Opened 4 years ago

Closed 4 years ago

#5086 closed enhancement (fixed)

Improve attribute-registration error reporting

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.3 (2021-05-13 06:57:20 UTC)
Description
Morph of #1 protein model with only protein chain and #2 protein model with split RNA and protein chain

Log:
UCSF ChimeraX version: 1.2.3 (2021-05-13)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/PublishedStructures/overlay_binary_catalytic.cxs

Log from Tue Jul 13 11:34:17 2021UCSF ChimeraX version: 1.2.3 (2021-05-13)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/PublishedStructures/overlay_binary_catalytic.cxs

Log from Tue Jul 13 11:23:26 2021UCSF ChimeraX version: 1.2.3 (2021-05-13)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/PublishedStructures/6c6b_1_2_real_space_refined_007.pdb
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/PublishedStructures/16c16b_model_10_cryosparc_pos_real_space_refined_040.pdb
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/PublishedStructures/SpCas9-sgRNA-
> binary_4zt0_x-ray.pdb
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/PublishedStructures/SpCas9-sgRNA-
> dsDNA-post-catalytic_6o0y_cryo.pdb
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/PublishedStructures/SpCas9-sgRNA-
> dsDNA-pre-catalytic_6o0z_cryo.pdb
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/PublishedStructures/SpCas9-sgRNA-
> dsDNA-product_6o0x_cryo.pdb

Summary of feedback from opening
C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/PublishedStructures/SpCas9-sgRNA-
binary_4zt0_x-ray.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 67 AH4 ALA C
59 ASP C 94 1 36  
Start residue of secondary structure not found: HELIX 68 AH5 SER C 96 GLU C
103 1 8  
Start residue of secondary structure not found: HELIX 69 AH6 ASN C 121 TYR C
132 1 12  
Start residue of secondary structure not found: HELIX 70 AH7 THR C 134 SER C
145 1 12  
Start residue of secondary structure not found: HELIX 71 AH8 ASP C 150 PHE C
164 1 15  
89 messages similar to the above omitted  
Cannot find LINK/SSBOND residue GLU (89 )  
Cannot find LINK/SSBOND residue MSE (90 )  
Cannot find LINK/SSBOND residue HIS (160 )  
Cannot find LINK/SSBOND residue MSE (161 )  
Cannot find LINK/SSBOND residue SER (320 )  
35 messages similar to the above omitted  
  
Chain information for 6c6b_1_2_real_space_refined_007.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for 16c16b_model_10_cryosparc_pos_real_space_refined_040.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
SpCas9-sgRNA-binary_4zt0_x-ray.pdb title:  
Crystal structure of catalytically-active streptococcus pyogenes CAS9 In
complex with single-guide RNA At 2.9 angstrom resolution [more info...]  
  
Chain information for SpCas9-sgRNA-binary_4zt0_x-ray.pdb #3  
---  
Chain | Description  
A | crispr-associated endonuclease CAS9  
B | single-guide RNA  
  
SpCas9-sgRNA-dsDNA-post-catalytic_6o0y_cryo.pdb title:  
Conformational states of CAS9-sgRNA-DNA ternary complex In the presence of
magnesium [more info...]  
  
Chain information for SpCas9-sgRNA-dsDNA-post-catalytic_6o0y_cryo.pdb #4  
---  
Chain | Description  
A | crispr-associated endonuclease CAS9/CSN1  
B | single guide RNA  
C | 5' product of target strand DNA  
D | non-target strand DNA  
c | 3' product of target strand DNA  
  
SpCas9-sgRNA-dsDNA-pre-catalytic_6o0z_cryo.pdb title:  
Conformational states of CAS9-sgRNA-DNA ternary complex In the presence of
magnesium [more info...]  
  
Chain information for SpCas9-sgRNA-dsDNA-pre-catalytic_6o0z_cryo.pdb #5  
---  
Chain | Description  
A | crispr-associated endonuclease CAS9/CSN1  
B | single guide RNA  
C | target strand DNA  
D | non-target strand DNA  
  
SpCas9-sgRNA-dsDNA-product_6o0x_cryo.pdb title:  
Conformational states of CAS9-sgRNA-DNA ternary complex In the presence of
magnesium [more info...]  
  
