Problem with intra-mol excluded H-bond detection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2019-12-24)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.92 (2019-12-24)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/bcrp_az628_in.pdb

bcrp_az628_in.pdb title:  
Structure of inhibitor-bound ABCG2 [more info...]  
  
Chain information for bcrp_az628_in.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Non-standard residues in bcrp_az628_in.pdb #1  
---  
CL — (CL)  
POPC — (popc)  
SPC — (SPC)  
  

> close session

> open /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/bcrp_az628_in.pdb

bcrp_az628_in.pdb title:  
Full System [more info...]  
  
Chain information for bcrp_az628_in.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Non-standard residues in bcrp_az628_in.pdb #1  
---  
CL — (CL)  
POPC — (popc)  
SPC — (SPC)  
  

Expected an objects specifier or a keyword  

> select #1/CL

Nothing selected  

> select ::name="CL"

23 atoms, 1 model selected  

> hide ::name="CL"

> hide ::name="SPC"

> hide ::name="POPC"

> hide #1 atoms

> show ::name="UNK"

Expected a keyword  

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> set bgColor white

> open /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/bcrp_az628_out.pdb

bcrp_az628_out.pdb title:  
Full System [more info...]  
  
Chain information for bcrp_az628_out.pdb #2  
---  
Chain | Description  
A B | No description available  
  
Non-standard residues in bcrp_az628_out.pdb #2  
---  
CL — (CL)  
POPC — (popc)  
SPC — (SPC)  
  

> hide ::name="CL" ::name="SPC" ::name="POPC"

> hide #2 atoms

> show ::name="UNK"

> show #2::name="UNK"

> show sel atoms

> hide sel atoms

> select ::name="UNK"

124 atoms, 134 bonds, 2 models selected  

> show sel atoms

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> close session

> open /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/bcrp_az628_in.pdb

bcrp_az628_in.pdb title:  
Full System [more info...]  
  
Chain information for bcrp_az628_in.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Non-standard residues in bcrp_az628_in.pdb #1  
---  
CL — (CL)  
POPC — (popc)  
SPC — (SPC)  
  

> open /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/bcrp_az628_out.pdb

bcrp_az628_out.pdb title:  
Full System [more info...]  
  
Chain information for bcrp_az628_out.pdb #2  
---  
Chain | Description  
A B | No description available  
  
Non-standard residues in bcrp_az628_out.pdb #2  
---  
CL — (CL)  
POPC — (popc)  
SPC — (SPC)  
  

> select up

Nothing selected  

> hide ::name="CL" ::name="SPC" ::name="POPC"

> hide atoms

> show ::name="UNK"

> toolshed show "Side View"

> lighting soft

> color ::name="UNK" byhetero

> color ::name="UNK" byhetero

> select #1 #2

275284 atoms, 216744 bonds, 24 pseudobonds, 4 models selected  

> select #1::name='UNK'

62 atoms, 67 bonds, 1 model selected  

> color #1::name='UNK' byhetero

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #2::name='UNK' #E97B74

> color #2::name='UNK' byhetero

> color #2::name='UNK' #9C5F9F

> color #2::name='UNK' byhetero

> select #2

137642 atoms, 108372 bonds, 12 pseudobonds, 2 models selected  

> ~select #2::name='UNK'

137580 atoms, 108305 bonds, 12 pseudobonds, 2 models selected  

> color sel #E7C69A

> color sel #E97B74

> ~select

Nothing selected  

> select #1/B:535-551 #1/A:392-412 #1/A:536-551 #1/A:438-450

1053 atoms, 1058 bonds, 1 model selected  

> select #1/B:535-551 #1/A:392-412 #1/A:536-551 #1/A:438-450 #2/B:535-551
> #2/A:392-412 #2/A:536-551 #2/A:438-450

2106 atoms, 2116 bonds, 2 models selected  

> select ~sel

273178 atoms, 214628 bonds, 24 pseudobonds, 4 models selected  

> ~select ::name='UNK'

273054 atoms, 214494 bonds, 24 pseudobonds, 4 models selected  

> transparency sel 100 target c

> ~select

Nothing selected  

> graphics silhouettes true

> toolshed show H-Bonds

> hbonds intraModel false twoColors true intraMol false intraRes false

18328 hydrogen bonds found  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds  
run(self.session, " ".join(self.gui.get_command()))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/cmd.py", line 144, in cmd_hbonds  
precise[:] = [hb for hb in precise is mol_map[hb[0]] != mol_map[hb[1]]]  
UnboundLocalError: local variable 'hb' referenced before assignment  
  
UnboundLocalError: local variable 'hb' referenced before assignment  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/cmd.py", line 144, in cmd_hbonds  
precise[:] = [hb for hb in precise is mol_map[hb[0]] != mol_map[hb[1]]]  
  
See log for complete Python traceback.  
  

