Opened 3 years ago

Closed 3 years ago

#7487 closed defect (fixed)

H-bonds: cannot import name 'report_exception' from 'chimerax.core.logger'

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.4 (2021-05-14 07:23:00 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.4 (2021-05-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Model Panel"

> ui tool show "Build Structure"

> build start nucleic "custom built" A-T-A-T-G-A-C-G-C-G-C-A-C-T-A-T- type dna
> form B

Sequence letter - is illegal for DNA  

> build start nucleic "custom built" ATATGACGCGCACTAT type dna form B

Chain information for custom built #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> show cartoons

> nucleotides atoms

> style nucleic stick

Changed 650 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 650 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 650 atom styles  

> nucleotides tube/slab shape box

> color bynucleotide

> nucleotides tube/slab shape box

> nucleotides fill

> style nucleic stick

Changed 650 atom styles  

> hbonds reveal true

46 hydrogen bonds found  

> nucleotides fill

> style nucleic stick

Changed 650 atom styles  

> nucleotides ladder

> nucleotides ladder

> nucleotides fill

> style nucleic stick

Changed 650 atom styles  

> nucleotides tube/slab shape box

> color bynucleotide

> save_pdb /Users/julian/Desktop/DNA.pdb

Unknown command: save_pdb /Users/julian/Desktop/DNA.pdb  

> from chimerax.core.commands import run

Unknown command: from chimerax.core.commands import run  

> opened_models = run(session, "open /path/to/file.pdb")

Unknown command: opened_models = run(session, "open /path/to/file.pdb")  

> select backbone

346 atoms, 376 bonds, 32 residues, 1 model selected  

> color sel forest green

> select ::name="A"

81 atoms, 89 bonds, 4 residues, 1 model selected  

> color sel cyan

> select strand

Nothing selected  

> select
> ::name="A"::name="C"::name="DA"::name="DC"::name="DG"::name="DT"::name="G"::name="T"

650 atoms, 728 bonds, 46 pseudobonds, 32 residues, 2 models selected  

> color sel bynucleotide

> select ::name="DA"

102 atoms, 112 bonds, 5 residues, 1 model selected  

> build start nucleic "custom built" DATATGACGCGCACTAT type dna form B

Sequence letter D is illegal for DNA  

> rainbow sel

> rainbow sel

> select sidechain

464 atoms, 512 bonds, 46 pseudobonds, 32 residues, 2 models selected  

> select backbone

346 atoms, 376 bonds, 32 residues, 1 model selected  

> color sel forest green

> hide sel cartoons

> show sel cartoons

> nucleotides sel fill

> style nucleic & sel stick

Changed 346 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 346 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 346 atom styles  

> color sel #74aa8dff

> color sel #74aa8d98

> color sel #74aa8d97

> color sel #74aa8d94

> color sel #74aa8d92

> color sel #74aa8d91

> color sel #74aa8d90

> color sel #74aa8d8f

> color sel #74aa8d8e

> color sel #74aa8d8d

> color sel #74aa8d8d

> color sel #74aa8d8d

> color sel #74aa8d8e

> color sel #74aa8d8f

> color sel #74aa8d91

> color sel #74aa8d91

> color sel #74aa8d92

> color sel #74aa8d92

> color sel #74aa8d93

> color sel #74aa8d94

> color sel #74aa8d94

> set bgColor white

> select clear

> hbonds reveal true

46 hydrogen bonds found  

> hbonds reveal true

46 hydrogen bonds found  

> ~hbonds

Alignment identifier is 1/B  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> interfaces ~solvent

1 buried areas: B A 728  
Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> color bynucleotide

> undo

> select ::name="A"

81 atoms, 89 bonds, 4 residues, 1 model selected  

> color sel #74aa8d94

> color sel #ff9300ff

> select ::name="DA"

102 atoms, 112 bonds, 5 residues, 1 model selected  

> color sel #ff9300ff

> select ::name="T" "DT"

Expected a keyword  

> select ::name="T" and "DT"

Expected a keyword  

> select ::name="T, DT"

Nothing selected  

> select ::name="T, DT"

Nothing selected  

> select ::name="T," "DT"

Expected a keyword  

> select ::name="T", "DT"

Expected an objects specifier or a keyword  

> select ::name="T"::name="DT"

180 atoms, 189 bonds, 9 residues, 1 model selected  

> color sel #fffb00ff

> select ::name="G"::name="DG"

154 atoms, 168 bonds, 7 residues, 1 model selected  

> color sel #73fa79ff

> color sel #73fdffff

> select ::name="C"::name="DC"

