Opened 3 years ago

Closed 3 years ago

#8790 closed defect (fixed)

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

Reported by: Jacob.Landeck@… 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:        Windows-10-10.0.22621
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
I am getting a consistant unparameterised Residue error. When I click "update" in the unparameterised residue widget I get this error. 

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"

Opened J377_006_volume_map_sharp.mrc as #1, grid size 352,352,352, pixel 0.87,
shown at level 0.0989, step 2, values float32  

> volume #1 level 0.2017

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377_startingModel.pdb"

Chain information for J377_startingModel.pdb #2  
---  
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  
  

> hide atoms

> show cartoons

> clipper associate #1 toModel #2

Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel
0.87, shown at level 0.329, step 1, values float32  
Chain information for J377_startingModel.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 145 residues in model #1.2 to IUPAC-IUB
standards.  

> volume #1.1.1.1 level 0.1754

> addh #1.2

Summary of feedback from adding hydrogens to J377_startingModel.pdb #1.2  
---  
warnings | Not adding hydrogens to /G GLN 123 OE1 because it is missing heavy-
atom bond partners  
Not adding hydrogens to /H DG 1 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond
partners  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /G GLN 123 OE1  
notes | Termini for J377_startingModel.pdb (#1.2) chain A determined from
SEQRES records  
Termini for J377_startingModel.pdb (#1.2) chain B determined from SEQRES
records  
Termini for J377_startingModel.pdb (#1.2) chain C determined from SEQRES
records  
Termini for J377_startingModel.pdb (#1.2) chain D determined from SEQRES
records  
Termini for J377_startingModel.pdb (#1.2) chain E determined from SEQRES
records  
4 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN
4, /D SER 2, /E MET 1, /F PRO -1, /G GLN 123  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO
368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A HIS 333  
Missing OXT added to C-terminal residue /B HIS 360  
Missing OXT added to C-terminal residue /C PRO 368  
Missing OXT added to C-terminal residue /D HIS 360  
Missing OXT added to C-terminal residue /E LEU 334  
1960 hydrogen bonds  
19191 hydrogens added  
  
Loading residue template for ADP from internal database  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Deleted the following atoms from residue ADP B400: H3B, H5', H5''  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> isolde sim start sel

ISOLDE: stopped sim  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> isolde sim start sel

ISOLDE: stopped sim  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> isolde sim start sel

> set selectionWidth 4

Loading residue template for ADP from internal database  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: stopped sim  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> close #1

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/postisolde.pdb"

Chain information for postisolde.pdb #1  
---  
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  
  

> hide atoms

> show cartoons

> set bgColor white

> set bgColor #ffffff00

> lighting simple

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"

Opened J377_006_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.87,
shown at level 0.0989, step 2, values float32  

> volume #2 level 0.197

> clipper associate #2 toModel #1

Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel
0.87, shown at level 0.329, step 1, values float32  
Chain information for postisolde.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
  

> start isolde

Unknown command: start isolde  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
Loading residue template for ADP from internal database  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> select #1

38623 atoms, 39043 bonds, 1 pseudobond, 2419 residues, 14 models selected  

> isolde sim start sel

ISOLDE: stopped sim  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> select add #1.1

38623 atoms, 39043 bonds, 2419 residues, 6 models selected  

> isolde sim start sel

ISOLDE: stopped sim  

> close

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"

Opened J377_006_volume_map_sharp.mrc as #1, grid size 352,352,352, pixel 0.87,
shown at level 0.0989, step 2, values float32  

> volume #1 level 0.1549

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/Open_CL_SC_ptDNA_J338_start_252-coot-0.pdb"

Chain information for Open_CL_SC_ptDNA_J338_start_252-coot-0.pdb #2  
---  
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  
  

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/Open_ptDNA_J338_start.pdb"

Summary of feedback from opening C:/Users/jtlan/OneDrive - UMass Chan Medical
School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/Open_ptDNA_J338_start.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 6
GLN A 8 1 3  
Start residue of secondary structure not found: HELIX 2 2 ARG A 10 GLN A 12 1
3  
Start residue of secondary structure not found: HELIX 3 3 PRO A 28 ASP A 36 1
9  
Start residue of secondary structure not found: HELIX 4 4 VAL A 38 ALA A 44 1
7  
Start residue of secondary structure not found: HELIX 5 5 TRP A 61 ILE A 64 1
4  
200 messages similar to the above omitted  
  
