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

[irisdyoung@…]

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Other unparameterized ALA resis could be fixed but this particular one somehow could not (B ALA 87 in attached). Disclaimer: I am doing some first aid on a model that a previous user had refined exclusively in Coot, and it is known to have a lot of issues. (Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.2.2-cp38-cp38-macosx_10_13_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.16.1 ChimeraX-ISOLDE-1.2.2  
Installed ChimeraX-Clipper (0.16.1)  
Installed ChimeraX-ISOLDE (1.2.2)  
Downloading bundle ChimeraX_ISOLDE-1.2.2-cp38-cp38-macosx_10_13_x86_64.whl  
Bundle installation canceled  
Downloading bundle ChimeraX_Phenix-0.3-py3-none-any.whl  
Successfully installed ChimeraX-Phenix-0.3  
Installed ChimeraX-Phenix (0.3)  

> open
> /Users/iris/Research/Oxazolidinones/maps/WT_LZD/70S_wt_Ldz_235_512_unsharpened_volume_29_updatedpixelsize.mrc

Opened 70S_wt_Ldz_235_512_unsharpened_volume_29_updatedpixelsize.mrc as #1,
grid size 512,512,512, pixel 0.812, shown at level 2.57, step 2, values
float32  

> open
> /Users/iris/Research/Oxazolidinones/refinement_wynton/combined_70S_model_no_tRNA.pdb

Summary of feedback from opening
/Users/iris/Research/Oxazolidinones/refinement_wynton/combined_70S_model_no_tRNA.pdb  
---  
warnings | Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
138734 messages similar to the above omitted  
  
Chain information for combined_70S_model_no_tRNA.pdb #2  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> select /1:3-81

1302 atoms, 1317 bonds, 79 residues, 1 model selected  

> select /1:3-81

1302 atoms, 1317 bonds, 79 residues, 1 model selected  

> select #2

238713 atoms, 250795 bonds, 3 pseudobonds, 10525 residues, 3 models selected  

> hide #!2 models

> hide #!1 models

> show #!2 models

> close #2

> open
> /Users/iris/Research/Oxazolidinones/refinement_wynton/combined_70S_model_no_tRNA.pdb

Summary of feedback from opening
/Users/iris/Research/Oxazolidinones/refinement_wynton/combined_70S_model_no_tRNA.pdb  
---  
warnings | Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
138734 messages similar to the above omitted  
  
Chain information for combined_70S_model_no_tRNA.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> select /A:3-81

1302 atoms, 1317 bonds, 79 residues, 1 model selected  

> select /I:1-2904

93545 atoms, 101010 bonds, 1 pseudobond, 2898 residues, 2 models selected  

> select /J:2-119

3810 atoms, 4109 bonds, 118 residues, 1 model selected  

> select /J:2-119

3810 atoms, 4109 bonds, 118 residues, 1 model selected  

> select /C:2-1540

50507 atoms, 54463 bonds, 1590 residues, 1 model selected  

> select /I:1-2904

93545 atoms, 101010 bonds, 1 pseudobond, 2898 residues, 2 models selected  

> select /J:2-119

3810 atoms, 4109 bonds, 118 residues, 1 model selected  

> select #2

238712 atoms, 250793 bonds, 3 pseudobonds, 10525 residues, 3 models selected  

> ~select #2

Nothing selected  

> show #!1 models

> nucleotides atoms

> style nucleic stick

Changed 146988 atom styles  

> hide #!1 models

> style sphere

Changed 238712 atom styles  

> style sphere

Changed 238712 atom styles  

> style sphere

Changed 238712 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 146988 atom styles  

> hide surfaces

> hide cartoons

> hide atoms

> show atoms

> hide atoms

> show cartoons

> hide cartoons

> show surfaces

> show atoms

> hide surfaces

> style stick

Changed 238712 atom styles  

> show #!1 models

> volume #1 level 1.729

> volume #1 color #b2b2b2a4

> volume #1 color #b2b2b293

> volume #1 color #b2b2b280

> ui tool show "Side View"

