ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.4.0-80-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.4 (2021-05-14 07:23:00 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
> close session

> camera ortho

> graphics bgColor white

> view orient

> view initial

> lighting depthCue false

> lighting default

> lighting shadows false

> cartoon style width 1.8 thickness 0.38

> cartoon style strand xsection barbell barScale 0.45 width 1.8 thickness 0.35

> cartoon style helix xsection barbell barScale 0.45 width 1.8 thickness 0.35

> cartoon style coil xsection barbell barScale 0.45 width 1.8 thickness 0.35

> size protein stickRadius 0.19

Changed 0 bond radii  

> size nucleic stickRadius 0.19

Changed 0 bond radii  

> windowsize 600 700

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  

> open
> /home/buttner/Documents/CVA6_build/r31_Full/cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063.mrc

Opened
cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063.mrc as
#1, grid size 320,320,320, pixel 1.06, shown at level 4.14, step 2, values
float32  

> volume #1 step 1

> volume #1 step 1 level 1.2 color gray(60%) style mesh surfaceSmoothing true
> subdivideSurface true smoothLines true squareMesh true dimTransparency true

> transparency #1 50 surfaces

> open
> /home/buttner/Documents/CVA6_build/r31_Full/cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc

Opened
cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc
as #2, grid size 320,320,320, pixel 1.06, shown at level 2.69, step 2, values
float32  

> ui tool show "Map Coordinates"

> hide #!1 models

> show #!1 models

> volume #2 step 1 level 1.2 color gray(60%) style mesh surfaceSmoothing true
> subdivideSurface true smoothLines true squareMesh true dimTransparency true

> transparency #2 50 surfaces

> close #1

> open
> /home/buttner/Documents/CVA6_build/r31_Full/RNA_modelled/RNA_ushf_strand_alt0_fitref-
> coot.pdb

Chain information for RNA_ushf_strand_alt0_fitref-coot.pdb #1  
---  
Chain | Description  
E | No description available  
  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> view #1

> color #1 byhetero

> color #1&nucleic & C magenta

> color #1 byhetero

> sym #1 i,222 range 75

> color #1&nucleic & C magenta

> color #all&nucleic & C magenta ;

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

> color #&nucleic & C magenta ;

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

> color #3&nucleic & C magenta

> color #3&nucleic magenta

> zonecol

Unknown command: zonecol  

> color zone

Missing or invalid "surfaces" argument: empty atom specifier  

> color zone #2 near #3 distance 8

> color zone #2 near #3 distance 6

> color zone #2 near #3 distance 5

> color zone #2 near #3 distance 4.5

> color zone #2 near #3 distance 4

> sym #1 i,222

> color zone #2 near #3 distance 4

> close #3

> sym #1 i,222

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #1 models

> show #1 models

> ~sym #1 i,222 ;

Unknown command: ~sym #1 i,222 ;  

> ~sym #1 ;

Unknown command: ~sym #1 ;  

> sym clear #1

> color unzone

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

> color single #2

> hide #!2 models

> hide #1 models

> show #1 models

> clip off

> view #1

> sym #1 i,222 copies true

> ]

Unknown command: ]  

> sym #1 i,222 copies true

> close #4

> close #3

> sym #1 i,222 copies true

> color single #2

> color zone #2 near #3 distance 4

> show #!2 models

> color #3&nucleic magenta

> color single #2

> color zone #2 near #3 distance 4

> view orient

> cofr #2

> cofr #2

> clip off

> clip front 0 back 30 position cofr

> cofr #2

> clip off

> clip front 0 back 90 position cofr

> cofr #2

> clip off

> clip front 0 back 130 position cofr

> cofr #2

> clip off

> clip front 0 position cofr

> volume #2 step 1 level 1.2 color gray(60%) style surface surfaceSmoothing
> true subdivideSurface true smoothLines true squareMesh true dimTransparency
> true

> color #2.1.1 white

> color #2.1.1 gray(20%)

> color #2.1.1 gray(40%)

> color #2.1.1 gray(50%)

> color #2.1.1 gray(50%)

> color #2.1.1 gray(20%)

> color #2.1.1 gray(70%)

> color #2.1.1 gray(90%)

> color #2.1.1 gray(80%)

> color #2.1.1 gray(60%)

> color #2.1.1 gray(80%)