133 atoms, 140 bonds, 7 residues, 1 model selected  

> color sel #73fa79ff

> select backbone

346 atoms, 376 bonds, 32 residues, 1 model selected  

> color sel #74aa8dff

> color sel #74aa8da1

> color sel #74aa8da1

> color sel #74aa8da0

> color sel #74aa8d9f

> color sel #74aa8d9d

> color sel #74aa8d9c

> color sel #74aa8d9a

> color sel #74aa8d98

> color sel #74aa8d96

> color sel #74aa8d94

> color sel #74aa8d93

> color sel #74aa8d93

> color sel #74aa8d92

> color sel #74aa8d91

> color sel #74aa8d90

> color sel #74aa8d90

> color sel #74aa8d8f

> color sel #74aa8d8e

> color sel #74aa8d8d

> color sel #74aa8d8c

> color sel #74aa8d8b

> color sel #74aa8d8b

> color sel #74aa8d8a

> color sel #74aa8d8a

> color sel #74aa8d89

> color sel #74aa8d88

> color sel #74aa8d87

> color sel #74aa8d86

> color sel #74aa8d85

> color sel #74aa8d84

> color sel #74aa8d83

> color sel #74aa8d83

> color sel #74aa8d82

> color sel #74aa8d81

> color sel #74aa8d80

> color sel #74aa8d76

> color sel #74aa8d76

> color sel #74aa8d75

> color sel #74aa8d76

> color sel #74aa8d75

> color sel #74aa8d74

> color sel #74aa8d74

> color sel #74aa8d74

> color sel #74aa8d75

> color sel #74aa8d76

> color sel #74aa8d76

> color sel #74aa8d78

> color sel #74aa8d79

> color sel #74aa8d7b

> color sel #74aa8d7b

> color sel #74aa8d7c

> color sel #74aa8d7c

> color sel #74aa8d7e

> color sel #74aa8d80

> select clear

> save /Users/julian/Desktop/DNA.cxs

> save /Users/julian/Desktop/DNA.png width 1984 height 1128 supersample 3
> transparentBackground true

> select backbone

346 atoms, 376 bonds, 32 residues, 1 model selected  

> color sel #74aa8dff

> select clear

> select ::name="C"::name="DC"

133 atoms, 140 bonds, 7 residues, 1 model selected  

> color sel forest green

> color sel medium blue

> undo

> select ::name="G"::name="DG"

154 atoms, 168 bonds, 7 residues, 1 model selected  

> color sel medium blue

> color sel #005493ff

> color sel #011993ff

> color sel #005493ff

> select ::name="T"::name="DT"