Chain information for SpCas9-sgRNA-dsDNA-product_6o0x_cryo.pdb #6  
---  
Chain | Description  
A | crispr-associated endonuclease CAS9/CSN1  
B | single guide RNA  
C | 5' product of target strand DNA  
D | non-target strand DNA  
c | 3' product of target strand DNA  
  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> lighting soft

> hide atoms

> show cartoons

> hide #3 models

> show #3 models

> hide #3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #3 models

> nucleotides tube/slab shape box

> color #1/B:1-56 dodger blue

> color #1/B:57-94 magenta

> color #1/B:95-174 gainsboro

> color #1/B:175-304 #C8C8FF

> color #1/B:305-494 gainsboro

> color #1/B:495-717 tan

> color #1/B:718-766 dodger blue

> color #1/B:767-925 yellow

> color #1/B:926-1099 dodger blue

> color #1/B:1100-1368 salmon

> color #2/B:1-56 dodger blue

> color #2/B:57-94 magenta

> color #2/B:95-174 gainsboro

> color #2/B:175-304 #C8C8FF

> color #2/B:305-494 gainsboro

> color #2/B:495-717 tan

> color #2/B:718-766 dodger blue

> color #2/B:767-925 yellow

> color #2/B:926-1099 dodger blue

> color #2/B:1100-1368 salmon

> color #3/A:1-56 dodger blue

> color #3/A:57-94 magenta

> color #3/A:95-174 gainsboro

> color #3/A:175-304 #C8C8FF

> color #3/A:305-494 gainsboro

> color #3/A:495-717 tan

> color #3/A:718-766 dodger blue

> color #3/A:767-925 yellow

> color #3/A:926-1099 dodger blue

> color #3/A:1100-1368 salmon

> color #4/A:1-56 dodger blue

> color #4/A:57-94 magenta

> color #4/A:95-174 gainsboro

> color #4/A:175-304 #C8C8FF

> color #4/A:305-494 gainsboro

> color #4/A:495-717 tan

> color #4/A:718-766 dodger blue

> color #4/A:767-925 yellow

> color #4/A:926-1099 dodger blue

> color #4/A:1100-1368 salmon

> color #5/A:1-56 dodger blue

> color #5/A:57-94 magenta

> color #5/A:95-174 gainsboro

> color #5/A:175-304 #C8C8FF

> color #5/A:305-494 gainsboro

> color #5/A:495-717 tan

> color #5/A:718-766 dodger blue

> color #5/A:767-925 yellow

> color #5/A:926-1099 dodger blue

> color #5/A:1100-1368 salmon

> color #6/A:1-56 dodger blue

> color #6/A:57-94 magenta

> color #6/A:95-174 gainsboro

> color #6/A:175-304 #C8C8FF

> color #6/A:305-494 gainsboro

> color #6/A:495-717 tan

> color #6/A:718-766 dodger blue

> color #6/A:767-925 yellow

> color #6/A:926-1099 dodger blue

> color #6/A:1100-1368 salmon

> color #1/A orange

> color #2/A orange

> color #3/B orange

> color #4/B orange

> color #5/B orange

> color #6/B orange

> color #1/C steel blue

> color #1/D royal blue

> color #2/C steel blue

> color #2/D royal blue

> color #3/C steel blue

> color #3/D royal blue

> color #4/C steel blue

> color #4/D royal blue

> color #5/C steel blue

> color #5/D royal blue

> color #6/C steel blue

> color #6/D royal blue

> hide #!1 models

> hide #!2 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #3 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #3 models