> color #2.1.1 gray(85%)

> color #2.1.1 gray(80%)

> color #2.1.1 gray(70%)

> color #2.1.1 gray(40%)

> color #2.1.1 gray(90%)

> color #2.1.1 gray(80%)

> color #2.1.1 gray(82%)

> lighting depthCue false

> clip off

> clip front 0 position cofr

> clip off

> clip front 0 position cofr

> view orient

> save
> /home/buttner/Documents/DocumentsSel/Data/Labbook/LB_silico/CVA6_SPA/210817_r31_cva6_2d3_full_unmaskedB100blur_cl1x2_RNA_sym_density.png
> format png width 700 supersample 3 transparentBackground true

> hide #3.1 models

> show #3.1 models

> hide #!2 models

> hide #3.1 models

> show #3.1 models

> hide #3.1 models

> show #3.1 models

> hide #3.60 models

> show #3.60 models

> hide #3.18 models

> show #3.18 models

> hide #3.9 models

> show #3.9 models

> hide #3.8 models

> show #3.8 models

> hide #3.6 models

> show #3.6 models

> hide #3.2 models

> show #3.2 models

> hide #3.10 models

> show #3.10 models

> hide #3.15 models

> show #3.15 models

> hide #3.16 models

> show #3.16 models

> hide #3.17 models

> show #3.17 models

> hide #3.22 models

> show #3.22 models

> hide #3.23 models

> show #3.23 models

> hide #3.26 models

> show #3.26 models

> hide #3.29 models

> show #3.29 models

> hide #3.32 models

> show #3.32 models

> hide #3.35 models

> show #3.35 models

> hide #3.38 models

> show #3.38 models

> hide #3.41 models

> show #3.41 models

> hide #3.40 models

> show #3.40 models

> hide #3.39 models

> show #3.39 models

> hide #3.41 models

> show #3.41 models

> hide #3.55 models

> show #3.55 models

> hide #3.54 models

> show #3.54 models

> view #3.7#3.45

> select #2

3 models selected  

> ~select #2

Nothing selected  

> show #!2 models

> hide #3.* target abc

> view orient

> save
> /home/buttner/Documents/DocumentsSel/Data/Labbook/LB_silico/CVA6_SPA/210817_r31_cva6_2d3_full_unmaskedB100blur_cl1x2_RNA_sym_density.png
> format png width 700 supersample 3 transparentBackground true

> save
> /home/buttner/Documents/DocumentsSel/Data/Labbook/LB_silico/CVA6_SPA/210817_r31_cva6_2d3_full_unmaskedB100blur_cl1x2_RNA_sym_density.png
> format png width 700 supersample 3 transparentBackground true

> view #3.7#3.45

No displayed objects specified.  

> show #3.7#3.45 target abc

> view #3.7#3.45

> volume #2 step 1 level 1.2 color gray(60%) style mesh surfaceSmoothing true
> subdivideSurface true smoothLines true squareMesh true dimTransparency true

> volume #2 step 1 level 1.2 color gray(60%) style mesh surfaceSmoothing true
> subdivideSurface true smoothLines true squareMesh true dimTransparency true

> transparency #2 50 surfaces

> volume #2 step 1 level 1.2 color gray(60%) style surface surfaceSmoothing
> true subdivideSurface true smoothLines true squareMesh true dimTransparency
> true