180 atoms, 189 bonds, 9 residues, 1 model selected  

> color sel #8e8b71ff

> color sel #8e886dff

> color sel #8e8568ff

> color sel #8e8464ff

> color sel #8e825dff

> color sel #8e825bff

> color sel #8e8258ff

> color sel #8e8257ff

> color sel #8e8256ff

> color sel #8e8255ff

> color sel #8e8254ff

> color sel #8e8252ff

> color sel #8e8350ff

> color sel #8e834fff

> color sel #8e844dff

> color sel #8e844cff

> color sel #8e844bff

> color sel #8e8548ff

> color sel #8e8544ff

> color sel #8e8541ff

> color sel #8e863eff

> color sel #8e863dff

> color sel #8e873dff

> color sel #8e873cff

> color sel #8e8839ff

> color sel #8e8838ff

> color sel #8e8a35ff

> color sel #8e8a34ff

> color sel #8e8a33ff

> color sel #8e8b33ff

> color sel #8e8b32ff

> color sel #8e8b31ff

> color sel #8e8c2eff

> color sel #8e8c2eff

> color sel #8e8c2dff

> color sel #8e8d2cff

> color sel #8e8c2cff

> color sel #8e8d2bff

> color sel #8e8c2bff

> color sel #8e8d2aff

> color sel #8e8d29ff

> color sel #8e8c29ff

> color sel #8e8d28ff

> color sel #8e8d29ff

> color sel #8f8e29ff

> color sel #908f29ff

> color sel #929029ff

> color sel #95932aff

> color sel #9a982cff

> color sel #9b9a2cff

> color sel #9d9c2dff

> color sel #9e9d2dff

> color sel #a3a12eff

> color sel #a4a32fff

> color sel #a6a42fff

> color sel #a8a630ff

> color sel #a9a830ff

> color sel #aeac31ff

> color sel #afad32ff

> color sel #b0ae32ff

> color sel #b0ae32ff

> color sel #b1af32ff

> color sel #b1af32ff

> color sel #b1b032ff

> color sel #b2b133ff

> color sel #b3b133ff

> color sel #b3b233ff

> color sel #b4b233ff

> color sel #b4b233ff

> color sel #b5b334ff

> color sel #b6b434ff

> color sel #b7b534ff

> color sel #b8b734ff

> color sel #bab835ff

> color sel #bbb935ff

> color sel #bcba35ff

> color sel #bcba35ff

> color sel #bdbb36ff

> color sel #bdbc36ff

> color sel #bebc36ff

> color sel #bebd36ff

> color sel #bfbd36ff

> color sel #c0be37ff

> color sel #c1bf37ff

> color sel #c2c037ff

> color sel #c2c037ff

> color sel #c3c137ff

> color sel #c3c238ff

> color sel #c4c238ff

> color sel #c6c438ff

> color sel #c7c538ff

> color sel #c9c739ff

> color sel #cac839ff

> color sel #cbc93aff

> color sel #ccca3aff

> color sel #cdcb3aff

> color sel #cdcb3aff

> color sel #cecc3bff

> color sel #cfcd3bff

> color sel #d0ce3bff

> color sel #d1cf3bff

> color sel #d2d03cff

> color sel #d2d03cff

> color sel #d4d23cff

> color sel #d5d33dff

> color sel #d6d43dff

> color sel #d7d53dff

> color sel #d8d63dff

> color sel #d7d53dff

> color sel #d7d53dff

> color sel #d6d43dff

> color sel #d6d43dff

> color sel #d5d33dff

> color sel #d5d33dff

> color sel #d4d23cff

> color sel #d4d23cff

> color sel #d4d23cff

> color sel #d3d13cff

> color sel #d2d03cff

> color sel #d1cf3cff

> color sel #d1cf3bff

> color sel #d0ce3bff

> color sel #cfcd3bff

> color sel #cfcc3bff

> color sel #cecc3aff

> color sel #cdcb3aff

> color sel #ccca3aff

> color sel #cbc93aff

> color sel #cac83aff

> color sel #cac839ff

> color sel #c9c739ff

> color sel #c9c739ff

> color sel #c8c639ff

> color sel #c8c639ff

> color sel #c7c539ff

> color sel #c6c438ff

> color sel #c5c338ff

> color sel #c5c338ff

> color sel #c4c238ff

> color sel #c4c238ff

> color sel #c3c238ff

> color sel #c3c137ff

> color sel #c3c137ff

> color sel #c1bf37ff

> color sel #bfbd36ff

> color sel #bebd36ff

> color sel #b3be2dff

> color sel #b3be2eff

> color sel #b3be31ff

> color sel #b3be32ff

> color sel #b3be33ff

> color sel #b3be34ff

> color sel #b3be34ff

> color sel #b2be35ff

> color sel #b3be35ff

> color sel #b2be36ff

> color sel #b2be36ff

> color sel #b1be36ff

> color sel #b1be37ff

> color sel #b0be38ff

> color sel #afbe38ff

> color sel #aebe38ff

> color sel #adbe39ff

> color sel #acbe39ff

> color sel #acbe39ff

> color sel #abbe3aff

> color sel #abbe3aff

> color sel #aabe3aff

> color sel #aabe3aff

> color sel #a9be3aff

> color sel #a8be3aff

> color sel #a7be3aff

> color sel #a7be3aff

> color sel #a6be3aff

> color sel #a6be3bff

> color sel #a7be3bff

> color sel #a7be3cff

> color sel #a8be3cff

> color sel #a8be3cff

> color sel #a8be3dff

> color sel #a9be3eff

> color sel #a9be3eff

> color sel #a9be3eff