> hide #3 models

> show #!4 models

> color #4/c steel blue

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> color #6/c steel blue

> show #1/A,C,D atoms

> show #2/A,C,D atoms

> show #3/B atoms

> show #4/B,C,c,D atoms

> show #5/B,C,D atoms

> show #6/B,C,c,D atoms

> hide #6.1 models

> hide #!6 models

> show #!5 models

> hide #5.1 models

> hide #!5 models

> hide #4.1 models

> show #!4 models

> hide #!4 models

> show #3 models

> hide #3 models

> show #!2 models

> hide #2.1 models

> ui mousemode right select

> select #2/C:0

21 atoms, 23 bonds, 1 residue, 1 model selected  

> select clear

> select #2/D:-2@O3'

1 atom, 1 residue, 1 model selected  

> hide sel target a

> hide #!2 models

> hide #1.1 models

> show #!1 models

> ui mousemode right select

> select clear

> save
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/PublishedStructures/overlay_binary_catalytic.cxs
> includeMaps true

> show #3 models

> hide #3 models

> show #!4 models

> hide #!4 models

> show #!4 models

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> hide #!1 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> show #!2 models

> hide #!5 models

> open
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/8c8b_1_1_real_space_refined_015.pdb
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/10c10b_1_3_real_space_refined_008.pdb
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/12c12b_1_5_cryosparc_pos_real_space_refined_041.pdb
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/14c14b_1_8_cryosparc_pos_real_space_refined_023.pdb
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/Cas9-CAZ15-10c10b_refine_172_molA.pdb
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/Cas9-CAZ15-10c10b_refine_172_molB.pdb

Summary of feedback from opening
C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/Cas9-CAZ15-10c10b_refine_172_molA.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 59 59 GLU E
60 VAL E 93 1 34  
Start residue of secondary structure not found: HELIX 60 60 PHE E 97 GLU E 102
1 6  
Start residue of secondary structure not found: HELIX 61 61 ILE E 122 LYS E
131 1 10  
Start residue of secondary structure not found: HELIX 62 62 ILE E 135 ASP E
144 1 10  
Start residue of secondary structure not found: HELIX 63 63 LEU E 151 LYS E
163 1 13  
69 messages similar to the above omitted  
  
Summary of feedback from opening
C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/Cas9-CAZ15-10c10b_refine_172_molB.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU B 60
ILE B 85 1 26  
Start residue of secondary structure not found: HELIX 2 2 SER B 87 VAL B 93 1
7  
Start residue of secondary structure not found: HELIX 3 3 PHE B 97 ARG B 100 1
4  
Start residue of secondary structure not found: HELIX 4 4 ILE B 122 LYS B 131
1 10  
Start residue of secondary structure not found: HELIX 5 5 ILE B 135 ASP B 144
1 10  
78 messages similar to the above omitted  
  
Chain information for 8c8b_1_1_real_space_refined_015.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for 10c10b_1_3_real_space_refined_008.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for 12c12b_1_5_cryosparc_pos_real_space_refined_041.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for 14c14b_1_8_cryosparc_pos_real_space_refined_023.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for Cas9-CAZ15-10c10b_refine_172_molA.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for Cas9-CAZ15-10c10b_refine_172_molB.pdb #12  
---  
Chain | Description  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
  

> hide #!2 models

> hide #!6 models

> show #!2 models

> ui tool show Matchmaker

> matchmaker #!7-12 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 16c16b_model_10_cryosparc_pos_real_space_refined_040.pdb, chain B
(#2) with 8c8b_1_1_real_space_refined_015.pdb, chain B (#7), sequence
alignment score = 6513.8  
RMSD between 806 pruned atom pairs is 0.961 angstroms; (across all 1338 pairs:
7.344)  
  
Matchmaker 16c16b_model_10_cryosparc_pos_real_space_refined_040.pdb, chain B
(#2) with 10c10b_1_3_real_space_refined_008.pdb, chain B (#8), sequence
alignment score = 6510.4  
RMSD between 1068 pruned atom pairs is 0.649 angstroms; (across all 1338
pairs: 6.713)  
  
Matchmaker 16c16b_model_10_cryosparc_pos_real_space_refined_040.pdb, chain B
(#2) with 12c12b_1_5_cryosparc_pos_real_space_refined_041.pdb, chain B (#9),
sequence alignment score = 5392.3  
RMSD between 1046 pruned atom pairs is 0.775 angstroms; (across all 1142
pairs: 1.644)  
  
