Opened 5 years ago

Last modified 5 years ago

#4016 assigned defect

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

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:        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  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.1.0-cp37-cp37m-macosx_10_13_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.15.0 ChimeraX-ISOLDE-1.1.0  
Installed ChimeraX-Clipper (0.15.0)  
Installed ChimeraX-ISOLDE (1.1.0)  

> open /Users/anne-xandervanderstel/OneDrive/DATA/Cryo-
> EM/tnaCwt/All_data_combined/Autosharpen_16/P-site_polished2_peptideselected_907A.mrc

Opened P-site_polished2_peptideselected_907A.mrc, grid size 408,408,408, pixel
0.907, shown at level 0.0244, step 2, values float32  
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.  
  

> open /Users/anne-xandervanderstel/OneDrive/DATA/Cryo-
> EM/tnaCwt/Modeling/TnaC/working_model_27102020_real_space_refined.pdb

Summary of feedback from opening /Users/anne-
xandervanderstel/OneDrive/DATA/Cryo-
EM/tnaCwt/Modeling/TnaC/working_model_27102020_real_space_refined.pdb  
---  
warnings | Ignored bad PDB record found on line 51  
LINK O4 U BB 1 N6 A BB 119  
  
Ignored bad PDB record found on line 52  
LINK N3 U BB 1 N1 A BB 119  
  
Ignored bad PDB record found on line 53  
LINK O6 G BB 2 N4 C BB 118  
  
Ignored bad PDB record found on line 54  
LINK N1 G BB 2 N3 C BB 118  
  
Ignored bad PDB record found on line 55  
LINK N2 G BB 2 O2 C BB 118  
  
9611 messages similar to the above omitted  
  
Chain information for working_model_27102020_real_space_refined.pdb #2  
---  
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  
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  
  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for working_model_27102020_real_space_refined.pdb  
---  
Chain | Description  
2.2/AA | No description available  
2.2/AB | No description available  
2.2/AC | No description available  
2.2/AD | No description available  
2.2/AE | No description available  
2.2/AF | No description available  
2.2/AG | No description available  
2.2/AH | No description available  
2.2/AI | No description available  
2.2/AJ | No description available  
2.2/AK | No description available  
2.2/AL | No description available  
2.2/AM | No description available  
2.2/AN | No description available  
2.2/AO | No description available  
2.2/AP | No description available  
2.2/AQ | No description available  
2.2/AR | No description available  
2.2/AS | No description available  
2.2/AT | No description available  
2.2/AU | No description available  
2.2/B0 | No description available  
2.2/B1 | No description available  
2.2/B2 | No description available  
2.2/B3 | No description available  
2.2/B4 | No description available  
2.2/B5 | No description available  
2.2/B7 | No description available  
2.2/B8 | No description available  
2.2/BA | No description available  
2.2/BB | No description available  
2.2/BC | No description available  
2.2/BD | No description available  
2.2/BE | No description available  
2.2/BF | No description available  
2.2/BG | No description available  
2.2/BH | No description available  
2.2/BI | No description available  
2.2/BJ | No description available  
2.2/BK | No description available  
2.2/BL | No description available  
2.2/BM | No description available  
2.2/BN | No description available  
2.2/BO | No description available  
2.2/BP | No description available  
2.2/BQ | No description available  
2.2/BS | No description available  
2.2/BT | No description available  
2.2/BU | No description available  
2.2/BV | No description available  
2.2/BW | No description available  
2.2/BX | No description available  
2.2/BY | No description available  
2.2/BZ | No description available  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to
working_model_27102020_real_space_refined.pdb #2.2  
---  
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  
6 messages similar to the above omitted  
Unknown hybridization for atoms (O4, O3, O5, O1, O2, O6) of residue type MO6;
not adding hydrogens to them  
Skipped 10 atom(s) with bad connectivities; see log for details  
notes | No usable SEQRES records for
working_model_27102020_real_space_refined.pdb (#2.2) chain AA; guessing
termini instead  
No usable SEQRES records for working_model_27102020_real_space_refined.pdb
(#2.2) chain AB; guessing termini instead  
No usable SEQRES records for working_model_27102020_real_space_refined.pdb
(#2.2) chain AC; guessing termini instead  
No usable SEQRES records for working_model_27102020_real_space_refined.pdb
(#2.2) chain AD; guessing termini instead  
No usable SEQRES records for working_model_27102020_real_space_refined.pdb
(#2.2) chain AE; guessing termini instead  
49 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, /BS MET 1, /BT MET 1, /BU ALA 2, /BV MET 1, /BW THR 10, /BX SER 2, /BY
LYS 2, /BZ ALA 2  
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 U 7, /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, /BS ARG 110, /BT LEU 93, /BU ILE 103, /BV ALA 94, /BW GLU 85, /BX
TYR 78, /BY ALA 63, /BZ GLU 59  
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 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 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /AS ARG 81 OXT  
  
5 messages similar to the above omitted  
15559 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  
96254 hydrogens added  
  
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.  
  