> color sel #aabe3fff

> color sel #aabe3eff

> color sel #abbe3fff

> color sel #abbe40ff

> color sel #acbe40ff

> color sel #acbe41ff

> color sel #adbe41ff

> color sel #adbe41ff

> color sel #aebe41ff

> color sel #aebe41ff

> color sel #afbe41ff

> color sel #b0be41ff

> color sel #b0be41ff

> color sel #b1be41ff

> color sel #b1be41ff

> color sel #b2be41ff

> color sel #b2be42ff

> color sel #b3be41ff

> color sel #b3be42ff

> color sel #b4be42ff

> color sel #b5be42ff

> color sel #b5be42ff

> color sel #b6be42ff

> color sel #b6be41ff

> color sel #b7be41ff

> color sel #b8be40ff

> color sel #b8be40ff

> color sel #b9be40ff

> color sel #b9be3fff

> color sel #babe3fff

> color sel #bbbe3fff

> color sel #bbbe3fff

> color sel #bcbe3fff

> color sel #bdbe3eff

> color sel #bdbe3eff

> color sel #bebe3eff

> color sel #bebe3dff

> color sel #bebe3dff

> color sel #bebd3dff

> color sel #bebd3cff

> color sel #bebc3cff

> color sel #bebc3cff

> color sel #bebb3bff

> color sel #bebb3bff

> color sel #beba3bff

> color sel #beba3aff

> color sel #beb93aff

> color sel #beb93aff

> color sel #beb839ff

> color sel #beb739ff

> color sel #beb739ff

> color sel #beb638ff

> color sel #beb638ff

> color sel #beb537ff

> color sel #beb537ff

> color sel #beb437ff

> color sel #beb436ff

> color sel #beb336ff

> color sel #beb236ff

> color sel #beb235ff

> color sel #beb135ff

> color sel #beb134ff

> color sel #beaf34ff

> color sel #beae34ff

> color sel #beac34ff

> color sel #beac34ff

> color sel #beab34ff

> color sel #beaa34ff

> color sel #bea934ff

> color sel #bea834ff

> color sel #bea833ff

> color sel #bea733ff

> color sel #bea633ff

> color sel #bea533ff

> color sel #bea534ff

> color sel #bea434ff

> color sel #bea435ff

> color sel #bea335ff

> color sel #bea336ff

> color sel #bea237ff

> color sel #bea237ff

> color sel #bea238ff

> color sel #bea339ff

> color sel #bea33aff

> color sel #bea33bff

> color sel #bea33cff

> color sel #bea33cff

> color sel #bea33dff

> color sel #bea43eff

> color sel #bea43fff

> color sel #bea43fff

> color sel #bea540ff

> color sel #bea440ff

> color sel #bea541ff

> color sel #bea541ff

> color sel #bea542ff

> color sel #bea642ff

> color sel #bea543ff

> color sel #bea645ff

> color sel #bea646ff

> color sel #bea646ff

> color sel #bea747ff

> color sel #bea648ff

> color sel #bea748ff

> color sel #bea749ff

> color sel #bea849ff

> color sel #bea84aff

> color sel #bea94bff

> color sel #bea94bff

> color sel #beaa4bff

> color sel #beaa4cff

> color sel #beab4cff

> color sel #beac4dff

> color sel #beac4dff

> color sel #bead4eff

> color sel #beae4eff

> color sel #beaf4fff

> color sel #beb050ff

> color sel #beb151ff

> color sel #beb351ff

> color sel #beb352ff

> color sel #beb452ff

> color sel #beb653ff

> color sel #beb653ff

> color sel #beb753ff

> color sel #beb854ff

> color sel #beb954ff

> color sel #bebd55ff

> color sel #bebe56ff

> color sel #bebe56ff

> color sel #bebe55ff

> color sel #bebe56ff

> color sel #bdbe56ff

> color sel #bcbe56ff

> color sel #bcbe57ff

> color sel #bcbe56ff

> color sel #bbbe56ff

> color sel #babe56ff

> color sel #babe56ff

> color sel #b9be56ff

> color sel #b8be55ff

> color sel #b8be56ff

> color sel #b8be55ff

> color sel #b7be55ff

> color sel #b7be55ff

> color sel #b6be55ff

> color sel #b6be55ff

> color sel #b5be55ff

> color sel #b5be54ff

> color sel #b6be54ff

> color sel #b5be53ff

> color sel #b5be52ff

> color sel #b5be52ff

> color sel #b6be52ff

> color sel #b5be51ff

> color sel #b5be50ff

> color sel #b4be4fff

> color sel #b4be4fff

> color sel #b4be4eff

> color sel #b4be4dff

> color sel #b4be4cff

> color sel #b4be4bff

> color sel #b4be49ff

> color sel #b4be48ff

> color sel #b5be47ff

> color sel #b4be47ff

> color sel #b4be46ff

> color sel #b5be45ff

> color sel #b5be44ff

> color sel #b5be42ff

> color sel #b4be41ff

> color sel #b5be3cff

> color sel #b4be3aff

> color sel #b4be39ff

> color sel #b4be38ff

> color sel #b3be36ff

> color sel #b2be34ff

> color sel #b2be33ff

> color sel #b1be32ff

> color sel #b0be30ff

> color sel #b0be2fff

> color sel #b0be2dff

> color sel #b0be2cff

> color sel #afbe2bff

> color sel #afbe29ff

> color sel #afbe27ff