> save image /Users/Jphild/Documents/Papers/*JW-
> AZ628_ABCG2/8_docking/md_az628.tif format tiff pixelSize 0.03 supersample 10

> cartoon style width 1.3

> cartoon style arrowScale 2

> lighting depthCueStart .4 depthCueEnd .8

> lighting gentle

> lighting soft

> graphics silhouettes width 1

> save image /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/md_az628.tif
> format tiff pixelSize 0.03 supersample 10

> color #2::name='UNK' #E97B74

> color #2::name='UNK' byhetero

> save image /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/md_az628.tif
> format tiff pixelSize 0.03 supersample 10

> save session /Users/Jphild/Documents/Papers/*JW-
> AZ628_ABCG2/9_md/md_az628.cxs

Expected fewer arguments  

> lighting depthCueStart 1 depthCueEnd 1

> save image /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/md_az628.tif
> format tiff pixelSize 0.03 supersample 10

> select #1 #2

275284 atoms, 216744 bonds, 24 pseudobonds, 4 models selected  

> transparency sel 0 target c

> ~select

Nothing selected  

> surface protein

> hide #1 atoms

> hide #2 atoms

> lighting simple

> lighting flat

> lighting simple

> show #1::name='UNK'

> show #2::name='UNK'

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

> lighting simple

> transparency #1 50

> transparency #2 50

> hide #1 cartoons

> hide #2 cartoons

> transparency #1 100

> transparency #1 0

> hide #2

> hide #2 surfaces

> show #1::name='UNK'

> show #2::name='UNK'

> lighting soft

> view

> view

> lighting soft

> lighting full

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> set bgColor gray

> set bgColor white

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft

> lighting gentle

> cartoon style width 1.3

> lighting depthCueStart .4 depthCueEnd .8

> lighting depthCueStart 1 depthCueEnd .8

> lighting depthCueStart 1 depthCueEnd 1

> lighting depthCueStart 0.5 depthCueEnd 1

> lighting depthCueStart 1 depthCueEnd 1

> save image /Users/Jphild/Documents/Papers/*JW-
> AZ628_ABCG2/9_md/md_az628_surf)full.tif format tiff pixelSize 0.03
> supersample 10

> lighting soft

> save image /Users/Jphild/Documents/Papers/*JW-
> AZ628_ABCG2/9_md/md_az628_surf.tif format tiff pixelSize 0.03 supersample 10

> surface #1::name='UNK'

> surface #2::name='UNK'

> transparency #2.4 50

> transparency #1.4 50

> transparency #1.4 60

> transparency #2.4 60

> save image /Users/Jphild/Documents/Papers/*JW-
> AZ628_ABCG2/9_md/md_az628_surf.tif format tiff pixelSize 0.03 supersample 10

> view

> save image /Users/Jphild/Documents/Papers/*JW-
> AZ628_ABCG2/9_md/md_az628_surf_full.tif format tiff pixelSize 0.03
> supersample 10

> save session /Users/Jphild/Documents/Papers/*JW-
> AZ628_ABCG2/9_md/md_az628_surf.cxs

> close session

> open /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/md_az628.cxs

opened ChimeraX session  

> toolshed show H-Bonds

> hbonds interModel false twoColors true intraMol false intraRes false

93601 hydrogen bonds found  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds  
run(self.session, " ".join(self.gui.get_command()))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/cmd.py", line 144, in cmd_hbonds  
precise[:] = [hb for hb in precise is mol_map[hb[0]] != mol_map[hb[1]]]  
UnboundLocalError: local variable 'hb' referenced before assignment  
  
UnboundLocalError: local variable 'hb' referenced before assignment  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/cmd.py", line 144, in cmd_hbonds  
precise[:] = [hb for hb in precise is mol_map[hb[0]] != mol_map[hb[1]]]  
  
See log for complete Python traceback.  
  

> hide #1

> hide #1 cartoons

> toolshed show "Side View"

> show #2/A:446 atoms

> show #2/A:446,535,538,539,542,545 #2/B:535,538-539,542 atoms

> color #2/A:446,535,538,539,542,545 #2/B:535,538-539,542 byhetero

> toolshed show H-Bonds

> hbonds interModel false twoColors true intraMol false intraRes false

93601 hydrogen bonds found  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds  
run(self.session, " ".join(self.gui.get_command()))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/cmd.py", line 144, in cmd_hbonds  
precise[:] = [hb for hb in precise is mol_map[hb[0]] != mol_map[hb[1]]]  
UnboundLocalError: local variable 'hb' referenced before assignment  
  
UnboundLocalError: local variable 'hb' referenced before assignment  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/cmd.py", line 144, in cmd_hbonds  
precise[:] = [hb for hb in precise is mol_map[hb[0]] != mol_map[hb[1]]]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.4.7
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.

[pett]

Has mistyped 'if' as 'is'