> transparency #2 50 surfaces

> nucleotides #3.1-60 atoms

> style nucleic & #3.1-60 stick

Changed 6180 atom styles  

> nucleotides #3.1-60 fill

> style nucleic & #3.1-60 stick

Changed 6180 atom styles  

> nucleotides #3.1-60 slab

> style nucleic & #3.1-60 stick

Changed 6180 atom styles  

> nucleotides #3.1-60 tube/slab shape box

> nucleotides #3.1-60 atoms

> style nucleic & #3.1-60 stick

Changed 6180 atom styles  

> nucleotides #3.1-60 tube/slab shape ellipsoid

> nucleotides #3.1-60 tube/slab shape muffler

> nucleotides #3.1-60 fill

> style nucleic & #3.1-60 stick

Changed 6180 atom styles  

> nucleotides #3.1-60 slab

> style nucleic & #3.1-60 stick

Changed 6180 atom styles  

> nucleotides #3.1-60 ladder

> nucleotides #3.1-60 stubs

> nucleotides #3.1-60 ladder

> nucleotides #3.1-60 stubs

> nucleotides #3.1-60 ladder

> nucleotides #3.1-60 tube/slab shape muffler

> nucleotides #3.1-60 tube/slab shape ellipsoid

> nucleotides #3.1-60 tube/slab shape box

> nucleotides #3.1-60 atoms

> style nucleic & #3.1-60 stick

Changed 6180 atom styles  

> hide #2.1.2 models

> show #2.1.2 models

> hide #2.1.1 models

> show #2.1.1 models

> hide #2.1.3 models

> show #2.1.3 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2 models

> show #!2 models

> volume #2 step 1 level 1.2 color gray(60%) style surface surfaceSmoothing
> true subdivideSurface true smoothLines true squareMesh true dimTransparency
> true

> transparency #2 50 surfaces

> view #3.7#3.45

> turn x 90

> turn x -90

> turn x -90

> view #3.7#3.45

> cofr #3.7#3.45

> turn x 90

> cofr #3.7#3.45

> turn x -90

> clip off

> clip front 0 position cofr

> clip off

> clip front 0 back 8 position cofr

> clip off

> clip front 0 back 12 position cofr

> clip off

> clip front 0 back 20 position cofr

> clip off

> clip front 0 back 30 position cofr

> clip off

> clip front -5 back 30 position cofr

> clip off

> clip front -8 back 30 position cofr

> clip off

> clip front -10 back 30 position cofr

> clip off

> clip front -14 back 30 position cofr

> clip off

> clip front -12 back 30 position cofr

> clip off

> clip front -12 back 30 position cofr

> clip off

> clip front -12 back 20 position cofr

> clip off

> clip front -12 back 15 position cofr

> clip off

> clip front -12 back 12 position cofr

> close session

> open
> /home/buttner/Documents/CVA6_build/RNA_modelled/RNA_ushf_strand_alt0_fitref-
> coot.pdb

No such file/path:
/home/buttner/Documents/CVA6_build/RNA_modelled/RNA_ushf_strand_alt0_fitref-
coot.pdb  

> open
> /home/buttner/Documents/CVA6_build/r31_Full/cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc

Opened
cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc
as #1, grid size 320,320,320, pixel 1.06, shown at level 2.69, step 2, values
float32  

> volume #2 step 1 level 1.2 color gray(60%) style surface surfaceSmoothing
> true subdivideSurface true smoothLines true squareMesh true dimTransparency
> true

No volumes specified  

> view orient

> close #1

> open
> /home/buttner/Documents/CVA6_build/RNA_modelled/RNA_ushf_strand_alt0_fitref-
> coot.pdb

No such file/path:
/home/buttner/Documents/CVA6_build/RNA_modelled/RNA_ushf_strand_alt0_fitref-
coot.pdb  

> open
> /home/buttner/Documents/CVA6_build/r31_Full/RNA_modelled/RNA_ushf_strand_alt0_fitref-
> coot.pdb

Chain information for RNA_ushf_strand_alt0_fitref-coot.pdb #1  
---  
Chain | Description  
E | No description available  
  

> open
> /home/buttner/Documents/CVA6_build/r31_Full/cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc

Opened
cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc
as #2, grid size 320,320,320, pixel 1.06, shown at level 2.69, step 2, values
float32  

> volume #2 step 1 level 1.2 color gray(60%) style surface surfaceSmoothing
> true subdivideSurface true smoothLines true squareMesh true dimTransparency
> true

> view orient

> lighting depthCue false

> sym #1 i,222 copies true

> color #3&nucleic magenta

> color single #2

> color zone #2 near #3 distance 4

> hide #3.* target abc

> cofr #2

> clip off

> clip front 0 position cofr

> color #2.1.1 gray(82%)

> view orient

> lighting depthCue false

> sym #1 i,222 copies true

> color #3&nucleic magenta

> color single #2

> color zone #2 near #3 distance 4

> hide #3.* target abc

> cofr #2

> clip off

> clip front 0 position cofr

> color #2.1.1 gray(82%)