Matchmaker 16c16b_model_10_cryosparc_pos_real_space_refined_040.pdb, chain B
(#2) with 14c14b_1_8_cryosparc_pos_real_space_refined_023.pdb, chain B (#10),
sequence alignment score = 6511.9  
RMSD between 1151 pruned atom pairs is 0.678 angstroms; (across all 1328
pairs: 6.710)  
  
Matchmaker 16c16b_model_10_cryosparc_pos_real_space_refined_040.pdb, chain B
(#2) with Cas9-CAZ15-10c10b_refine_172_molA.pdb, chain B (#11), sequence
alignment score = 5921.5  
RMSD between 902 pruned atom pairs is 0.674 angstroms; (across all 1240 pairs:
3.956)  
  
Matchmaker 16c16b_model_10_cryosparc_pos_real_space_refined_040.pdb, chain B
(#2) with Cas9-CAZ15-10c10b_refine_172_molB.pdb, chain E (#12), sequence
alignment score = 5403.7  
RMSD between 965 pruned atom pairs is 0.762 angstroms; (across all 1155 pairs:
2.899)  
  

> hide #!2 models

> nucleotides tube/slab shape box

> color #7/B:1-56 dodger blue

> color #7/B:57-94 magenta

> color #7/B:95-174 gainsboro

> color #7/B:175-304 #C8C8FF

> color #7/B:305-494 gainsboro

> color #7/B:495-717 tan

> color #7/B:718-766 dodger blue

> color #7/B:767-925 yellow

> color #7/B:926-1099 dodger blue

> color #7/B:1100-1368 salmon

> color #8/B:1-56 dodger blue

> color #8/B:57-94 magenta

> color #8/B:95-174 gainsboro

> color #8/B:175-304 #C8C8FF

> color #8/B:305-494 gainsboro

> color #8/B:495-717 tan

> color #8/B:718-766 dodger blue

> color #8/B:767-925 yellow

> color #8/B:926-1099 dodger blue

> color #8/B:1100-1368 salmon

> color #9/B:1-56 dodger blue

> color #9/B:57-94 magenta

> color #9/B:95-174 gainsboro

> color #9/B:175-304 #C8C8FF

> color #9/B:305-494 gainsboro

> color #9/B:495-717 tan

> color #9/B:718-766 dodger blue

> color #9/B:767-925 yellow

> color #9/B:926-1099 dodger blue

> color #9/B:1100-1368 salmon

> color #13/B:1-56 dodger blue

> color #13/B:57-94 magenta

> color #13/B:95-174 gainsboro

> color #13/B:175-304 #C8C8FF

> color #13/B:305-494 gainsboro

> color #13/B:495-717 tan

> color #13/B:718-766 dodger blue

> color #13/B:767-925 yellow

> color #13/B:926-1099 dodger blue

> color #13/B:1100-1368 salmon

> color #11/B:1-56 dodger blue

> color #11/B:57-94 magenta

> color #11/B:95-174 gainsboro

> color #11/B:175-304 #C8C8FF

> color #11/B:305-494 gainsboro

> color #11/B:495-717 tan

> color #11/B:718-766 dodger blue

> color #11/B:767-925 yellow

> color #11/B:926-1099 dodger blue

> color #11/B:1100-1368 salmon

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

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> show #!7 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> color #10/B:1-56 dodger blue