Deleted the following atoms from residue C AA311: OP1  
Deleted the following atoms from residue C AA576: OP1  
Fetching CCD GMP from http://ligand-expo.rcsb.org/reports/G/GMP/GMP.cif  
Deleted the following atoms from residue G AA587: OP1  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 177, in
_fix_selected_unparameterised_residue  
indices = [i for i in range(table.rowCount()) if table.item(i, 0).data[0].name
== residue.name]  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 177, in
<listcomp>  
indices = [i for i in range(table.rowCount()) if table.item(i, 0).data[0].name
== residue.name]  
AttributeError: 'NoneType' object has no attribute 'data'  
  
AttributeError: 'NoneType' object has no attribute 'data'  
  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 177, in  
indices = [i for i in range(table.rowCount()) if table.item(i, 0).data[0].name
== residue.name]  
  
See log for complete Python traceback.  
  
Deleted the following atoms from residue G AA1233: OP1  
Traceback (most recent call last):  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 177, in
_fix_selected_unparameterised_residue  
indices = [i for i in range(table.rowCount()) if table.item(i, 0).data[0].name
== residue.name]  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 177, in
<listcomp>  
indices = [i for i in range(table.rowCount()) if table.item(i, 0).data[0].name
== residue.name]  
AttributeError: 'NoneType' object has no attribute 'data'  
  
AttributeError: 'NoneType' object has no attribute 'data'  
  
File "/Users/anne-xandervanderstel/Library/Application
Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 177, in  
indices = [i for i in range(table.rowCount()) if table.item(i, 0).data[0].name
== residue.name]  
  
See log for complete Python traceback.  
  
Deleted the following atoms from residue G BA1025: OP1  
Deleted the following atoms from residue C BA1348: OP1  
Deleted the following atoms from residue U BA1781: OP1  
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.  
  

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

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

> isolde ignore sel

ISOLDE: currently ignoring 37 residues in model 2.2  

> select /AB

3536 atoms, 3567 bonds, 224 residues, 1 model selected  
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

2778 atoms, 1784 bonds, 564 pseudobonds, 523 residues, 2 models selected  

> isolde ignore sel

ISOLDE: currently ignoring 523 residues in model 2.2  

> select clear

> select /C

Nothing selected  

> select /C1308

Nothing selected  
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.  
  




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 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 5 days 22:55

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
    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
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by pett, 5 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: OpenMM: residue_graph: edges should be a n x 2 array of unsigned ints!

comment:2 by Tristan Croll, 5 years ago

I see what's happening here: your model includes the residue MO6 (a Mg2+ ion with 6 coordinated waters - FYI, this is obsoleted by the wwPDB and shouldn't be used anymore). ChimeraX doesn't really know what to do with this - the magnesium-oxygen bonds are converted to metal coordination pseudobonds, and AddH refuses to add hydrogens to the oxygens. ISOLDE doesn't have any parameterisation for clusters like this - you'll need to model it as a MG with individual HOH residues. If the density isn't great, you'll want to use ISOLDE's interactive distance restraints tool to restrain the Mg-O distances - just ctrl-click on the Mg, ctrl-shift-click on an O, and on ISOLDE's Rebuild tab find the distance restraints widget near the bottom, set the distance you want (and probably increase the spring constant to about 500), and click the add-restraint button. Sorry this is a bit involved - I'm still looking for a better, more general solution to handling metal coordination geometry.

The actual source of the error is that for unrecognised residues ISOLDE tries to use a graph-matching algorithm to match the residue to potential templates, allowing for possible missing or extraneous atoms. The problem is, due to the issues above your MO6 comes out having 7 graph nodes (atoms) and 0 edges (bonds). Not a scenario I'd foreseen, hence the traceback. Will adjust to give a more informative error message in such cases.

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