> volume #2 originIndex 160,160,160

> clip off

> view orient

> lighting depthCue false

> sym #1 i,222 copies true

> color #3&nucleic magenta

> color single #2

> color zone #2 near #3 distance 4

> hide #3.* target abc

> cofr #2

> clip off

> clip front 0 position cofr

> color #2.1.1 gray(82%)

> show #3.7#3.45 target abc

> view #3.7#3.45

> cofr #3.7#3.45

> volume #2 step 1 level 1.2 color gray(60%) style surface surfaceSmoothing
> true subdivideSurface true smoothLines true squareMesh true dimTransparency
> true

> transparency #2 50 surfaces

> turn x -90

> clip off

> clip front -12 back 12 position cofr

> surface dust #2 size 4

> surface dust #2 size 3.5

> surface dust #2 size 3.5

> close #5

> close #4

> close #3

> sym #1 i,222 copies true

> color #3&nucleic magenta

> color single #2

> color zone #2 near #3 distance 4

> hide #3.* target abc

> cofr #2

> clip off

> clip front 0 position cofr

> color #2.1.1 gray(82%)

> color #2.1.1 gray(82%)

> view orient

> clip off

> clip off

> clip front 0 position cofr

> color #2.1.1 gray(82%)

> show #3.7#3.45 target abc

> view #3.7#3.45

> cofr #3.7#3.45

> volume #2 step 1 level 1.2 color gray(60%) style surface surfaceSmoothing
> true subdivideSurface true smoothLines true squareMesh true dimTransparency
> true

> transparency #2 50 surfaces

> turn x -90

> clip off

> clip front -12 back 12 position cofr

> clip off

> turn x 90

> zoom 0.9

> view #3.7#3.45

> view zoom 0.9

Expected an objects specifier or a view name or a keyword  

> view #3.7#3.45

> view #3.7#3.45

> zoom 0.9

> view #3.7#3.45

> zoom 0.8

> nucleotides #3.1-60 fill

> style nucleic & #3.1-60 stick

Changed 6180 atom styles  

> transparency #2 70 surfaces

> zone

> zone #3.7#3.45 surfaceDistance 8

Must specify a single residue, 10 specified  

> zone #3.7/E/2 residueDistance 5 surfaceDistance 8

Must specify a single residue, 5 specified  

> zone #3.7/E:2 residueDistance 5 surfaceDistance 8

> zone #3.7/E/2 residueDistance 5 surfaceDistance 12

Must specify a single residue, 5 specified  

> zone #3.7/E:2 residueDistance 5 surfaceDistance 12

> zone #3.7/E:2 residueDistance 12 surfaceDistance 12

> zone #3.7/E:2 surfaceDistance 12

> zone clear

> zone #3.7/E:2 surfaceDistance 12

> zone clear

> zone #3.7/E:2 surfaceDistance 20

> zone clear

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for RNA_ushf_strand_alt0_fitref-coot.pdb  
---  
Chain | Description  
1.2/E | No description available  
  
Done loading forcefield  

> hide #!2 models

> hide #!3 models

> hide #1.3 models

> hide #1.1 models

> show #1.1 models

> show #!1.2 models

> show #1.3 models

> hide #1.3 models

Opened
cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc
as #1.1.1.1, grid size 320,320,320, pixel 1.06, shown at step 1, values
float32  