> color #10/B:57-94 magenta

> color #10/B:95-174 gainsboro

> color #10/B:175-304 #C8C8FF

> color #10/B:305-494 gainsboro

> color #10/B:495-717 tan

> color #10/B:718-766 dodger blue

> color #10/B:767-925 yellow

> color #10/B:926-1099 dodger blue

> color #10/B:1100-1368 salmon

> color #12/E:1-56 dodger blue

> color #12/E:57-94 magenta

> color #12/E:95-174 gainsboro

> color #12/E:175-304 #C8C8FF

> color #12/E:305-494 gainsboro

> color #12/E:495-717 tan

> color #12/E:718-766 dodger blue

> color #12/E:767-925 yellow

> color #12/E:926-1099 dodger blue

> color #12/E:1100-1368 salmon

> color #7/A orange

> color #8/A orange

> color #9/A orange

> color #10/A orange

> color #11/A orange

> color #12/F orange

> hide #!7-12 atoms

> show #!7-12 cartoons

> hide #7.1 models

> hide #8.1 models

> hide #9.1 models

> hide #10.1 models

> hide #11.1 models

> hide #12.1 models

> show #7/A,C,D atoms

> show #8/A,C,D atoms

> show #9/A,C,D atoms

> show #10/A,C,D atoms

> show #11/A,C,D atoms

> show #12/F,G,H atoms

> color #7/C steel blue

> color #7/D royal blue

> color #8/C steel blue

> color #8/D royal blue

> color #9/C steel blue

> color #9/D royal blue

> color #10/C steel blue

> color #10/D royal blue

> color #11/C steel blue

> color #11/D royal blue

> color #12/G steel blue

> color #12/H royal blue

> hide #!8 models

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> hide #!11 models

> hide #!12 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!9 models

> select clear

> hide #9/C:13

> hide #!9 models

> show #!10 models

> hide #!10 models

> show #!11 models

> hide #!11 models

> show #!12 models

> show #!11 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!11 models

> save
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/PublishedStructures/overlay_binary_catalytic.cxs
> includeMaps true

——— End of log from Tue Jul 13 11:23:26 2021 ———

opened ChimeraX session  

> hide #!12 models

> show #!2 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

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> show #!5 models

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> show #!5 models

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> show #!5 models

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> show #!5 models

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> show #!5 models

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> show #!5 models

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> show #!5 models

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> show #!5 models

> hide #!2 models

> show #!2 models

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> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!5 models

> show #!2 models

> hide #2/C:18

> save
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Analysis_210712/PublishedStructures/overlay_binary_catalytic.cxs
> includeMaps true

——— End of log from Tue Jul 13 11:34:17 2021 ———

opened ChimeraX session  

> ui tool show Matchmaker

> matchmaker #3#!2,4-12 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6c6b_1_2_real_space_refined_007.pdb, chain B (#1) with
SpCas9-sgRNA-binary_4zt0_x-ray.pdb, chain A (#3), sequence alignment score =
6631.7  
RMSD between 654 pruned atom pairs is 0.887 angstroms; (across all 1356 pairs:
8.839)  
  
Matchmaker 6c6b_1_2_real_space_refined_007.pdb, chain B (#1) with
16c16b_model_10_cryosparc_pos_real_space_refined_040.pdb, chain B (#2),
sequence alignment score = 6491.4  
RMSD between 808 pruned atom pairs is 0.765 angstroms; (across all 1338 pairs:
10.761)  
  
Matchmaker 6c6b_1_2_real_space_refined_007.pdb, chain B (#1) with
SpCas9-sgRNA-dsDNA-post-catalytic_6o0y_cryo.pdb, chain A (#4), sequence
alignment score = 5210.2  
RMSD between 717 pruned atom pairs is 1.014 angstroms; (across all 1138 pairs:
15.032)  
  
Matchmaker 6c6b_1_2_real_space_refined_007.pdb, chain B (#1) with
SpCas9-sgRNA-dsDNA-pre-catalytic_6o0z_cryo.pdb, chain A (#5), sequence
alignment score = 5979.9  
RMSD between 886 pruned atom pairs is 1.029 angstroms; (across all 1288 pairs:
7.481)  
  
Matchmaker 6c6b_1_2_real_space_refined_007.pdb, chain B (#1) with
SpCas9-sgRNA-dsDNA-product_6o0x_cryo.pdb, chain A (#6), sequence alignment
score = 5064.8  
RMSD between 736 pruned atom pairs is 1.114 angstroms; (across all 1112 pairs:
7.704)  
  
