Opened 3 years ago

Closed 11 months ago

#6977 closed defect (fixed)

PDB two-letter chain ID sometimes not recognized if TER missing

Reported by: apadavannil@… Owned by: pett
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by pett) 

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

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

> open
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/ND1-ND3/ND1-ND3_Closed.cxs

Log from Wed May 25 17:26:43 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/ClosedConfiguration/ClosedConfiguration.cxs

Log from Wed May 25 10:51:47 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_19/Dro_real_space_refined_017-coot-1_real_space_refined_019.pdb

Summary of feedback from opening
/Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_19/Dro_real_space_refined_017-coot-1_real_space_refined_019.pdb  
---  
warnings | Ignored bad PDB record found on line 504  
LINK SG CYS V1 394 FE4 SF4 V1 502  
  
Ignored bad PDB record found on line 505  
LINK SG CYS V1 400 FE1 SF4 V1 502  
  
Ignored bad PDB record found on line 506  
LINK SG CYS V1 440 FE2 SF4 V1 502  
  
Ignored bad PDB record found on line 507  
LINK SG CYS V1 397 FE3 SF4 V1 502  
  
Ignored bad PDB record found on line 508  
LINK SG CYS V2 128 FE1 FES V2 301  
  
61 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 331 331 PROA7 10 LEUA7
20 1 11  
Start residue of secondary structure not found: HELIX 332 332 TYRA7 57 ARGA7
60 5 4  
Start residue of secondary structure not found: HELIX 333 333 GLYA7 62 GLUA7
65 1 4  
Start residue of secondary structure not found: HELIX 334 334 LEUA7 72 ALAA7
81 1 10  
  
Chain information for
Dro_real_space_refined_017-coot-1_real_space_refined_019.pdb #1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
4L | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
A1 | No description available  
A3 | No description available  
A5 | No description available  
A6 | No description available  
A8 | No description available  
A9 | No description available  
AB AC | No description available  
AL | No description available  
AM | No description available  
AN | No description available  
AO | No description available  
B1 | No description available  
B2 | No description available  
B3 | No description available  
B4 | No description available  
B5 | No description available  
B6 | No description available  
B7 | No description available  
B8 | No description available  
B9 | No description available  
BL | No description available  
BM | No description available  
C2 | No description available  
S1 | No description available  
S2 | No description available  
S3 | No description available  
S4 | No description available  
S5 | No description available  
S6 | No description available  
S7 | No description available  
S8 | No description available  
V1 | No description available  
V2 | No description available  
V3 | No description available  
  

> set bgColor white

> hide atoms

> show cartoons

> open
> /Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_19/Dro_real_space_refined_017-coot-1_real_space_refined_019.pdb

Summary of feedback from opening
/Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_19/Dro_real_space_refined_017-coot-1_real_space_refined_019.pdb  
---  
warnings | Ignored bad PDB record found on line 504  
LINK SG CYS V1 394 FE4 SF4 V1 502  
  
Ignored bad PDB record found on line 505  
LINK SG CYS V1 400 FE1 SF4 V1 502  
  
Ignored bad PDB record found on line 506  
LINK SG CYS V1 440 FE2 SF4 V1 502  
  
Ignored bad PDB record found on line 507  
LINK SG CYS V1 397 FE3 SF4 V1 502  
  
Ignored bad PDB record found on line 508  
LINK SG CYS V2 128 FE1 FES V2 301  
  
61 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 331 331 PROA7 10 LEUA7
20 1 11  
Start residue of secondary structure not found: HELIX 332 332 TYRA7 57 ARGA7
60 5 4  
Start residue of secondary structure not found: HELIX 333 333 GLYA7 62 GLUA7
65 1 4  
Start residue of secondary structure not found: HELIX 334 334 LEUA7 72 ALAA7
81 1 10  
  