> hide #!2 models

> show #!2 models

> hide #2.54 models

> hide #2.53 models

> hide #2.52 models

> hide #2.51 models

> hide #2.50 models

> hide #2.49 models

> hide #2.48 models

> hide #2.47 models

> hide #2.46 models

> hide #2.45 models

> hide #2.44 models

> hide #2.43 models

> hide #2.42 models

> hide #2.41 models

> hide #2.40 models

> hide #2.39 models

> hide #2.38 models

> hide #2.37 models

> hide #2.36 models

> hide #2.35 models

> hide #2.34 models

> hide #2.33 models

> hide #2.32 models

> hide #2.31 models

> hide #2.30 models

> hide #2.29 models

> hide #2.28 models

> hide #2.27 models

> hide #2.26 models

> hide #2.25 models

> hide #2.24 models

> hide #2.23 models

> hide #2.22 models

> hide #2.21 models

> hide #2.20 models

> hide #2.19 models

> hide #2.18 models

> hide #2.17 models

> hide #2.16 models

> hide #2.15 models

> hide #2.14 models

> hide #2.13 models

> hide #2.10 models

> hide #2.9 models

> hide #2.8 models

> hide #2.7 models

> hide #2.6 models

> hide #2.12 models

> hide #2.11 models

> hide #2.5 models

> hide #2.4 models

> hide #2.3 models

> hide #2.2 models

> hide #2.1 models

> view #2 clip false

> show #!2 target m

> show #!2 target m

> ui tool show "Model Panel"

> select /C

50507 atoms, 54463 bonds, 1590 residues, 1 model selected  

> select /C

50507 atoms, 54463 bonds, 1590 residues, 1 model selected  

> select clear

> select /C

50507 atoms, 54463 bonds, 1590 residues, 1 model selected  

> select clear

> select /C

50507 atoms, 54463 bonds, 1590 residues, 1 model selected  

> select clear

> close #2.3

> select down

Nothing selected  

> close #2.4-54

> select /A

1302 atoms, 1317 bonds, 79 residues, 1 model selected  

> hide #* target a

> show sel target ab

> select clear

> select /A

1302 atoms, 1317 bonds, 79 residues, 1 model selected  

> view sel

> select clear

> show atoms

> hide atoms

> show atoms

> show cartoons

> hide atoms

> hide atoms

> show atoms

> hide cartoons

> nucleotides #1#!2 tube/slab

> nucleotides #1#!2 ladder

> color #1#!2 byelement

> view chain A and resi 1

Expected an objects specifier or a view name or a keyword  

> view chain A and residue 1`

Expected an objects specifier or a view name or a keyword  

> view chain A and residue 1

Expected an objects specifier or a view name or a keyword  

> view chain A

Expected an objects specifier or a view name or a keyword  

> hide

> show /A

> view /A

> view /A/1

> view /A

> ui tool show "Show Sequence Viewer"

> close #2

> open
> /Users/iris/Research/Oxazolidinones/refinement_wynton/combined_70S_model_no_tRNA.pdb

Summary of feedback from opening
/Users/iris/Research/Oxazolidinones/refinement_wynton/combined_70S_model_no_tRNA.pdb  
---  
warnings | Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
138734 messages similar to the above omitted  
  
Chain information for combined_70S_model_no_tRNA.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #2.1 models

> show #2.1 models

> style stick

Changed 238712 atom styles  

> volume #1 step 1

> view /A:1

No objects specified.  

> view /A:10

> view /A:9

> view /A:8

> view /A:7

> view /A:6

> view /A:5

> view /A:4

> view /A:3

> view /A:2

No objects specified.  