Chain information for Open_ptDNA_J338_start.pdb  
---  
Chain | Description  
3.1/A 3.3/A | No description available  
3.1/B 3.3/B | No description available  
3.1/C 3.3/C | No description available  
3.1/D 3.3/D | No description available  
3.1/E 3.3/E | No description available  
3.1/F 3.3/F | No description available  
3.1/G 3.3/G | No description available  
3.2/G 3.3/J | No description available  
3.1/H 3.3/H | No description available  
3.1/I 3.3/I | No description available  
  

> hide #!2 models

> show #!2 models

> close #2

> hide #!3.3 models

> show #!3.3 models

> hide #!3.3 models

> delete 33.3

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete #3.3

> hide #3.2 models

> show #3.2 models

> delete #3.1

> hide #3.2 models

> show #3.2 models

> hide #3.2 models

> hide #!3 models

> show #!3 models

> show #3.2 models

> delete #3

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/Open_CL_fullSC_ptDNA.pdb"

Chain information for Open_CL_fullSC_ptDNA.pdb #2  
---  
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  
  

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #!2 models

> show #!2 models

> hide #3 models

> show #3 models

> hide #3 models

> close #3

> delete #2/G:1-123

> show cartoons

> hide atoms

> delete #2/J

> volume #1 level 0.2063

> clipper associate #1 toModel #2

Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel
0.87, shown at level 0.329, step 1, values float32  
Chain information for Open_CL_fullSC_ptDNA.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 145 residues in model #1.2 to IUPAC-IUB
standards.  

> addh #1.2

Summary of feedback from adding hydrogens to Open_CL_fullSC_ptDNA.pdb #1.2  
---  
warnings | Not adding hydrogens to /H DG 1 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond
partners  
notes | Termini for Open_CL_fullSC_ptDNA.pdb (#1.2) chain A determined from
SEQRES records  
Termini for Open_CL_fullSC_ptDNA.pdb (#1.2) chain B determined from SEQRES
records  
Termini for Open_CL_fullSC_ptDNA.pdb (#1.2) chain C determined from SEQRES
records  
Termini for Open_CL_fullSC_ptDNA.pdb (#1.2) chain D determined from SEQRES
records  
Termini for Open_CL_fullSC_ptDNA.pdb (#1.2) chain E determined from SEQRES
records  
4 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN
4, /D SER 2, /E MET 1, /F PRO -1  
Chain-initial residues that are not actual N termini: /G SER 124  
Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO
368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A HIS 333  
Missing OXT added to C-terminal residue /B HIS 360  
Missing OXT added to C-terminal residue /C PRO 368  
Missing OXT added to C-terminal residue /D HIS 360  
Missing OXT added to C-terminal residue /E LEU 334  
1960 hydrogen bonds  
Adding 'H' to /G SER 124  
19189 hydrogens added  
  
Loading residue template for ADP from internal database  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Deleted the following atoms from residue ADP B400: H3B, H5', H5''  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> isolde sim start sel

ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: stopped sim  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> isolde sim start sel

ISOLDE: stopped sim  

> save "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/test.pdb"

> close

> open "C:\Users\jtlan\OneDrive - UMass Chan Medical
> School\BacterialClampLoader\ModelBuilding\Open_CL_SC_ptDNA\test.pdb" format
> pdb

Chain information for test.pdb #1  
---  
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  
  

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"

Opened J377_006_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.87,
shown at level 0.0989, step 2, values float32  

> assoc #2 to #1

Unknown command: assoc #2 to #1  

> clipper associate #2 toModel #1

Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel
0.87, shown at level 0.329, step 1, values float32  
Chain information for test.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Loading residue template for ADP from internal database  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> isolde sim start sel

ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: stopped sim  

> close

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/PostRefinement/WorkingModel_ptDNA_del-
> cha-G-1-123-coot-133.pdb"

Chain information for WorkingModel_ptDNA_del-cha-G-1-123-coot-133.pdb #1  
---  
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  
  

> lighting simple

> hide atoms

[Repeated 1 time(s)]

> show cartoons

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"

Opened J377_006_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.87,
shown at level 0.0989, step 2, values float32  

> ui mousemode right "rotate selected models"

> select add #1

19426 atoms, 19846 bonds, 1 pseudobond, 2419 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select add #1

19426 atoms, 19846 bonds, 1 pseudobond, 2419 residues, 2 models selected  

> view matrix models
> #1,0.9347,0.019254,-0.3549,66.455,-0.029687,-0.99081,-0.13194,359.78,-0.35418,0.13386,-0.92555,355.63

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.9347,0.019254,-0.3549,60.04,-0.029687,-0.99081,-0.13194,345.52,-0.35418,0.13386,-0.92555,348.75