Chain information for
Dro_real_space_refined_017-coot-1_real_space_refined_019.pdb #2  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
4L | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
A1 | No description available  
A3 | No description available  
A5 | No description available  
A6 | No description available  
A8 | No description available  
A9 | No description available  
AB AC | No description available  
AL | No description available  
AM | No description available  
AN | No description available  
AO | No description available  
B1 | No description available  
B2 | No description available  
B3 | No description available  
B4 | No description available  
B5 | No description available  
B6 | No description available  
B7 | No description available  
B8 | No description available  
B9 | No description available  
BL | No description available  
BM | No description available  
C2 | No description available  
S1 | No description available  
S2 | No description available  
S3 | No description available  
S4 | No description available  
S5 | No description available  
S6 | No description available  
S7 | No description available  
S8 | No description available  
V1 | No description available  
V2 | No description available  
V3 | No description available  
  

> hide atoms

> show cartoons

> hide #!2 models

> hide #1 cartoons

> select #1

66587 atoms, 68159 bonds, 110 pseudobonds, 8178 residues, 2 models selected  

> select clear

> show #1 surfaces

> lighting soft

> transparenccy #1 100

Unknown command: transparenccy #1 100  

> transparency #1 100

> select #1

66587 atoms, 68159 bonds, 110 pseudobonds, 8178 residues, 2 models selected  

> graphics selection color black width 2

> graphics silhouettes true

> show #!2 models

> color #2/V1 #DC050C

> color #2/V2 #E8601C

> color #2/S1 #F1932D

> color #2/S2 #F6C141

> color #2/S3 #F7F056

> color #2/S7 #CAE0AB

> color #2/S8 #90C987

> color #2/1 #7BAFDE

> color #2/2 #D1BBD7

> color #2/A1 #B8221E

> color #2/3 #4EB265

> color #2/A3 #69B190

> color #2/4 #AE76A3

> color #2/A5 #95211b

> color #2/4L #1965B0

> color #2/A6 #DF4828

> color #2/5 #882E72

> color #2/A7 #4D8AC6

> color #2/6 #5289C7

> color #2/A8 #C3A8D1

> color #2/A9 #6F4C9B

> color #2/AL #59A5A9

> color #2/AM #FEDA8B

> color #2/AN #D1B541

> color #2/AO #BEBC48

> color #2/AB #B58FC2

> color #2/AC #B58FC2

> color #2/B1 #DA2222

> color #2/B2 #E78C35

> color #2/B3 #77B77D

> color #2/B4 #D1B541

> color #2/B5 #4A7BB7

> color #2/B6 #D1B541

> color #2/B7 #DDAA3C

> color #2/B8 #E67932

> color #2/B9 #E49C39

> color #2/BL #95211B

> color #2/BM #E4632D

> color #2/C2 #8CBC68

> color #2/S4 #8C4E99

> color #2/S5 #60AB9E

> color #2/S6 #721E17

> color #2/V3 #A778B4

> hide #2 cartoons

> graphics silhouettes false

> transparency #1 50

> transparency #1 0

> hide #2 surfaces

> hide #1 surfaces

> show #2/S7 :89-93 :115-121 /S2 :90-101 /6 :49-110 /1 :183-247 /3 :1-81
> cartoons

> graphics silhouettes true

> show #1 surfaces

> transparency #1 100

> graphics silhouettes false

> graphics silhouettes #2 true

Expected true or false or a keyword  

> graphics silhouettes true

> cartoon style (#!1 & sel) modeHelix tube sides 20

> cartoon style (#!1 & sel) modeHelix tube sides 20

> select #2

66587 atoms, 68159 bonds, 110 pseudobonds, 8178 residues, 2 models selected  

> cartoon style (#!2 & sel) modeHelix tube sides 20

> select #1

66587 atoms, 68159 bonds, 110 pseudobonds, 8178 residues, 2 models selected  

> select ::name="FES"

16 atoms, 16 bonds, 4 pseudobonds, 4 residues, 4 models selected  

> show sel atoms

> style (#!1-2 & sel) sphere

Changed 16 atom styles  

> color sel byhetero

> setattr sel a radius 1.2

Assigning radius attribute to 16 items  

> select clear

> select ::name="SF4"

96 atoms, 216 pseudobonds, 12 residues, 4 models selected  

> show sel atoms

> color sel byhetero

> setattr sel a radius 1.2

Assigning radius attribute to 96 items  

> select clear

> select #1

66587 atoms, 68159 bonds, 110 pseudobonds, 8178 residues, 2 models selected  

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/OpenConfiguration/Open_Config_ActiveSiteLoops.cxs