> color sel #b0be26ff

> color sel #b0be24ff

> color sel #b1be23ff

> color sel #b1be22ff

> color sel #b1be20ff

> color sel #b2be1fff

> color sel #b2be1fff

> color sel #b2be1eff

> color sel #b3be1cff

> color sel #b3be1cff

> color sel #b4be1aff

> color sel #b5be19ff

> color sel #b6be18ff

> color sel #b6be17ff

> color sel #b7be17ff

> color sel #b7be16ff

> color sel #b7be16ff

> color sel #b7be15ff

> color sel #b7be15ff

> color sel #b7be15ff

> color sel #b7be16ff

> color sel #b7be16ff

> color sel #b7be17ff

> color sel #b7be18ff

> color sel #b7be18ff

> color sel #b7be19ff

> color sel #b7be19ff

> color sel #b7be1aff

> color sel #b7be1aff

> color sel #b6be1bff

> color sel #b6be1cff

> color sel #b6be1dff

> color sel #b6be1fff

> color sel #b6be1fff

> color sel #b6be20ff

> color sel #b5be21ff

> color sel #b5be23ff

> color sel #b5be24ff

> color sel #b4be25ff

> color sel #b5be25ff

> color sel #b4be26ff

> color sel #b5be27ff

> color sel #b5be28ff

> color sel #b4be2aff

> color sel #b4be2aff

> color sel #b4be2bff

> color sel #b4be2dff

> color sel #b4be2dff

> color sel #b4be2dff

> color sel #b4be2eff

> color sel #b4be2eff

> color sel #b4be2fff

> color sel #b4be30ff

> color sel #b4be30ff

> color sel #b4be31ff

> color sel #b4be31ff

> color sel #b4be32ff

> color sel #b4be32ff

> color sel #b3be33ff

> color sel #b3be34ff

> color sel #b3be34ff

> color sel #b3be35ff

> color sel #b2be35ff

> color sel #b2be35ff

> color sel #b2be36ff

> color sel #b2be36ff

> color sel #b2be37ff

> color sel #b3be37ff

> color sel #b3be37ff

> color sel #b4be37ff

> color sel #b5be37ff

> color sel #b6be37ff

> color sel #b7be38ff

> color sel #b7be38ff

> color sel #b8be38ff

> color sel #b8be38ff

> color sel #babe38ff

> color sel #babe38ff

> color sel #bbbe38ff

> color sel #bcbe38ff

> color sel #bdbe38ff

> color sel #bdbe38ff

> color sel #bebe37ff

> color sel #bebe38ff

> color sel #bebe37ff

> color sel #bebd37ff

> color sel #bebd37ff

> color sel #bebc37ff

> color sel #bebb37ff

> color sel #beba37ff

> color sel #beba36ff

> color sel #beb936ff

> color sel #beb836ff

> color sel #beb836ff

> color sel #beb736ff

> color sel #beb736ff

> color sel #beb737ff

> color sel #beb636ff

> color sel #beb637ff

> color sel #beb537ff

> color sel #beb537ff

> color sel #beb438ff

> color sel #beb439ff

> color sel #beb339ff

> color sel #beb439ff

> color sel #beb439ff

> color sel #beb439ff

> color sel #beb539ff

> color sel #beb639ff

> color sel #beb739ff

> color sel #beb839ff

> color sel #beb839ff

> color sel #beb938ff

> color sel #beba38ff

> color sel #bebb38ff

> color sel #bebb38ff

> color sel #bebc38ff

> color sel #bebc38ff

> color sel #bebc38ff

> color sel #bebd38ff

> color sel #bebd38ff

> color sel #bebe38ff

> color sel #bebe38ff

> color sel #bdbe38ff

> color sel #bdbe38ff

> color sel #bdbe38ff

> color sel #bcbe38ff

> color sel #bbbe38ff

> color sel #bbbe38ff

> color sel #babe38ff

> color sel #b9be38ff

> color sel #b8be38ff

> color sel #b8be38ff

> color sel #b7be38ff

> color sel #b7be37ff

> color sel #b7be38ff

> color sel #b6be38ff

> color sel #b6be37ff

> color sel #b5be38ff

> color sel #b5be38ff

> color sel #b4be37ff

> color sel #b4be38ff

> color sel #b3be38ff

> color sel #b3be38ff

> color sel #b2be37ff

> color sel #b2be38ff

> color sel #b1be38ff

> color sel #b1be38ff

> color sel #b0be39ff

> color sel #b0be39ff

> color sel #afbe39ff

> color sel #aebe39ff

> color sel #aebe3aff

> color sel #adbe3aff

> color sel #adbe3aff

> color sel #adbe3bff

> color sel #adbe3bff

> color sel #acbe3bff

> color sel #abbe3bff

> color sel #abbe3cff

> color sel #abbe3dff

> color sel #aabe3dff

> color sel #aabe3dff

> color sel #a8be3dff

> color sel #a8be3eff

> color sel #a7be3fff

> color sel #a6be3fff

> color sel #a5be40ff

> color sel #a5be40ff

> color sel #a3be41ff

> color sel #a3be41ff

> color sel #a3be42ff

> color sel #a2be42ff

> color sel #a1be43ff

> color sel #a1be43ff

> color sel #a0be43ff

> color sel #a0be44ff

> color sel #a0be44ff

> color sel #9fbe44ff

> color sel #a1be42ff

> color sel #a1be42ff

> color sel #a2be41ff

> color sel #a1be41ff

> color sel #a2be41ff

> color sel #a3be40ff

> color sel #a4be41ff