Matchmaker 6c6b_1_2_real_space_refined_007.pdb, chain B (#1) with
8c8b_1_1_real_space_refined_015.pdb, chain B (#7), sequence alignment score =
6703.6  
RMSD between 986 pruned atom pairs is 0.681 angstroms; (across all 1357 pairs:
7.013)  
  
Matchmaker 6c6b_1_2_real_space_refined_007.pdb, chain B (#1) with
10c10b_1_3_real_space_refined_008.pdb, chain B (#8), sequence alignment score
= 6669  
RMSD between 957 pruned atom pairs is 0.732 angstroms; (across all 1357 pairs:
8.780)  
  
Matchmaker 6c6b_1_2_real_space_refined_007.pdb, chain B (#1) with
12c12b_1_5_cryosparc_pos_real_space_refined_041.pdb, chain B (#9), sequence
alignment score = 5390.8  
RMSD between 805 pruned atom pairs is 0.885 angstroms; (across all 1148 pairs:
8.538)  
  
Matchmaker 6c6b_1_2_real_space_refined_007.pdb, chain B (#1) with
14c14b_1_8_cryosparc_pos_real_space_refined_023.pdb, chain B (#10), sequence
alignment score = 6557.4  
RMSD between 943 pruned atom pairs is 0.844 angstroms; (across all 1334 pairs:
8.433)  
  
Matchmaker 6c6b_1_2_real_space_refined_007.pdb, chain B (#1) with
Cas9-CAZ15-10c10b_refine_172_molA.pdb, chain B (#11), sequence alignment score
= 6109.7  
RMSD between 855 pruned atom pairs is 0.867 angstroms; (across all 1259 pairs:
10.241)  
  
Matchmaker 6c6b_1_2_real_space_refined_007.pdb, chain B (#1) with
Cas9-CAZ15-10c10b_refine_172_molB.pdb, chain E (#12), sequence alignment score
= 5580.5  
RMSD between 849 pruned atom pairs is 0.823 angstroms; (across all 1174 pairs:
8.171)  
  

> show #!1 models

> show #3 models

> show #!4 models

> show #!5 models

> show #!6 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #3 models

> hide #!2 models

> hide #!1 models

> show #3 models

> open "C:/Users/Patch/Desktop/Structure/Projects/anti-
> CRISPR_design/Structures/Class2_Cas_Effectors/Type II-A/SpCas9-apo_4cmp_x-
> ray.pdb"

SpCas9-apo_4cmp_x-ray.pdb title:  
Crystal structure of S. Pyogenes CAS9 [more info...]  
  
Chain information for SpCas9-apo_4cmp_x-ray.pdb #13  
---  
Chain | Description  
A B | CAS9  
  
Non-standard residues in SpCas9-apo_4cmp_x-ray.pdb #13  
---  
MG — magnesium ion  
SO4 — sulfate ion  
  

> hide #!13 models

> show #!13 models

> hide #3 models

> hide #!13 models

> show #!13 models

> show #13 ribbons

> hide #!13 models

> show #!13 models

> ui tool show Matchmaker

> matchmaker #!13 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker SpCas9-sgRNA-binary_4zt0_x-ray.pdb, chain A (#3) with
SpCas9-apo_4cmp_x-ray.pdb, chain B (#13), sequence alignment score = 6353.8  
RMSD between 523 pruned atom pairs is 0.739 angstroms; (across all 1166 pairs:
36.263)  
  

> close #13

> open
> C:/Users/Patch/Desktop/Structure/Projects/Thesis/Figures_Cas9/SpCas9-apo_4cmp_x-
> ray.pdb

Summary of feedback from opening
C:/Users/Patch/Desktop/Structure/Projects/Thesis/Figures_Cas9/SpCas9-apo_4cmp_x-
ray.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 58
LEU A 64 1 7  
Start residue of secondary structure not found: HELIX 2 2 THR A 67 ASP A 94 1
28  
Start residue of secondary structure not found: HELIX 3 3 SER A 96 LEU A 101 1
6  
Start residue of secondary structure not found: HELIX 4 4 ASN A 121 TYR A 132
1 12  
Start residue of secondary structure not found: HELIX 5 5 THR A 134 SER A 145
1 12  
79 messages similar to the above omitted  
  
SpCas9-apo_4cmp_x-ray.pdb title:  
Crystal structure of S. Pyogenes CAS9 [more info...]  
  