> hide #1 surfaces

> hide #1 atoms

> select clear

> graphics silhouettes false

> graphics silhouettes true

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/OpenConfiguration/Open_Config_ActiveSiteLoops_Zoomed.cxs

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/OpenConfiguration/Open_Config_ActiveSiteLoops_Zoomed.png
> width 1235 height 858 supersample 3

> show #1 surfaces

> select #1

66587 atoms, 68159 bonds, 110 pseudobonds, 8178 residues, 2 models selected  

> view matrix

camera position:
-0.33102,0.018704,0.94344,1102.5,0.52355,-0.82816,0.20012,437.02,0.78506,0.56018,0.26435,490.2  
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1.35,1,0,0,0,0,1,0,0,0,0,1,0,#1.36,1,0,0,0,0,1,0,0,0,0,1,0,#1.37,1,0,0,0,0,1,0,0,0,0,1,0,#1.38,1,0,0,0,0,1,0,0,0,0,1,0,#1.39,1,0,0,0,0,1,0,0,0,0,1,0,#1.40,1,0,0,0,0,1,0,0,0,0,1,0,#1.41,1,0,0,0,0,1,0,0,0,0,1,0,#1.42,1,0,0,0,0,1,0,0,0,0,1,0,#1.43,1,0,0,0,0,1,0,0,0,0,1,0,#1.44,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> open
> /Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_20/Dro_real_space_refined_real_space_refined_018_coot-0_real_space_refined_020.pdb

Summary of feedback from opening
/Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_20/Dro_real_space_refined_real_space_refined_018_coot-0_real_space_refined_020.pdb  
---  
warnings | Ignored bad PDB record found on line 504  
LINK SG CYS V1 394 FE4 SF4 V1 502  
  
Ignored bad PDB record found on line 505  
LINK SG CYS V1 400 FE1 SF4 V1 502  
  
Ignored bad PDB record found on line 506  
LINK SG CYS V1 440 FE2 SF4 V1 502  
  
Ignored bad PDB record found on line 507  
LINK SG CYS V1 397 FE3 SF4 V1 502  
  
Ignored bad PDB record found on line 508  
LINK SG CYS V2 128 FE1 FES V2 301  
  
58 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 140 140 LEUA8 34 CYSA8
38 1 5  
Start residue of secondary structure not found: HELIX 141 141 ALAA8 41 GLUA8
51 1 11  
Start residue of secondary structure not found: HELIX 142 142 CYSA8 58 LYSA8
78 1 21  
Start residue of secondary structure not found: HELIX 143 143 HISA8 81 SERA8
94 1 14  
Start residue of secondary structure not found: HELIX 144 144 LYSA8 105 PHEA8
118 1 14  
  
Chain information for
Dro_real_space_refined_real_space_refined_018_coot-0_real_space_refined_020.pdb
#3  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
4L | No description available  
5 | No description available  
6 | No description available  
8 | No description available  
A1 | No description available  
A3 | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A9 | No description available  
AB | No description available  
AC | No description available  
AL | No description available  
AM | No description available  
AN | No description available  
AO | No description available  
B1 | No description available  
B2 | No description available  
B3 | No description available  
B4 | No description available  
B5 | No description available  
B6 | No description available  
B7 | No description available  
B8 | No description available  
B9 | No description available  
BL | No description available  
BM | No description available  
C2 | No description available  
S1 | No description available  
S2 | No description available  
S3 | No description available  
S4 | No description available  
S5 | No description available  
S6 | No description available  
S7 | No description available  
S8 | No description available  
V1 | No description available  
V2 | No description available  
V3 | No description available  
  

> hide #!2 models

> hide #!1 models

> hide #!3 atoms

> show #!3 cartoons

> open
> /Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_20/Dro_real_space_refined_real_space_refined_018_coot-0_real_space_refined_020.pdb

Summary of feedback from opening
/Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_20/Dro_real_space_refined_real_space_refined_018_coot-0_real_space_refined_020.pdb  
---  
warnings | Ignored bad PDB record found on line 504  
LINK SG CYS V1 394 FE4 SF4 V1 502  
  