> view #1

> volume #1.1.1.1 level 1

> volume #1.1.1.1 level 1.2

> view #1

> clipper spotlight radius 13.00

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

> clipper spotlight radius 16.00

> volume #1.1.1.1 style surface

> transparencey #1.1.1.1 70 surfaces

Unknown command: transparencey #1.1.1.1 70 surfaces  

> transparency #1.1.1.1 70 surfaces

> transparency #1.1.1.1 80 surfaces

> transparency #1.1.1.1 90 surfaces

> transparency #1.1.1.1 70 surfaces

> hide #1.2 target c

> clipper spotlight radius 15.00

> clipper spotlight radius 16.00

> clipper spotlight radius 17.00

> clipper spotlight radius 18.00

> clipper spotlight radius 19.00

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

103 atoms, 113 bonds, 5 residues, 1 model selected  
ISOLDE: stopped sim  

> addH

Unknown command: addH  

> isolde start

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Not adding hydrogens to RNA_ushf_strand_alt0_fitref-coot.pdb #3.1/E
U 1 P because it is missing heavy-atom bond partners  
Not adding hydrogens to RNA_ushf_strand_alt0_fitref-coot.pdb #3.2/E U 1 P
because it is missing heavy-atom bond partners  
Not adding hydrogens to RNA_ushf_strand_alt0_fitref-coot.pdb #3.3/E U 1 P
because it is missing heavy-atom bond partners  
Not adding hydrogens to RNA_ushf_strand_alt0_fitref-coot.pdb #3.4/E U 1 P
because it is missing heavy-atom bond partners  
Not adding hydrogens to RNA_ushf_strand_alt0_fitref-coot.pdb #3.5/E U 1 P
because it is missing heavy-atom bond partners  
56 messages similar to the above omitted  
notes | No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb
(#3.1) chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.1/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.1/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.2) chain
E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.2/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.2/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.3) chain
E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.3/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.3/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.4) chain
E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.4/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.4/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.5) chain
E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.5/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.5/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.6) chain
E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.6/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.6/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.7) chain
E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.7/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.7/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.8) chain
E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.8/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.8/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.9) chain
E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.9/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.9/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.10)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.10/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.10/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.11)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.11/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.11/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.12)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.12/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.12/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.13)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.13/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.13/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.14)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.14/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.14/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.15)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.15/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.15/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.16)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.16/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.16/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.17)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.17/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.17/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.18)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.18/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.18/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.19)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.19/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.19/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.20)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.20/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.20/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.21)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.21/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.21/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.22)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.22/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.22/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.23)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.23/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.23/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.24)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.24/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.24/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.25)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.25/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.25/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.26)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.26/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.26/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.27)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.27/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.27/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.28)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.28/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.28/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.29)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.29/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.29/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.30)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.30/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.30/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.31)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.31/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.31/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.32)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.32/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.32/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.33)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.33/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.33/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.34)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.34/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.34/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.35)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.35/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.35/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.36)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.36/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.36/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.37)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.37/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.37/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.38)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.38/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.38/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.39)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.39/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.39/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.40)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.40/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.40/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.41)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.41/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.41/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.42)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.42/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.42/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.43)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.43/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.43/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.44)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.44/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.44/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.45)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.45/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.45/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.46)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.46/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.46/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.47)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.47/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.47/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.48)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.48/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.48/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.49)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.49/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.49/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.50)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.50/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.50/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.51)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.51/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.51/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.52)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.52/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.52/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.53)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.53/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.53/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.54)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.54/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.54/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.55)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.55/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.55/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.56)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.56/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.56/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.57)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.57/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.57/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.58)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.58/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.58/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.59)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.59/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.59/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#3.60)
chain E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.60/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #3.60/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
No usable SEQRES records for RNA_ushf_strand_alt0_fitref-coot.pdb (#1.2) chain
E; guessing termini instead  
Chain-initial residues that are actual N termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #1.2/E U 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: RNA_ushf_strand_alt0_fitref-
coot.pdb #1.2/E G 5  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
3172 hydrogens added  
  

> hide HC

> show HC

> show #1.2

> show #1.2 target abc

> show #1.2 &nucleic

ISOLDE: started sim  
reverting to start  
ISOLDE: stopped sim  

> isolde restrain ligands #1

> open
> /home/buttner/Documements/CVA6_build/r31_Full/RNA_modelled/ASU_unshifted_w_RNA_mergestrands_alt0-for-
> ISOLDE_coot-01.pdb

No such file/path:
/home/buttner/Documements/CVA6_build/r31_Full/RNA_modelled/ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb  

> open
> /home/buttner/Documents/CVA6_build/r31_Full/RNA_modelled/ASU_unshifted_w_RNA_mergestrands_alt0-for-
> ISOLDE_coot-01.pdb

ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb title:  
\--- [more info...]  
  
Chain information for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  
Non-standard residues in ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb #2  
---  
PLM — (PLM)  
  

> hide #!2 models

> show #!2 models

> hide #2 target abc

> style #2 stick

Changed 6620 atom styles  

> show #2 target abc

> hide #2 target abc

> style #2 stick

Changed 6620 atom styles  

> show #2 target ab

> hide #2 target abc

> style #2 stick

Changed 6620 atom styles  

> show #2 target c

> style #2 stick

Changed 6620 atom styles  

> show #2 target abc

> hide #2&nucleic target c

> close #1.2

Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb title:  
\--- [more info...]  
  