> view matrix models
> #1,0.9347,0.019254,-0.3549,50.213,-0.029687,-0.99081,-0.13194,345.63,-0.35418,0.13386,-0.92555,344.19

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.98389,0.15313,-0.092211,-23.895,0.14922,-0.98764,-0.04799,301.41,-0.09842,0.033457,-0.99458,329.85

> toolshed show

> ui tool show "Fit in Map"

> fitmap #1 inMap #2

Fit molecule WorkingModel_ptDNA_del-cha-G-1-123-coot-133.pdb (#1) to map
J377_006_volume_map_sharp.mrc (#2) using 19426 atoms  
average map value = 0.3212, steps = 100  
shifted from previous position = 3.15  
rotated from previous position = 7.64 degrees  
atoms outside contour = 3704, contour level = 0.098888  
  
Position of WorkingModel_ptDNA_del-cha-G-1-123-coot-133.pdb (#1) relative to
J377_006_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.97784985 0.20896876 -0.01190552 -42.80492843  
0.20927960 -0.97706676 0.03927582 273.89654349  
-0.00342507 -0.04089744 -0.99915748 327.74385785  
Axis -0.99444478 -0.10518895 0.00385563  
Axis point 0.00000000 142.53424951 160.99615186  
Rotation angle (degrees) 177.68974898  
Shift along axis 15.01990745  
  

> volume #2 level 0.1802

> save "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/postref_fitJ377.pdb"
> relModel #2

> close #1

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/postref_fitJ377.pdb"

Chain information for postref_fitJ377.pdb #1  
---  
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  
  

> show cartoons

> hide atoms

> clipper associate #2 toModel #1

Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel
0.87, shown at level 0.329, step 1, values float32  
Chain information for postref_fitJ377.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 145 residues in model #1.2 to IUPAC-IUB
standards.  

> addh #1.2

Summary of feedback from adding hydrogens to postref_fitJ377.pdb #1.2  
---  
warnings | Not adding hydrogens to /G GLN 123 OE1 because it is missing heavy-
atom bond partners  
Not adding hydrogens to /H DG 1 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond
partners  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /G GLN 123 OE1  
notes | Termini for postref_fitJ377.pdb (#1.2) chain A determined from SEQRES
records  
Termini for postref_fitJ377.pdb (#1.2) chain B determined from SEQRES records  
Termini for postref_fitJ377.pdb (#1.2) chain C determined from SEQRES records  
Termini for postref_fitJ377.pdb (#1.2) chain D determined from SEQRES records  
Termini for postref_fitJ377.pdb (#1.2) chain E determined from SEQRES records  
4 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN
4, /D SER 2, /E MET 1, /F PRO -1, /G GLN 123  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO
368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A HIS 333  
Missing OXT added to C-terminal residue /B HIS 360  
Missing OXT added to C-terminal residue /C PRO 368  
Missing OXT added to C-terminal residue /D HIS 360  
Missing OXT added to C-terminal residue /E LEU 334  
1960 hydrogen bonds  
19191 hydrogens added  
  
Loading residue template for ADP from internal database  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> volume #1.1.1.1 level 0.231

> view matrix models
> #1.2,0.90086,-0.34939,0.25765,28.828,0.20337,0.86401,0.46058,-81.584,-0.38353,-0.36252,0.8494,137.56

> view matrix models
> #1.2,0.97911,0.17871,0.096979,-39.202,-0.19579,0.95733,0.21257,3.5952,-0.054852,-0.22712,0.97232,47.484

> undo

[Repeated 1 time(s)]

> ui mousemode right select

> volume #1.1.1.1 level 0.1832

> isolde sim start sel

ISOLDE: stopped sim  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 182, in
_fix_button_clicked_cb  
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 182, in
<listcomp>  
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]  
AttributeError: 'NoneType' object has no attribute 'data'  
  
AttributeError: 'NoneType' object has no attribute 'data'  
  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 182, in  
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]  
  
See log for complete Python traceback.  
  
Deleted the following atoms from residue ADP B400: H3B, H5', H5''  

> isolde sim start sel

ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> select 1

Expected an objects specifier or a keyword  

> select #1

38623 atoms, 39043 bonds, 1 pseudobond, 2419 residues, 19 models selected  

> select #2

Nothing selected  

> hide #!1.2 models

> show #!1.2 models

> select #1.2

38623 atoms, 39043 bonds, 1 pseudobond, 2419 residues, 12 models selected  

> isolde sim start sel

Simulation already running!  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: stopped sim  

> undo

Undo failed, probably because structures have been modified.  

> undo

[Repeated 2 time(s)]Undo failed, probably because structures have been
modified.  