Ignored bad PDB record found on line 505  
LINK SG CYS V1 400 FE1 SF4 V1 502  
  
Ignored bad PDB record found on line 506  
LINK SG CYS V1 440 FE2 SF4 V1 502  
  
Ignored bad PDB record found on line 507  
LINK SG CYS V1 397 FE3 SF4 V1 502  
  
Ignored bad PDB record found on line 508  
LINK SG CYS V2 128 FE1 FES V2 301  
  
58 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 140 140 LEUA8 34 CYSA8
38 1 5  
Start residue of secondary structure not found: HELIX 141 141 ALAA8 41 GLUA8
51 1 11  
Start residue of secondary structure not found: HELIX 142 142 CYSA8 58 LYSA8
78 1 21  
Start residue of secondary structure not found: HELIX 143 143 HISA8 81 SERA8
94 1 14  
Start residue of secondary structure not found: HELIX 144 144 LYSA8 105 PHEA8
118 1 14  
  
Chain information for
Dro_real_space_refined_real_space_refined_018_coot-0_real_space_refined_020.pdb
#4  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
4L | No description available  
5 | No description available  
6 | No description available  
8 | No description available  
A1 | No description available  
A3 | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A9 | No description available  
AB | No description available  
AC | No description available  
AL | No description available  
AM | No description available  
AN | No description available  
AO | No description available  
B1 | No description available  
B2 | No description available  
B3 | No description available  
B4 | No description available  
B5 | No description available  
B6 | No description available  
B7 | No description available  
B8 | No description available  
B9 | No description available  
BL | No description available  
BM | No description available  
C2 | No description available  
S1 | No description available  
S2 | No description available  
S3 | No description available  
S4 | No description available  
S5 | No description available  
S6 | No description available  
S7 | No description available  
S8 | No description available  
V1 | No description available  
V2 | No description available  
V3 | No description available  
  

> hide #!3-4 atoms

> hide #!3-4 cartoons

> show #!3-4 cartoons

> hide #3 cartoons

> show #3 surfaces

> transparency #3 100

> color #4/V1 #DC050C

> color #4/V2 #E8601C

> color #4/S1 #F1932D

> color #4/S2 #F6C141

> color #4/S3 #F7F056

> color #4/S7 #CAE0AB

> color #4/S8 #90C987

> color #4/1 #7BAFDE

> color #4/2 #D1BBD7

> color #4/A1 #B8221E

> color #4/3 #4EB265

> color #4/A3 #69B190

> color #4/4 #AE76A3

> color #4/A5 #95211b

> color #4/4L #1965B0

> color #4/A6 #DF4828

> color #4/5 #882E72

> color #4/A7 #4D8AC6

> color #4/6 #5289C7

> color #4/A8 #C3A8D1

> color #4/A9 #6F4C9B

> color #4/AL #59A5A9

> color #4/AM #FEDA8B

> color #4/AN #D1B541

> color #4/AO #BEBC48

> color #4/AB #B58FC2

> color #4/AC #B58FC2

> color #4/B1 #DA2222

> color #4/B2 #E78C35

> color #4/B3 #77B77D

> color #4/B4 #D1B541

> color #4/B5 #4A7BB7

> color #4/B6 #D1B541

> color #4/B7 #DDAA3C

> color #4/B8 #E67932

> color #4/B9 #E49C39

> color #4/BL #95211B

> color #4/BM #E4632D

> color #4/C2 #8CBC68

> color #4/S4 #8C4E99

> color #4/S5 #60AB9E

> color #4/S6 #721E17

> color #4/V3 #A778B4

> hide #4 cartoons

> show #4/S7 :89-93 :115-121 /S2 :90-101 /6 :49-110 /1 :183-247 /3 :1-81
> cartoons

> select #4

66019 atoms, 67574 bonds, 113 pseudobonds, 8112 residues, 3 models selected  

> cartoon style (#!4 & sel) modeHelix tube sides 20

> select clear

> select ::name="FES"