> view /A:3

> volume #1 level 0.8816

> volume #1 level 1.575

> volume #1 level 1.96

> volume #1 color #b2b2b280

> volume #1 style mesh

> volume #1 style image

> volume #1 style surface

> volume #1 style image

> volume #1 level -0.5029,0 level 2.571,0.8 level 24.7,1

> volume #1 level -0.5029,0 level 1.411,0.8588 level 24.7,1

> volume #1 color white color #fffb00 color white

> volume #1 level -0.5029,0 level 0.4824,0.9029 level 24.7,1

> volume #1 level -0.5029,0 level 0.6371,1 level 24.7,1

> volume #1 level -0.5029,0 level 0.6371,0.9118 level 24.7,1

> volume #1 level -0.5029,0 level 0.7144,0.9706 level 24.7,1

> volume #1 level -0.5029,0 level 0.5597,1 level 24.7,1

> view /A:3

> volume #1 color white color #fffb00d9 color white

> volume #1 color white color #fffb00 color white

> volume #1 color white color #fffb00 color white

> volume #1 level -0.5029,0 level 0.5597,0.9559 level 24.7,1

> volume #1 level -0.5029,0 level 0.5597,1 level 24.7,1

> volume #1 level -0.5029,0 level 1.333,1 level 24.7,1

> volume #1 level -0.5029,0 level 2.803,1 level 24.7,1

> volume #1 style surface

> volume #1 color #0433ff

> volume #1 color #0433ff4c

> volume #1 color #0433ff4d

> view /A

> hide /

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide atoms

> show atoms /A

Expected ',' or a keyword  

> show atoms, /A

Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'  

> show /A, atoms

> volume #1 color #0433ff80

> volume #1 color #0096ff

> volume #1 color #0096ffcd

> volume #1 color #0433ff

> volume #1 color #0433ff

> volume #1 color #0433ffcf

> hide @H

> hide @H*

> volume #1 color #0433ff81

> volume #1 color #0433ffa5

> volume #1 color #0433ffa6

> toolshed show

> clipper associate #1 toModel #2

Opened 70S_wt_Ldz_235_512_unsharpened_volume_29_updatedpixelsize.mrc as
#1.1.1.1, grid size 512,512,512, pixel 0.812, shown at level 4.56, step 1,
values float32  
Chain information for combined_70S_model_no_tRNA.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | 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  
1.2/J | No description available  
1.2/K | No description available  
1.2/L | No description available  
1.2/M | No description available  
1.2/N | No description available  
1.2/O | No description available  
1.2/P | No description available  
1.2/Q | No description available  
1.2/R | No description available  
1.2/S | No description available  
1.2/T | No description available  
1.2/U | No description available  
1.2/V | No description available  
1.2/W | No description available  
1.2/X | No description available  
1.2/Y | No description available  
1.2/Z | No description available  
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  
1.2/j | No description available  
1.2/k | No description available  
1.2/l | No description available  
1.2/m | No description available  
1.2/n | No description available  
1.2/o | No description available  
1.2/p | No description available  
1.2/q | No description available  
1.2/r | No description available  
1.2/s | No description available  
1.2/t | No description available  
1.2/u | No description available  
1.2/v | No description available  
1.2/w | No description available  
1.2/x | No description available  
1.2/y | No description available  
1.2/z | No description available  
  

> show atoms

> show atoms

> hide cartoons

> show cartoons

> show atoms

> hide atoms

> volume #1.1.1.1 level 3.063

> show atoms

> hide cartoons

> hide @H*

> show cartoons

/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/app/desmonddmsfile.py:411: SyntaxWarning: "is" with a
literal. Did you mean "=="?  
if implicitSolvent is 'AGBNP3':  
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/app/desmonddmsfile.py:433: SyntaxWarning: "is" with a
literal. Did you mean "=="?  
if implicitSolvent is 'GVolSA':  
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/app/desmonddmsfile.py:440: SyntaxWarning: "is" with a
literal. Did you mean "=="?  
if implicitSolvent is 'AGBNP':  

> isolde start

> set selectionWidth 4

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  
Matplotlib is building the font cache; this may take a moment.  
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  