Chain information for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb  
---  
Chain | Description  
63.2/A | No description available  
63.2/B | No description available  
63.2/C | No description available  
63.2/D | No description available  
63.2/E | No description available  
  
Non-standard residues in ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb #63.2  
---  
PLM — (PLM)  
  

> close #1

Deleting atomic symmetry model...  

> close #2

> close #4

> close

> open
> /home/buttner/Documents/CVA6_build/r31_Full/RNA_modelled/ASU_unshifted_w_RNA_mergestrands_alt0-for-
> ISOLDE_coot-01.pdb format pdb

ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb title:  
\--- [more info...]  
  
Chain information for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  
Non-standard residues in ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb #1  
---  
PLM — (PLM)  
  
ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb title:  
\--- [more info...]  
  
Chain information for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
  
Non-standard residues in ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb #1.2  
---  
PLM — (PLM)  
  

> open
> /home/buttner/Documents/CVA6_build/r31_Full/cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc
> format mrc

Opened
cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc
as #2, grid size 320,320,320, pixel 1.06, shown at level 2.69, step 2, values
float32  

> ui tool show "Map Coordinates"

> volume #2 level 1.3

> volume #2 level 1.2

> volume #2 step 1

> transparency #2 70 surfaces

> transparency #2 50 surfaces

Opened
cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc
as #1.1.1.1, grid size 320,320,320, pixel 1.06, shown at step 1, values
float32  

> volume #1.1.1.1 level 1.2

> show 1.2#nucleic target ab

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

> show 1.2#nucleic

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  
Loading residue template for PLM from internal database  

> show #2&nucleic target c

> show #2&nucleic target abc

> show #1.2&nucleic target abc

> show #1.2.2&nucleic target abc

> show #1.2.1&nucleic target abc

> hide #1.2.2 models

> show #1.2.2 models

> close #1.2

Deleting atomic symmetry model...  
Deleting atomic symmetry model...  

> open
> /home/buttner/Documents/CVA6_build/r31_Full/RNA_modelled/ASU_unshifted_w_RNA_mergestrands_alt0-for-
> ISOLDE_coot-01.pdb

ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb title:  
\--- [more info...]  
  
Chain information for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  
Non-standard residues in ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb #2  
---  
PLM — (PLM)  
  
Deleting atomic symmetry model...  
ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb title:  
\--- [more info...]  
  
Chain information for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
2.2/C | No description available  
2.2/D | No description available  
2.2/E | No description available  
  
Non-standard residues in ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb #2.2  
---  
PLM — (PLM)  
  

> close #1

Deleting atomic symmetry model...  

> addh

Summary of feedback from adding hydrogens to
ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb #2.2  
---  
warnings | Not adding hydrogens to /B GLN 144 C because it is missing heavy-
atom bond partners  
Not adding hydrogens to /E U 1 P because it is missing heavy-atom bond
partners  
notes | No usable SEQRES records for
ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb (#2.2) chain A;
guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain B; guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain C; guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain D; guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain E; guessing termini instead  
Chain-initial residues that are actual N termini: /A ALA 11, /B GLY 8, /C GLY
1, /D THR 24, /E U 1  
Chain-initial residues that are not actual N termini: /E U 10  
Chain-final residues that are actual C termini: /B GLN 256, /C GLN 240, /D GLN
69, /E G 14  
Chain-final residues that are not actual C termini: /A PRO 301, /E G 5  
645 hydrogen bonds  
/A PRO 301 is not terminus, removing H atom from 'C'  
6352 hydrogens added  
  

> open
> /home/buttner/Documents/CVA6_build/r31_Full/cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc

Opened
cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc
as #1, grid size 320,320,320, pixel 1.06, shown at level 2.69, step 2, values
float32  

> clipper associate #1 toModel #2

Opened
cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc
as #2.1.1.1, grid size 320,320,320, pixel 1.06, shown at step 1, values
float32  