> color sel #a5be41ff

> color sel #a6be41ff

> color sel #a6be42ff

> color sel #a6be43ff

> color sel #a7be43ff

> color sel #a8be44ff

> color sel #a8be44ff

> color sel #a8be45ff

> color sel #a9be46ff

> color sel #a9be46ff

> color sel #a9be48ff

> color sel #a9be49ff

> color sel #a9be4aff

> color sel #a9be4bff

> color sel #a9be4bff

> color sel #aabe4cff

> color sel #aabe4dff

> color sel #aabe4dff

> color sel #abbe4eff

> color sel #abbe4fff

> color sel #acbe4eff

> color sel #acbe4fff

> color sel #adbe4fff

> color sel #adbe4fff

> color sel #aebe50ff

> color sel #aebe4fff

> color sel #afbe50ff

> color sel #afbe50ff

> color sel #b0be50ff

> color sel #b0be50ff

> color sel #b0be51ff

> color sel #b1be51ff

> color sel #b1be51ff

> color sel #b2be51ff

> color sel #b2be52ff

> color sel #b3be51ff

> color sel #b3be52ff

> color sel #b3be52ff

> color sel #b4be53ff

> color sel #b3be52ff

> color sel #b3be52ff

> color sel #b3be51ff

> color sel #b2be51ff

> color sel #b2be50ff

> color sel #b2be4fff

> color sel #b1be4fff

> color sel #b2be4eff

> color sel #b1be4dff

> color sel #b1be4bff

> color sel #b1be4aff

> color sel #b1be4aff

> color sel #b1be49ff

> color sel #b1be48ff

> color sel #b0be48ff

> color sel #b1be46ff

> color sel #b1be44ff

> color sel #b2be43ff

> color sel #b2be42ff

> color sel #b2be42ff

> color sel #b2be41ff

> color sel #b2be40ff

> color sel #b3be40ff

> color sel #b2be3fff

> color sel #b3be3fff

> color sel #b4be3eff

> color sel #b3be3cff

> color sel #b4be3bff

> color sel #b4be3aff

> color sel #b5be39ff

> color sel #b5be38ff

> color sel #b5be38ff

> color sel #b5be37ff

> color sel #b6be36ff

> color sel #b5be35ff

> color sel #b6be34ff

> color sel #b5be34ff

> color sel #b5be33ff

> color sel #b5be32ff

> color sel #b5be31ff

> color sel #b4be30ff

> color sel #b4be30ff

> color sel #b4be2fff

> color sel #b4be2fff

> select ::name="A"::name="DA"

183 atoms, 201 bonds, 9 residues, 1 model selected  

> color sel #be8842ff

> color sel #be8942ff

> color sel #be8941ff

> color sel #be8940ff

> color sel #be8a3eff

> color sel #be8a3dff

> color sel #be8a3cff

> color sel #be8a3aff

> color sel #be8a39ff

> color sel #be8a38ff

> color sel #be8936ff

> color sel #be8a36ff

> color sel #be8935ff

> color sel #be8934ff

> color sel #be8834ff

> color sel #be8933ff

> color sel #be8833ff

> color sel #be8832ff

> color sel #be8731ff

> color sel #be8731ff

> color sel #be8630ff

> color sel #be862fff

> color sel #be852fff

> color sel #be852eff

> color sel #be842dff

> color sel #be842dff

> color sel #be832cff

> color sel #be822aff

> color sel #be812aff

> color sel #be8129ff

> color sel #be8029ff

> color sel #be8028ff

> color sel #be7f28ff

> color sel #be7e27ff

> color sel #be7e27ff

> color sel #be7d26ff

> color sel #be7d25ff

> color sel #be7b24ff

> color sel #be7a23ff

> color sel #be7922ff

> color sel #be7822ff

> color sel #be7621ff

> color sel #be7521ff

> color sel #be7520ff

> color sel #be7420ff

> color sel #be7320ff

> color sel #be731fff

> color sel #be721fff

> color sel #be701eff

> color sel #be701dff

> color sel #be6e1dff

> color sel #be6d1cff

> color sel #be6d1cff

> color sel #be6c1bff

> color sel #be6c1bff

> color sel #be6b1bff

> color sel #be6b1bff

> color sel #be6a1bff

> color sel #be691aff

> color sel #be691aff

> color sel #be681aff

> color sel #be681aff

> color sel #be671bff

> color sel #be671bff

> color sel #be661aff

> color sel #be661bff

> color sel #be661bff

> color sel #be661bff

> color sel #be671bff

> color sel #be671bff

> color sel #be671bff

> color sel #be681bff

> color sel #be681bff

> color sel #be691aff

> color sel #be691bff

> select backbone

346 atoms, 376 bonds, 32 residues, 1 model selected  

> color sel #74aa8dff

> select clear

> nucleotides fill

> style nucleic stick

Changed 650 atom styles  

> nucleotides ladder

> undo

> undo

> undo

> nucleotides ladder

> undo

> save /Users/julian/Desktop/DNAv2.png width 1984 height 1128 supersample 3
> transparentBackground true

> ui mousemode right select

Drag select of 6 atoms, 6 bonds  
Drag select of 8 atoms, 1 residues, 9 bonds  
Drag select of 8 atoms, 9 bonds  
Drag select of 8 atoms, 9 bonds  