> select clear

> select clear

> select clear

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

Chain C, residue 4 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 5 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 6 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 7 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 8 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 9 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 10 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 11 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 12 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 13 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 14 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 15 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 16 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 17 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 18 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 19 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 20 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 21 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 22 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 23 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 24 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 25 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 26 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 27 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 28 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 29 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 30 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 31 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 32 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 33 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 34 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 35 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 36 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 37 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 38 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 39 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 40 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 41 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 42 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 43 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 44 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 45 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 46 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 47 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 48 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 49 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 50 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 51 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 52 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 53 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 54 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Fetching CCD ALA_LL from http://ligand-
expo.rcsb.org/reports/A/ALA_LL/ALA_LL.cif  
Traceback (most recent call last):  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 185, in
_fix_selected_unparameterised_residue  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 329, in
fix_residue_to_match_md_template  
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 203, in
fix_residue_from_template  
matched_nodes, residue_extra, template_extra =
find_maximal_isomorphous_fragment(residue, template,
limit_template_indices=template_indices, match_by=match_by)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 156, in
find_maximal_isomorphous_fragment  
rg = residue_graph(residue, label=match_by)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 102, in residue_graph  
return make_graph_from_residue(residue, label=label)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
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/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Deleted the following atoms from residue ALA 287: OXT, H  
Fetching CCD ARG_LL from http://ligand-
expo.rcsb.org/reports/A/ARG_LL/ARG_LL.cif  
Fetching CCD ARG_LL_DHH22 from http://ligand-
expo.rcsb.org/reports/A/ARG_LL_DHH22/ARG_LL_DHH22.cif  
Fetching CCD ARG_LEO2 from http://ligand-
expo.rcsb.org/reports/A/ARG_LEO2/ARG_LEO2.cif  
Fetching CCD NMM from http://ligand-expo.rcsb.org/reports/N/NMM/NMM.cif  
Fetching CCD ARG_LFZW from http://ligand-
expo.rcsb.org/reports/A/ARG_LFZW/ARG_LFZW.cif  
Fetching CCD 2MR from http://ligand-expo.rcsb.org/reports/2/2MR/2MR.cif  
Fetching CCD DA2 from http://ligand-expo.rcsb.org/reports/D/DA2/DA2.cif  
Fetching CCD AAG from http://ligand-expo.rcsb.org/reports/A/AAG/AAG.cif  
Fetching CCD ASN_LL from http://ligand-
expo.rcsb.org/reports/A/ASN_LL/ASN_LL.cif  
Fetching CCD ASN_LEO2 from http://ligand-
expo.rcsb.org/reports/A/ASN_LEO2/ASN_LEO2.cif  
Fetching CCD MEN from http://ligand-expo.rcsb.org/reports/M/MEN/MEN.cif  
Traceback (most recent call last):  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 185, in
_fix_selected_unparameterised_residue  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 329, in
fix_residue_to_match_md_template  
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 203, in
fix_residue_from_template  
matched_nodes, residue_extra, template_extra =
find_maximal_isomorphous_fragment(residue, template,
limit_template_indices=template_indices, match_by=match_by)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 156, in
find_maximal_isomorphous_fragment  
rg = residue_graph(residue, label=match_by)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 102, in residue_graph  
return make_graph_from_residue(residue, label=label)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
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/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 185, in
_fix_selected_unparameterised_residue  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 329, in
fix_residue_to_match_md_template  
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 203, in
fix_residue_from_template  
matched_nodes, residue_extra, template_extra =
find_maximal_isomorphous_fragment(residue, template,
limit_template_indices=template_indices, match_by=match_by)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 156, in
find_maximal_isomorphous_fragment  
rg = residue_graph(residue, label=match_by)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 102, in residue_graph  
return make_graph_from_residue(residue, label=label)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
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/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.25
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

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      Model Identifier: MacBookPro14,3
      Processor Name: Intel Core i7
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      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
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      SMC Version (system): 2.45f0

Software:

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      Revision ID: 0x0004
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      EFI Driver Version: 01.A0.927
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Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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File attachment: combined_70S_model_no_tRNA.pdb

combined_70S_model_no_tRNA.pdb​

[irisdyoung@…]

Added by email2trac

[Eric Pettersen]

Reported by Iris Young

[Tristan Croll]

Really sorry for my ridiculously slow response to this - it's been a rather fraught few months (well... a rather fraught year and a half, really!). Anyway, this turned out to be a really good test case for a bunch of improvements to the handling of unparameterised residues... it still won't fix *everything*, but it does a much better job at pointing in the right direction.