> isolde sim start sel

ISOLDE: stopped sim  

> close

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377_startingModel-
> coot-0.pdb"

Chain information for J377_startingModel-coot-0.pdb #1  
---  
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  
  

> show cartoons

> hide atoms

> lighting simple

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"

Opened J377_006_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.87,
shown at level 0.0989, step 2, values float32  

> volume #2 level 0.1502

> clipper associate #2 toModel #1

Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel
0.87, shown at level 0.329, step 1, values float32  
Chain information for J377_startingModel-coot-0.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 145 residues in model #1.2 to IUPAC-IUB
standards.  

> addh #1.2

Summary of feedback from adding hydrogens to J377_startingModel-coot-0.pdb
#1.2  
---  
warnings | Not adding hydrogens to /G GLN 123 OE1 because it is missing heavy-
atom bond partners  
Not adding hydrogens to /H DG 1 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond
partners  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /G GLN 123 OE1  
notes | Termini for J377_startingModel-coot-0.pdb (#1.2) chain A determined
from SEQRES records  
Termini for J377_startingModel-coot-0.pdb (#1.2) chain B determined from
SEQRES records  
Termini for J377_startingModel-coot-0.pdb (#1.2) chain C determined from
SEQRES records  
Termini for J377_startingModel-coot-0.pdb (#1.2) chain D determined from
SEQRES records  
Termini for J377_startingModel-coot-0.pdb (#1.2) chain E determined from
SEQRES records  
4 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN
4, /D SER 2, /E MET 1, /F PRO -1, /G GLN 123  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO
368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A HIS 333  
Missing OXT added to C-terminal residue /B HIS 360  
Missing OXT added to C-terminal residue /C PRO 368  
Missing OXT added to C-terminal residue /D HIS 360  
Missing OXT added to C-terminal residue /E LEU 334  
1961 hydrogen bonds  
19190 hydrogens added  
  
Loading residue template for ADP from internal database  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> close

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"

Opened J377_006_volume_map_sharp.mrc as #1, grid size 352,352,352, pixel 0.87,
shown at level 0.0989, step 2, values float32  

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377_startingModel-
> coot-1.pdb"

Chain information for J377_startingModel-coot-1.pdb #2  
---  
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  
  

> volume #1 level 0.193

> show cartoons

> hide atoms

> clipper associate #1 toModel #2

Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel
0.87, shown at level 0.329, step 1, values float32  
Chain information for J377_startingModel-coot-1.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 146 residues in model #1.2 to IUPAC-IUB
standards.  

> addh #1.2

Summary of feedback from adding hydrogens to J377_startingModel-coot-1.pdb
#1.2  
---  
warnings | Not adding hydrogens to /G GLN 123 OE1 because it is missing heavy-
atom bond partners  
Not adding hydrogens to /H DG 1 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond
partners  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /G GLN 123 OE1  
notes | Termini for J377_startingModel-coot-1.pdb (#1.2) chain A determined
from SEQRES records  
Termini for J377_startingModel-coot-1.pdb (#1.2) chain B determined from
SEQRES records  
Termini for J377_startingModel-coot-1.pdb (#1.2) chain C determined from
SEQRES records  
Termini for J377_startingModel-coot-1.pdb (#1.2) chain D determined from
SEQRES records  
Termini for J377_startingModel-coot-1.pdb (#1.2) chain E determined from
SEQRES records  
4 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN
4, /D SER 2, /E MET 1, /F PRO -1, /G GLN 123  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO
368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A HIS 333  
Missing OXT added to C-terminal residue /B HIS 360  
Missing OXT added to C-terminal residue /C PRO 368  
Missing OXT added to C-terminal residue /D HIS 360  
Missing OXT added to C-terminal residue /E LEU 334  
1961 hydrogen bonds  
19191 hydrogens added  
  
Loading residue template for ADP from internal database  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1.2

38623 atoms, 39043 bonds, 1 pseudobond, 2419 residues, 12 models selected  

> isolde sim start sel

ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: stopped sim  

> close

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377_startingModel-
> coot-1.pdb"

Chain information for J377_startingModel-coot-1.pdb #1  
---  
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  
  

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"

Opened J377_006_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.87,
shown at level 0.0989, step 2, values float32  

> volume #2 level 0.1631

> clipper associate #2 toModel #1

Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel
0.87, shown at level 0.329, step 1, values float32  
Chain information for J377_startingModel-coot-1.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 146 residues in model #1.2 to IUPAC-IUB
standards.  