> select clear

Drag select of 8 atoms, 9 bonds  

> color sel red

> save /Users/julian/Desktop/DNAMe.cxs

> select backbone

346 atoms, 376 bonds, 32 residues, 1 model selected  

> select backbone

346 atoms, 376 bonds, 32 residues, 1 model selected  

> ui mousemode right select

> select /B:15

326 atoms, 365 bonds, 16 residues, 1 model selected  

> select backbone

346 atoms, 376 bonds, 32 residues, 1 model selected  

> color sel dim gray

> undo

> color sel gray

> color sel #d0e1d8ff

> color sel #74aa8dff

> select clear

> save /Users/julian/Desktop/DNAMe.cxs

> save /Users/julian/Desktop/DNAMe.png width 1984 height 1128 supersample 3
> transparentBackground true

> open /Users/julian/Desktop/hPNAN/D13.pdb

> open /Users/julian/Desktop/hPNAN/h13.pdb

Chain information for h13.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

Drag select of 35 atoms, 38 bonds  
Drag select of 30 atoms, 34 bonds  

> ui mousemode right select

Drag select of 9 residues  

> ui mousemode right translate

> show sel atoms

> select

1472 atoms, 1612 bonds, 73 residues, 3 models selected  

> show sel & #2-3 atoms

> show sel & #2-3 cartoons

> color sel & #2-3 bynucleotide

> open /Users/julian/Desktop/hPNAN/D13c.pdb

Chain information for D13c.pdb #4  
---  
Chain | Description  
B | No description available  
  

> close #2

> show sel & #3 atoms

> nucleotides sel & #3 ladder

> nucleotides sel & #3 fill

> style nucleic & sel & #3 stick

Changed 0 atom styles  

> nucleotides sel & #3 atoms

> style nucleic & sel & #3 stick

Changed 0 atom styles  

> select

1472 atoms, 1612 bonds, 88 residues, 3 models selected  

> nucleotides sel & #3-4 atoms

> style nucleic & sel & #3-4 stick

Changed 325 atom styles  

> open /Users/julian/Desktop/hPNAN/D34.pdb

Chain information for D34.pdb #2  
---  
Chain | Description  
B | No description available  
  

> open /Users/julian/Desktop/hPNAN/h34.pdb

Summary of feedback from opening /Users/julian/Desktop/hPNAN/h34.pdb  
---  
warning | Duplicate atom serial number found: 669  
  
Chain information for h34.pdb #5  
---  
Chain | Description  
A | No description available  
  

> hide #3 models

> hide #2 models

> hide #4 models

> show #2 models

> nucleotides #2,5 atoms

> style nucleic & #2,5 stick

Changed 325 atom styles  

> show #2,5 atoms

> hide #5 models

> hide #2 models

> show #3 models

> show #4 models

> show sel & #3-4 atoms

> select backbone

1093 atoms, 1152 bonds, 166 residues, 5 models selected  

> select #1

650 atoms, 728 bonds, 32 residues, 1 model selected  

> ~select #1

Nothing selected  

> select #3

497 atoms, 520 bonds, 40 residues, 1 model selected  

> color sel gray

> select ::name="A"::name="DA"::name="DPA"

541 atoms, 585 bonds, 27 residues, 5 models selected  

> ui tool show "Color Actions"

> color sel #be691bff

> select ::name="A"::name="DA"::name="DPA"

541 atoms, 585 bonds, 27 residues, 5 models selected  

> color sel #be691bff

> select ::name="T"::name="DT"::name="DPT"

516 atoms, 535 bonds, 27 residues, 5 models selected  

> color sel #b4be2fff

> select ::name="C"::name="DC"::name="DPC"

383 atoms, 396 bonds, 21 residues, 5 models selected  

> color sel forest green

> select ::name="G"::name="DG"

330 atoms, 360 bonds, 15 residues, 3 models selected  

> color sel #005493ff

> select #2

325 atoms, 364 bonds, 16 residues, 1 model selected  

> ~select #2

Nothing selected  

> select #4

325 atoms, 364 bonds, 16 residues, 1 model selected  

> select backbone

1093 atoms, 1152 bonds, 166 residues, 5 models selected  

> select #3

497 atoms, 520 bonds, 40 residues, 1 model selected  

> select #4

325 atoms, 364 bonds, 16 residues, 1 model selected  

> color sel gray

> undo

> select backbone

1093 atoms, 1152 bonds, 166 residues, 5 models selected  

> hide #3 models

> show #3 models

> select #3

497 atoms, 520 bonds, 40 residues, 1 model selected  

> select #4

325 atoms, 364 bonds, 16 residues, 1 model selected  

> select #4

325 atoms, 364 bonds, 16 residues, 1 model selected  

> select #4 backbone

Expected a keyword  

> select #4 :: slecet backbone

Expected a keyword  

> select #4 :: select backbone

Expected a keyword  

> select backbone

1093 atoms, 1152 bonds, 166 residues, 5 models selected  

> select backbone #4

Expected a keyword  

> select ::name="G"::name="DG"::name="DPG"