> isolde start

> addh

Summary of feedback from adding hydrogens to
ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb #2.2  
---  
warnings | Not adding hydrogens to /B GLN 144 C because it is missing heavy-
atom bond partners  
Not adding hydrogens to /E U 1 P because it is missing heavy-atom bond
partners  
notes | No usable SEQRES records for
ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb (#2.2) chain A;
guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain B; guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain C; guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain D; guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain E; guessing termini instead  
Chain-initial residues that are actual N termini: /A ALA 11, /B GLY 8, /C GLY
1, /D THR 24, /E U 1  
Chain-initial residues that are not actual N termini: /E U 10  
Chain-final residues that are actual C termini: /B GLN 256, /C GLN 240, /D GLN
69, /E G 14  
Chain-final residues that are not actual C termini: /A PRO 301, /E G 5  
598 hydrogen bonds  
/A PRO 301 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  

> ui tool show Rotamers

> swapaa interactive sel GLN rotLib Dunbrack

/B GLN 144: phi 35.0, psi 159.2 trans  
Changed 648 bond radii  

> swapaa #2.2/B:144 GLN criteria 88 rotLib Dunbrack retain false

Using Dunbrack library  
ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb #2.2/B GLN 144:
phi 35.0, psi 159.2 trans  
Applying GLN rotamer (chi angles: 66.7 -84.8 30.5) to
ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb #2.2/B GLN 144  

> volume #2.1.1.1 style surface

> volume #2.1.1.1 level 1.2

> volume #2.1.1.1

> volume #2.1.1.1 level 0.2

> select up

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select up

309 atoms, 329 bonds, 10 residues, 1 model selected  

> select up

330 atoms, 350 bonds, 11 residues, 1 model selected  

> select up

600 atoms, 626 bonds, 30 residues, 1 model selected  

> volume #2.1.1.1 level -0.6057

> volume #2.1.1.1 level -0.5401

> close #2.1.1.1

> close #2.1.1

> open
> /home/buttner/Documents/CVA6_build/r31_Full/cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063.mrc
> format mrc

Opened
cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063.mrc as
#1, grid size 320,320,320, pixel 1.06, shown at level 4.14, step 2, values
float32  

> close #1

> open
> /home/buttner/Documents/CVA6_build/r31_Full/cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc
> format mrc

Opened
cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc
as #1, grid size 320,320,320, pixel 1.06, shown at level 2.69, step 2, values
float32  

> volume #1 level 1.2

> volume #1 step 1

> select up

4113 atoms, 4191 bonds, 259 residues, 1 model selected  

> select up

12973 atoms, 13166 bonds, 837 residues, 1 model selected  

> select up

12973 atoms, 13166 bonds, 837 residues, 3 models selected  

> select up

12973 atoms, 13166 bonds, 837 residues, 4 models selected  

> select up

12973 atoms, 13166 bonds, 837 residues, 6 models selected  

> select up

12973 atoms, 13166 bonds, 837 residues, 6 models selected  

> select up

12973 atoms, 13166 bonds, 837 residues, 6 models selected  

> select up

12973 atoms, 13166 bonds, 837 residues, 6 models selected  
Opened
cva6_r31_2-2d3_full_refine18_unmasked_flip_p1_shift_origin_320px_1_063_B100blur.mrc
as #2.1.1.1, grid size 320,320,320, pixel 1.06, shown at step 1, values
float32  

> volume #2.1.1.1 level -0.5842

> volume #2.1.1.1 level -0.6068

> volume #2.1.1.1 style surface

> volume #2.1.1.1 level -0.5955

> ui tool show "Map Coordinates"

> volume #2.1.1.1 level -0.6681

> addh

Summary of feedback from adding hydrogens to
ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb #2.2  
---  
warning | Not adding hydrogens to /E U 1 P because it is missing heavy-atom
bond partners  
notes | No usable SEQRES records for
ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb (#2.2) chain A;
guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain B; guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain C; guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain D; guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain E; guessing termini instead  
Chain-initial residues that are actual N termini: /A ALA 11, /B GLY 8, /C GLY
1, /D THR 24, /E U 1  
Chain-initial residues that are not actual N termini: /E U 10  
Chain-final residues that are actual C termini: /B GLN 256, /C GLN 240, /D GLN
69, /E G 14  
Chain-final residues that are not actual C termini: /A PRO 301, /E G 5  
598 hydrogen bonds  
/A PRO 301 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  