Chain information for SpCas9-apo_4cmp_x-ray.pdb #13  
---  
Chain | Description  
B | CAS9  
  
Non-standard residues in SpCas9-apo_4cmp_x-ray.pdb #13  
---  
MG — magnesium ion  
SO4 — sulfate ion  
  

> hide #!13 atoms

> show #!1 models

> hide #!1 models

> show #3 models

> ui tool show Matchmaker

> matchmaker #!13 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker SpCas9-sgRNA-binary_4zt0_x-ray.pdb, chain A (#3) with
SpCas9-apo_4cmp_x-ray.pdb, chain B (#13), sequence alignment score = 5318.3  
RMSD between 523 pruned atom pairs is 0.739 angstroms; (across all 1166 pairs:
36.263)  
  

> color #13/A:1-56 dodger blue

> color #13/A:57-94 magenta

> color #13/A:95-174 gainsboro

> color #13/A:175-304 #aaaaff

> color #13/A:305-494 gainsboro

> color #13/A:495-717 tan

> color #13/A:718-766 dodger blue

> color #13/A:767-925 yellow

> color #13/A:926-1099 dodger blue

> color #13/A:1100-1368 salmon

> hide #3 models

> color #13/B:1-56 dodger blue

> color #13/B:57-94 magenta

> color #13/B:95-174 gainsboro

> color #13/B:175-304 #aaaaff

> color #13/B:305-494 gainsboro

> color #13/B:495-717 tan

> color #13/B:718-766 dodger blue

> color #13/B:767-925 yellow

> color #13/B:926-1099 dodger blue

> color #13/B:1100-1368 salmon

> hide #13.1 models

> hide #13.2 models

> show #13.1 models

> hide #13.1 models

> save
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Figures_210815/MorphMovie/AlignedModels.cxs

> show #!1 models

> show #!2 models

> show #3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> show #!9 models

> show #!10 models

> show #!11 models

> show #!12 models

> hide #!13 models

> color #1/B:175-304 #aaaaff

> color #2/B:175-304 #aaaaff

> color #3/A:175-304 #aaaaff

> color #4/A:175-304 #aaaaff

> color #5/A:175-304 #aaaaff

> color #6/A:175-304 #aaaaff

> color #7/B:175-304 #aaaaff

> color #8/B:175-304 #aaaaff

> color #9/B:175-304 #aaaaff

> color #10/B:175-304 #aaaaff

> hide #!11 models

> hide #!10 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #3 models

> hide #!2 models

> hide #!1 models

> show #!11 models

> color #11/B:175-304 #aaaaff

> hide #!11 models

> hide #!12 models

> show #!12 models

> color #12/E:175-304 #aaaaff

> color #12/H medium blue

> show #!11 models

> show #!10 models

> show #!9 models

> show #!8 models

> show #!7 models

> show #!6 models

> show #!5 models

> show #!4 models

> show #3 models

> show #!2 models

> show #!1 models

> hide #!12 models

> color #11/D medium blue

> hide #!11 models

> color #10/D medium blue

> color #9/D medium blue

> color #8/D medium blue

> color #7/D medium blue

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> color #6/D medium blue

> color #5/D medium blue

> color #4/D medium blue

> color #2/D medium blue

> color #1/D medium blue

> save
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Figures_210815/MorphMovie/AlignedModels.cxs

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #3 models

> hide #!2 models

> hide #!1 models

> show #!13 models

> show #3 models

> hide #!13 models

> split #3

Split SpCas9-sgRNA-binary_4zt0_x-ray.pdb (#3) into 2 models  
Chain information for SpCas9-sgRNA-binary_4zt0_x-ray.pdb A #3.1  
---  
Chain | Description  
A | No description available  
  