32 atoms, 32 bonds, 8 pseudobonds, 8 residues, 8 models selected  

> show sel atoms

> style (#!3-4 & sel) sphere

Changed 16 atom styles  

> color sel byhetero

> setattr sel a radius 1.2

Assigning radius attribute to 32 items  

> select clear

> select ::name="SF4"

192 atoms, 432 pseudobonds, 24 residues, 8 models selected  

> show sel atoms

> color sel byhetero

> setattr sel a radius 1.2

Assigning radius attribute to 192 items  

> select clear

> hide #3 atoms

> select #3

66019 atoms, 67574 bonds, 113 pseudobonds, 8112 residues, 3 models selected  

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/ClosedConfiguration/ClosedConfiguration.cxs

——— End of log from Wed May 25 10:51:47 2022 ———

opened ChimeraX session  

> hide cartoons

> hide atoms

> show #!2 models

> hide #!3 models

> show #!3 models

> show #!1 models

> hide #!2 models

> hide #!4 models

> show #!2 models

> hide #!1 models

> hide #!3 models

> show #!4 models

> show #!3 models

> show #!1 models

> hide #!3 models

> hide #!4 models

> show #2/A9 /6 cartoons

> show #2/A9 /6 /3 cartoons

> hide #1/3 cartoons

> hide #2/3 cartoons

> select #1

66587 atoms, 68159 bonds, 110 pseudobonds, 8178 residues, 2 models selected  

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/A9-ND6/A9-ND6_Open.cxs

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/A9-ND6/A9-ND6_Open.png
> width 1235 height 858 supersample 3

> hide #1 surfaces

> select ::name="NDP"

192 atoms, 208 bonds, 4 residues, 4 models selected  

> show sel atoms

> color sel byhetero

> select clear

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/A9-ND6/A9-ND6_Open_Zoomed.cxs

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/A9-ND6/A9-ND6_Open_Zoomed.png
> width 1235 height 858 supersample 3

> show #1 surfaces

> select #1

66587 atoms, 68159 bonds, 110 pseudobonds, 8178 residues, 2 models selected  

> view matrix

camera position:
0.77744,-0.03122,0.62818,862.33,0.38745,-0.76298,-0.51743,-290.25,0.49545,0.64566,-0.58108,-352.41  
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1.35,1,0,0,0,0,1,0,0,0,0,1,0,#1.36,1,0,0,0,0,1,0,0,0,0,1,0,#1.37,1,0,0,0,0,1,0,0,0,0,1,0,#1.38,1,0,0,0,0,1,0,0,0,0,1,0,#1.39,1,0,0,0,0,1,0,0,0,0,1,0,#1.40,1,0,0,0,0,1,0,0,0,0,1,0,#1.41,1,0,0,0,0,1,0,0,0,0,1,0,#1.42,1,0,0,0,0,1,0,0,0,0,1,0,#1.43,1,0,0,0,0,1,0,0,0,0,1,0,#1.44,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#3.3,1,0,0,0,0,1,0,0,0,0,1,0,#3.4,1,0,0,0,0,1,0,0,0,0,1,0,#3.5,1,0,0,0,0,1,0,0,0,0,1,0,#3.6,1,0,0,0,0,1,0,0,0,0,1,0,#3.7,1,0,0,0,0,1,0,0,0,0,1,0,#3.8,1,0,0,0,0,1,0,0,0,0,1,0,#3.9,1,0,0,0,0,1,0,0,0,0,1,0,#3.10,1,0,0,0,0,1,0,0,0,0,1,0,#3.11,1,0,0,0,0,1,0,0,0,0,1,0,#3.12,1,0,0,0,0,1,0,0,0,0,1,0,#3.13,1,0,0,0,0,1,0,0,0,0,1,0,#3.14,1,0,0,0,0,1,0,0,0,0,1,0,#3.15,1,0,0,0,0,1,0,0,0,0,1,0,#3.16,1,0,0,0,0,1,0,0,0,0,1,0,#3.17,1,0,0,0,0,1,0,0,0,0,1,0,#3.18,1,0,0,0,0,1,0,0,0,0,1,0,#3.19,1,0,0,0,0,1,0,0,0,0,1,0,#3.20,1,0,0,0,0,1,0,0,0,0,1,0,#3.21,1,0,0,0,0,1,0,0,0,0,1,0,#3.22,1,0,0,0,0,1,0,0,0,0,1,0,#3.23,1,0,0,0,0,1,0,0,0,0,1,0,#3.24,1,0,0,0,0,1,0,0,0,0,1,0,#3.25,1,0,0,0,0,1,0,0,0,0,1,0,#3.26,1,0,0,0,0,1,0,0,0,0,1,0,#3.27,1,0,0,0,0,1,0,0,0,0,1,0,#3.28,1,0,0,0,0,1,0,0,0,0,1,0,#3.29,1,0,0,0,0,1,0,0,0,0,1,0,#3.30,1,0,0,0,0,1,0,0,0,0,1,0,#3.31,1,0,0,0,0,1,0,0,0,0,1,0,#3.32,1,0,0,0,0,1,0,0,0,0,1,0,#3.33,1,0,0,0,0,1,0,0,0,0,1,0,#3.34,1,0,0,0,0,1,0,0,0,0,1,0,#3.35,1,0,0,0,0,1,0,0,0,0,1,0,#3.36,1,0,0,0,0,1,0,0,0,0,1,0,#3.37,1,0,0,0,0,1,0,0,0,0,1,0,#3.38,1,0,0,0,0,1,0,0,0,0,1,0,#3.39,1,0,0,0,0,1,0,0,0,0,1,0,#3.40,1,0,0,0,0,1,0,0,0,0,1,0,#3.41,1,0,0,0,0,1,0,0,0,0,1,0,#3.42,1,0,0,0,0,1,0,0,0,0,1,0,#3.43,1,0,0,0,0,1,0,0,0,0,1,0,#3.44,1,0,0,0,0,1,0,0,0,0,1,0,#3.45,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.2,1,0,0,0,0,1,0,0,0,0,1,0  
  