> isolde start

> hide #!2.2 models

> show #!2.2 models

> select up

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select up

309 atoms, 329 bonds, 10 residues, 1 model selected  

> volume #2.1.1.1 level -0.6733

> volume #2.1.1.1 level 0.9681

> volume #2.1.1.1

> isolde start

> set selectionWidth 4

Done loading forcefield  
Loading residue template for PLM from internal database  

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

> clipper spotlight radius 16.00

> clipper spotlight radius 17.00

> clipper spotlight radius 18.00

> clipper spotlight radius 19.00

> clipper spotlight radius 18.00

> clipper spotlight radius 17.00

> clipper spotlight radius 16.00

> clipper spotlight radius 17.00

> clipper spotlight radius 18.00

> clipper spotlight radius 19.00

> volume #2.1.1.1 level 1.218

> volume #2.1.1.1 level 1.2

> select up

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select up

309 atoms, 329 bonds, 10 residues, 1 model selected  

> select up

12973 atoms, 13166 bonds, 837 residues, 1 model selected  

> select down

309 atoms, 329 bonds, 10 residues, 1 model selected  

> addh

Summary of feedback from adding hydrogens to
ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb #2.2  
---  
warning | Not adding hydrogens to /E U 1 P because it is missing heavy-atom
bond partners  
notes | No usable SEQRES records for
ASU_unshifted_w_RNA_mergestrands_alt0-for-ISOLDE_coot-01.pdb (#2.2) chain A;
guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain B; guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain C; guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain D; guessing termini instead  
No usable SEQRES records for ASU_unshifted_w_RNA_mergestrands_alt0-for-
ISOLDE_coot-01.pdb (#2.2) chain E; guessing termini instead  
Chain-initial residues that are actual N termini: /A ALA 11, /B GLY 8, /C GLY
1, /D THR 24, /E U 1  
Chain-initial residues that are not actual N termini: /E U 10  
Chain-final residues that are actual C termini: /B GLN 256, /C GLN 240, /D GLN
69, /E G 14  
Chain-final residues that are not actual C termini: /A PRO 301, /E G 5  
598 hydrogen bonds  
/A PRO 301 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  
Traceback (most recent call last):  
File "/soft/UCSF-ChimeraX/chimerax-1.2.4-rc-2021.05.14/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/soft/UCSF-ChimeraX/chimerax-1.2.4-rc-2021.05.14/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/soft/UCSF-ChimeraX/chimerax-1.2.4-rc-2021.05.14/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/soft/UCSF-ChimeraX/chimerax-1.2.4-rc-2021.05.14/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
ISOLDE: started sim  
Traceback (most recent call last):  
File "/soft/UCSF-ChimeraX/chimerax-1.2.4-rc-2021.05.14/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/soft/UCSF-ChimeraX/chimerax-1.2.4-rc-2021.05.14/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/soft/UCSF-ChimeraX/chimerax-1.2.4-rc-2021.05.14/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
[**so** many of these deleted]

Traceback (most recent call last):  
File "/soft/UCSF-ChimeraX/chimerax-1.2.4-rc-2021.05.14/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  

> select #2/B:83,105,107,109,125,182,205,213,239

70 atoms, 65 bonds, 9 residues, 1 model selected  
Traceback (most recent call last):  
File "/soft/UCSF-ChimeraX/chimerax-1.2.4-rc-2021.05.14/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  

> select #2/B:84,106,108,110,126,183,206,214,240

77 atoms, 70 bonds, 9 residues, 1 model selected  
Traceback (most recent call last):  
File "/soft/UCSF-ChimeraX/chimerax-1.2.4-rc-2021.05.14/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  

> close #2

Traceback (most recent call last):  
File "/soft/UCSF-ChimeraX/chimerax-1.2.4-rc-2021.05.14/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  

> close #1

Traceback (most recent call last):  
File "/soft/UCSF-ChimeraX/chimerax-1.2.4-rc-2021.05.14/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/buttner/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 460.91.03
OpenGL renderer: Quadro RTX 5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD EPYC 7302P 16-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          125Gi        19Gi        83Gi       161Mi        22Gi       105Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	81:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 5000] [10de:1eb0] (rev a1)	
	Subsystem: NVIDIA Corporation TU104GL [Quadro RTX 5000] [10de:129f]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    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-Clipper: 0.16.0
    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-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 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
    distro: 1.5.0
    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
    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: 1.2.0