA 84, /AU ALA 57, /B1 ILE 54, /B5 PRO 24, /BA C 885, /BH
GLU 149, /BI ILE 66, /BK LEU 123, /BN ARG 118  
Skipping possible acceptor with bad geometry: /AS ARG 81 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /AS ARG 81 OXT  
  
Skipping possible acceptor with bad geometry: /AS ARG 81 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /AS ARG 81 OXT  
  
Skipping possible acceptor with bad geometry: /AS ARG 81 O  
Wrong number of grandchild atoms for phi/psi acceptor /AS ARG 81 O  
  
Skipping possible acceptor with bad geometry: /AS ARG 81 O  
Wrong number of grandchild atoms for phi/psi acceptor /AS ARG 81 O  
  
Skipping possible acceptor with bad geometry: /AS ARG 81 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /AS ARG 81 OXT  
  
3 messages similar to the above omitted  
16253 hydrogen bonds  
/AB GLN 227 is not terminus, removing H atom from 'C'  
/AE ILE 164 is not terminus, removing H atom from 'C'  
/AF LYS 106 is not terminus, removing H atom from 'C'  
/AS ALA 84 is not terminus, removing H atom from 'C'  
/AU ALA 57 is not terminus, removing H atom from 'C'  
6 messages similar to the above omitted  
97661 hydrogens added  
  
Loading residue template for MGC from internal database  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 48, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 87, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 319, in find_possible_templates  
rgraph = self.residue_graph(res)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 87, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 319, in find_possible_templates  
rgraph = self.residue_graph(res)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> ui mousemode right "contour level"

> volume #1.1.1.1 level 7.01

Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2727, in
start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 616, in __init__  
raise e  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 595, in __init__  
isolde.forcefield_mgr)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1348, in __init__  
sim_params, residue_templates)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1430, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2707, in
_start_sim_or_toggle_pause  
self.start_sim()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2740, in
start_sim  
self._unparam_mgr._sim_unparam_res_cb()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 207, in
_sim_unparam_res_cb  
self._show_main_frame()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 48, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 87, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 319, in find_possible_templates  
rgraph = self.residue_graph(res)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2727, in
start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 616, in __init__  
raise e  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 595, in __init__  
isolde.forcefield_mgr)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1348, in __init__  
sim_params, residue_templates)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1430, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2707, in
_start_sim_or_toggle_pause  
self.start_sim()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2740, in
start_sim  
self._unparam_mgr._sim_unparam_res_cb()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 207, in
_sim_unparam_res_cb  
self._show_main_frame()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 48, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 87, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 319, in find_possible_templates  
rgraph = self.residue_graph(res)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2727, in
start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 616, in __init__  
raise e  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 595, in __init__  
isolde.forcefield_mgr)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1348, in __init__  
sim_params, residue_templates)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1430, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2707, in
_start_sim_or_toggle_pause  
self.start_sim()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2740, in
start_sim  
self._unparam_mgr._sim_unparam_res_cb()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 207, in
_sim_unparam_res_cb  
self._show_main_frame()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 48, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 87, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 319, in find_possible_templates  
rgraph = self.residue_graph(res)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> select
> :PSU:5MU:1MG:5MU:6MZ:2MG:3TD:5MU:5MC:G7M:OMG:H2U:OMC:2MA:OMU:4OC:UR3:MA6:D2T:H2U:OMC:4D4:MO6:K:MG

1256 atoms, 1309 bonds, 37 residues, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 37 residues in model 1.2  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2727, in
start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 616, in __init__  
raise e  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 595, in __init__  
isolde.forcefield_mgr)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1348, in __init__  
sim_params, residue_templates)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1430, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2707, in
_start_sim_or_toggle_pause  
self.start_sim()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2740, in
start_sim  
self._unparam_mgr._sim_unparam_res_cb()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 207, in
_sim_unparam_res_cb  
self._show_main_frame()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 48, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 87, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 319, in find_possible_templates  
rgraph = self.residue_graph(res)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 87, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 319, in find_possible_templates  
rgraph = self.residue_graph(res)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.1.0-cp37-cp37m-macosx_10_13_x86_64.whl  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/help_viewer/tool.py", line 389, in download_finished  
session=self.session)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2727, in
start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 616, in __init__  
raise e  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 595, in __init__  
isolde.forcefield_mgr)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1348, in __init__  
sim_params, residue_templates)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1430, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2707, in
_start_sim_or_toggle_pause  
self.start_sim()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/isolde.py", line 2740, in
start_sim  
self._unparam_mgr._sim_unparam_res_cb()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 207, in
_sim_unparam_res_cb  
self._show_main_frame()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 48, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 87, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 319, in find_possible_templates  
rgraph = self.residue_graph(res)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> select
> :PSU:5MU:1MG:5MU:6MZ:2MG:3TD:5MU:5MC:G7M:OMG:H2U:OMC:2MA:OMU:4OC:UR3:MA6:D2T:H2U:OMC:4D4:MO6:K:MG

1256 atoms, 1309 bonds, 37 residues, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 37 residues in model 1.2  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 87, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 319, in find_possible_templates  
rgraph = self.residue_graph(res)  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-packages/chimerax/isolde/openmm/forcefields.py",
line 270, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-14.0.32 355.11.11.10.10.143
OpenGL renderer: NVIDIA GeForce GT 650M OpenGL Engine
OpenGL vendor: NVIDIA CorporationHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro9,1
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.3 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
      Boot ROM Version: 232.0.0.0.0
      SMC Version (system): 2.1f175
      Sudden Motion Sensor:
          State: Enabled

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H15)
      Kernel Version: Darwin 19.6.0
      Time since boot: 1 day 18:59

Graphics/Displays:

    Intel HD Graphics 4000:

      Chipset Model: Intel HD Graphics 4000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0166
      Revision ID: 0x0009
      Automatic Graphics Switching: Supported
      gMux Version: 1.9.23
      Metal: Supported, feature set macOS GPUFamily1 v4

    NVIDIA GeForce GT 650M:

      Chipset Model: NVIDIA GeForce GT 650M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 512 MB
      Vendor: NVIDIA (0x10de)
      Device ID: 0x0fd5
      Revision ID: 0x00a2
      ROM Revision: 3682
      Automatic Graphics Switching: Supported
      gMux Version: 1.9.23
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
          UI Looks like: 1440 x 900
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        BenQ LCD:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 59 Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: R8G06730019 
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    decorator: 4.4.2
    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: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    versioneer: 0.19
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[Eric Pettersen]

Duplicate of #4016