> hide #!1 models

> hide #!2 models

> show #3 surfaces

> show #!3 models

> show #4/A9 /6 cartoons

> show #!4 models

> view matrix camera
> 0.77744,-0.03122,0.62818,862.33,0.38745,-0.76298,-0.51743,-290.25,0.49545,0.64566,-0.58108,-352.41

> select #3

66019 atoms, 67574 bonds, 113 pseudobonds, 8112 residues, 3 models selected  

> view matrix camera
> 0.77744,-0.03122,0.62818,862.33,0.38745,-0.76298,-0.51743,-290.25,0.49545,0.64566,-0.58108,-352.41

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/A9-ND6/A9-ND6_Closed.cxs

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/A9-ND6/A9-ND6_Closed.png
> width 1235 height 858 supersample 3

> hide #3 surfaces

> view matrix camera
> 0.77744,-0.03122,0.62818,862.33,0.38745,-0.76298,-0.51743,-290.25,0.49545,0.64566,-0.58108,-352.41

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/A9-ND6/A9-ND6_Closed_Zoomed.cxs

> select clear

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/A9-ND6/A9-ND6_Closed_Zoomed.png
> width 1235 height 858 supersample 3

> view matrix camera
> 0.77744,-0.03122,0.62818,862.33,0.38745,-0.76298,-0.51743,-290.25,0.49545,0.64566,-0.58108,-352.41

> hide #!4 models

> hide #!3 models

> show #!2 models

> hide cartoons

> hide atoms

> show #2/1 /3 cartoons

> show #1 surfaces

> show #!1 models

> show #2/A9 cartoons

> view matrix camera
> 0.77744,-0.03122,0.62818,862.33,0.38745,-0.76298,-0.51743,-290.25,0.49545,0.64566,-0.58108,-352.41

> hide #2/A9 cartoons

> view matrix camera
> 0.77744,-0.03122,0.62818,862.33,0.38745,-0.76298,-0.51743,-290.25,0.49545,0.64566,-0.58108,-352.41

> select #1

66587 atoms, 68159 bonds, 110 pseudobonds, 8178 residues, 2 models selected  

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/ND1-ND3/ND1-ND3_Open.cxs

> hide #1 surfaces

> show #1 surfaces

> view matrix camera
> 0.77744,-0.03122,0.62818,862.33,0.38745,-0.76298,-0.51743,-290.25,0.49545,0.64566,-0.58108,-352.41