> select 1.2

Expected an objects specifier or a keyword  

> select #1.2

19426 atoms, 19846 bonds, 1 pseudobond, 2419 residues, 7 models selected  

> addh #1.2

Summary of feedback from adding hydrogens to J377_startingModel-coot-1.pdb
#1.2  
---  
warnings | Not adding hydrogens to /G GLN 123 OE1 because it is missing heavy-
atom bond partners  
Not adding hydrogens to /H DG 1 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond
partners  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /G GLN 123 OE1  
notes | Termini for J377_startingModel-coot-1.pdb (#1.2) chain A determined
from SEQRES records  
Termini for J377_startingModel-coot-1.pdb (#1.2) chain B determined from
SEQRES records  
Termini for J377_startingModel-coot-1.pdb (#1.2) chain C determined from
SEQRES records  
Termini for J377_startingModel-coot-1.pdb (#1.2) chain D determined from
SEQRES records  
Termini for J377_startingModel-coot-1.pdb (#1.2) chain E determined from
SEQRES records  
4 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN
4, /D SER 2, /E MET 1, /F PRO -1, /G GLN 123  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO
368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A HIS 333  
Missing OXT added to C-terminal residue /B HIS 360  
Missing OXT added to C-terminal residue /C PRO 368  
Missing OXT added to C-terminal residue /D HIS 360  
Missing OXT added to C-terminal residue /E LEU 334  
1961 hydrogen bonds  
19191 hydrogens added  
  
Loading residue template for ADP from internal database  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> close

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"

Opened J377_006_volume_map_sharp.mrc as #1, grid size 352,352,352, pixel 0.87,
shown at level 0.0989, step 2, values float32  

> volume #1 level 0.2316

> open "C:/Users/jtlan/OneDrive - UMass Chan Medical
> School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377_startingModel-
> coot-2.pdb"

Chain information for J377_startingModel-coot-2.pdb #2  
---  
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  
  

> hide atoms

> show cartoons

> clipper associate #1 toModel #2

Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel
0.87, shown at level 0.329, step 1, values float32  
Chain information for J377_startingModel-coot-2.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 145 residues in model #1.2 to IUPAC-IUB
standards.  

> addh #1.2

Summary of feedback from adding hydrogens to J377_startingModel-coot-2.pdb
#1.2  
---  
warnings | Not adding hydrogens to /G GLN 123 OE1 because it is missing heavy-
atom bond partners  
Not adding hydrogens to /H DG 1 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond
partners  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /G GLN 123 OE1  
notes | Termini for J377_startingModel-coot-2.pdb (#1.2) chain A determined
from SEQRES records  
Termini for J377_startingModel-coot-2.pdb (#1.2) chain B determined from
SEQRES records  
Termini for J377_startingModel-coot-2.pdb (#1.2) chain C determined from
SEQRES records  
Termini for J377_startingModel-coot-2.pdb (#1.2) chain D determined from
SEQRES records  
Termini for J377_startingModel-coot-2.pdb (#1.2) chain E determined from
SEQRES records  
4 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN
4, /D SER 2, /E MET 1, /F PRO -1, /G GLN 123  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO
368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A HIS 333  
Missing OXT added to C-terminal residue /B HIS 360  
Missing OXT added to C-terminal residue /C PRO 368  
Missing OXT added to C-terminal residue /D HIS 360  
Missing OXT added to C-terminal residue /E LEU 334  
1963 hydrogen bonds  
19192 hydrogens added  
  
Loading residue template for ADP from internal database  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> select #1.2

38623 atoms, 39043 bonds, 1 pseudobond, 2419 residues, 7 models selected  

> isolde sim start sel

ISOLDE: stopped sim  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 95, in
_populate_unparameterised_residue_table  
by_name, by_comp = ff.find_possible_templates(r)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 317, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, 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 "C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\openmm\forcefields.py", line 268, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  

> volume #1.1.1.1 step 2

> volume #1.1.1.1 step 1




OpenGL version: 3.3.0 - Build 31.0.101.4032
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: LENOVO
Model: 21DJ
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 16,874,135,552
MaxProcessMemory: 137,438,953,344
CPU: 12 12th Gen Intel(R) Core(TM) i7-1255U
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.19.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.5
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StarMap: 1.1.70
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    pyqtgraph: 0.13.1
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0

Change History (2)

comment:1 by pett, 3 years ago

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

comment:2 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

The problem was three BEF residues in the model, which each contain four atoms but were instantiated in ChimeraX with no internal bonds (the PDB file contains CONECT records, but I'm guessing they don't cover these atoms). I had a sanity-check on the number of *atoms*, but not the number of *bonds*. Fix will be in the next release.

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