450 atoms, 486 bonds, 21 residues, 5 models selected  

> color sel #005493ff

> hbonds sel & #3-4 reveal true

Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  

Skipped 13 atom(s) with bad connectivities; see log for details  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1285, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 1333, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 389, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 407, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 326, in run  
f(s)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 568, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 511, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/cmd.py", line 83, in cmd_hbonds  
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 694, in find_hbonds  
from chimerax.core.logger import report_exception  
ImportError: cannot import name 'report_exception' from 'chimerax.core.logger'
(/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/logger.py)  
  
ImportError: cannot import name 'report_exception' from 'chimerax.core.logger'
(/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/logger.py)  
  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 694, in find_hbonds  
from chimerax.core.logger import report_exception  
  
See log for complete Python traceback.  
  

> open /Users/julian/Desktop/hPNAN/hD13R.pdb

Chain information for hD13R.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #4 models

> hide #3 models

> nucleotides #6 atoms

> style nucleic & #6 stick

Changed 325 atom styles  

> show #6 atoms

> select ::name="A"::name="DA"::name="DPA"

720 atoms, 776 bonds, 36 residues, 6 models selected  

> color sel #be691bff

> select ::name="T"::name="DT"::name="DPT"

684 atoms, 708 bonds, 36 residues, 6 models selected  

> color sel #b4be2fff

> select ::name="C"::name="DC"::name="DPC"

508 atoms, 524 bonds, 28 residues, 6 models selected  

> color sel forest green

> select ::name="G"::name="DG"

418 atoms, 456 bonds, 19 residues, 4 models selected  

> color sel #005493ff

> select ::name="A"::name="DA"::name="DPA"

720 atoms, 776 bonds, 36 residues, 6 models selected  

> color sel #be691bff

> select ::name="T"::name="DT"::name="DPT"

684 atoms, 708 bonds, 36 residues, 6 models selected  

> color sel #b4be2fff

> select ::name="C"::name="DC"::name="DPC"

508 atoms, 524 bonds, 28 residues, 6 models selected  

> color sel forest green

> select ::name="G"::name="DG"::name="DPG"

598 atoms, 645 bonds, 28 residues, 6 models selected  

> color sel #005493ff

> hbonds sel & #6 reveal true

Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  

Skipped 13 atom(s) with bad connectivities; see log for details  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1285, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 1333, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 389, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 407, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 326, in run  
f(s)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 568, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 511, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/cmd.py", line 83, in cmd_hbonds  
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 694, in find_hbonds  
from chimerax.core.logger import report_exception  
ImportError: cannot import name 'report_exception' from 'chimerax.core.logger'
(/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/logger.py)  
  
ImportError: cannot import name 'report_exception' from 'chimerax.core.logger'
(/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/logger.py)  
  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 694, in find_hbonds  
from chimerax.core.logger import report_exception  
  
See log for complete Python traceback.  
  

> select backbone

1421 atoms, 1493 bonds, 222 residues, 6 models selected  

> color (#6 & sel) gray

> select clear

> hbonds #6 reveal true

Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  
Skipping possible acceptor with bad geometry: h34.pdb #5/A GLU 2 O  
Wrong number of grandchild atoms for phi/psi acceptor h34.pdb #5/A GLU 2 O  
  

Skipped 13 atom(s) with bad connectivities; see log for details  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1285, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 1333, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 389, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 407, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 326, in run  
f(s)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 568, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 511, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/cmd.py", line 83, in cmd_hbonds  
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 694, in find_hbonds  
from chimerax.core.logger import report_exception  
ImportError: cannot import name 'report_exception' from 'chimerax.core.logger'
(/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/logger.py)  
  
ImportError: cannot import name 'report_exception' from 'chimerax.core.logger'
(/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/logger.py)  
  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 694, in find_hbonds  
from chimerax.core.logger import report_exception  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4,2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 40 GB
      System Firmware Version: 451.140.1.0.0
      OS Loader Version: 540.120.3~19
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 12.5.1 (21G83)
      Kernel Version: Darwin 21.6.0
      Time since boot: 4 days 7:06

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        S24D330:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Adapter Firmware Version: ff.c1

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.4
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.4
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.0
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → H-bonds: cannot import name 'report_exception' from 'chimerax.core.logger'

comment:2 by Eric Pettersen, 3 years ago

Resolution: → fixed
Status: accepted → closed

Fix: ​https://github.com/RBVI/ChimeraX/commit/50b7baf7fa844b0f2dd5a6b20b28e915e5f55491

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