Chain information for SpCas9-sgRNA-binary_4zt0_x-ray.pdb B #3.2  
---  
Chain | Description  
B | No description available  
  

> hide #3.2 models

> show #3.2 models

> hide #3.1 models

> hide #!3 models

> hide #3.2 models

> show #3.2 models

> nucleotides #3.2 tube/slab shape box

> show #3.1 models

> hide #3.1 models

> colour #3.2 orange

> show #3.1 models

> save
> C:/Users/Patch/Desktop/Structure/Projects/Bubbles_Cas9/Figures_210815/MorphMovie/AlignedModels.cxs

> morph #13,3.1

Require at least 2 structures for morph  

> morph #13,#3.1

Missing or invalid "structures" argument: only initial part "#13" of atom
specifier valid  

> morph #13,3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\morph\morph.py", line 73, in morph  
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph  
res_groups = motion.interpolate(mol, res_interp)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\morph\motion.py", line 139, in interpolate  
nc = sm.coordset_size  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 61, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError  
  
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError  
  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> morph #13,3.1

Require at least 2 structures for morph  

> morph #13, 3.1

Require at least 2 structures for morph  

> morph #13, 3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\morph\morph.py", line 73, in morph  
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph  
res_groups = motion.interpolate(mol, res_interp)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\morph\motion.py", line 139, in interpolate  
nc = sm.coordset_size  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 61, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError  
  
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError  
  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> hide #3.2 models

> morph #13, 3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\morph\morph.py", line 73, in morph  
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph  
res_groups = motion.interpolate(mol, res_interp)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\morph\motion.py", line 139, in interpolate  
nc = sm.coordset_size  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 61, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError  
  
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError  
  
File "C:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.13596 Core Profile Forward-Compatible Context 20.10.35.02 27.20.1034.6
OpenGL renderer: Radeon (TM) RX 480 Graphics
OpenGL vendor: ATI Technologies Inc.
Manufacturer: MSI
Model: MS-7920
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 17,129,168,896
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-4790K CPU @ 4.00GHz
OSLanguage: cs-CZ
Locale: ('en_GB', 'cp1252')
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: 1.2.3
    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: 1.1.2
    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-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
    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
    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
    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
    pywin32: 228
    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
    WMI: 1.5.1

Change History (7)

comment:1 by pett, 4 years ago

Cc: pett added
Component: Unassigned → Structure Comparison
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Structure.coordset_size failed during morph

comment:2 by Tom Goddard, 4 years ago

Cc: Tom Goddard added; pett removed
Owner: changed from Tom Goddard to pett

The attribute registration code has crippled our ability to debug an error in a property. All we get is "Some attribute error occurred when calling the property". This needs to be fixed. We can't spend hours debugging because our code design has suppressed errors.

comment:3 by pett, 4 years ago

Component: Structure Comparison → Core
Status: assigned → accepted
Summary: Structure.coordset_size failed during morph → Improve attribute-registration error reporting
Type: defect → enhancement

I think this can be done by eliminating support for returning a default value when the registered attribute is missing.

comment:4 by pett, 4 years ago

Status: accepted → feedback

I've made the code changes to not support default values for custom attributes, which therefore removes the necessity of overriding __getattr__, which in turn enables normal tracebacks for missing attributes during property access instead of "Execution of 'X' object's 'y' property raised AttributeError".

I *could* push it. I lean against pushing it since it's a fairly major change close to a release, though having it in there will make debugging some reports significantly easier. Opinion?

in reply to:  5 ; comment:5 by goddard@…, 4 years ago 

Sound like a good change.  I agree, don't push until after 1.3.  It does not cause problems often enough to try to squeeze it in right before the 1.3 release.

comment:6 by pett, 4 years ago

Status: feedback → accepted

comment:7 by pett, 4 years ago

Resolution: → fixed
Status: accepted → closed

Fixed on develop, not release 1.3

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