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/ND1-ND3/ND1-ND3_Open.png
> width 1235 height 858 supersample 3

> hide #1 surfaces

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/ND1-ND3/ND1-ND3_Open_Zoomed.cxs

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/ND1-ND3/ND1-ND3_Open_Zoomed.png
> width 1235 height 858 supersample 3

> view matrix camera
> 0.77744,-0.03122,0.62818,862.33,0.38745,-0.76298,-0.51743,-290.25,0.49545,0.64566,-0.58108,-352.41

> hide #2 cartoons

> show #3 surfaces

> show #!3 models

> show #4/1 /3 cartoons

> show #!4 models

> select #3

66019 atoms, 67574 bonds, 113 pseudobonds, 8112 residues, 3 models selected  

> save
> /Users/apadavan/Desktop/Drosophila_processing/Drosophila_Figures/ND1-ND3/ND1-ND3_Closed.cxs

——— End of log from Wed May 25 17:26:43 2022 ———

opened ChimeraX session  

> hide cartoons

> select
> ::name="3PE"::name="ALAA"::name="ARGA"::name="ASNA"::name="ASPA"::name="ATP"::name="CDL"::name="CYSA"::name="FES"::name="FMN"::name="GLNA"::name="GLUA"::name="GLYA"::name="HISA"::name="ILEA"::name="K"::name="LEUA"::name="LYSA"::name="META"::name="NDP"::name="PC1"::name="PHEA"::name="PROA"::name="SERA"::name="SF4"::name="THRA"::name="TRPA"::name="TYRA"::name="U10"::name="VALA"::name="ZMP"::name="ZN"

9698 atoms, 9516 bonds, 440 pseudobonds, 718 residues, 8 models selected  

> hide #3 surfaces

> show #1 surfaces

> show sel atoms

> hide #!3 models

> hide #!4 models

> hide #1/7 atoms

> transparency 100

> hide #1/7 atoms

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!1 models

> style (#!1 & sel) sphere

Changed 2162 atom styles  

> setattr sel a radius 1.2

Assigning radius attribute to 9698 items  

> select clear

> select ::name="U10"

126 atoms, 126 bonds, 2 residues, 2 models selected  

> style (#!1 & sel) ball

Changed 63 atom styles  

> select clear

> show #!2 models

> hide #!2 models

> hide #1 surfaces

Drag select of 1 atoms  

> hide sel atoms

> show #2 surfaces

> show #!2 models

> transparency #2 100

> select #2

66587 atoms, 68159 bonds, 110 pseudobonds, 8178 residues, 2 models selected  

> select clear

> hide #!1 models

> hide #2 atoms

> show #!1 models

> select ::name="NDP"

192 atoms, 208 bonds, 4 residues, 4 models selected  

> select ::name="FMN"

124 atoms, 132 bonds, 4 residues, 4 models selected  

> style (#!1-2 & sel) ball

Changed 62 atom styles  

> select clear

> graphics silhouettes false

> select #2

66587 atoms, 68159 bonds, 110 pseudobonds, 8178 residues, 2 models selected  

> graphics silhouettes true

> select clear

> select #2

66587 atoms, 68159 bonds, 110 pseudobonds, 8178 residues, 2 models selected  

> select clear

> graphics silhouettes false

> graphics silhouettes true

> hide #!2 models

Drag select of 1 atoms  

> hide sel atoms

> show #!2 models

> hide #!2 models

Drag select of 863 atoms  

> style sel ball

Changed 863 atom styles  

> select clear

Drag select of 508 atoms, 156 bonds  

> style sel ball

Changed 508 atom styles  

> select clear

> show #!2 models

> select
> ::name="3PE"::name="ALAA"::name="ARGA"::name="ASNA"::name="ASPA"::name="ATP"::name="CDL"::name="CYSA"::name="FES"::name="FMN"::name="GLNA"::name="GLUA"::name="GLYA"::name="HISA"::name="ILEA"::name="K"::name="LEUA"::name="LYSA"::name="META"::name="NDP"::name="PC1"::name="PHEA"::name="PROA"::name="SERA"::name="SF4"::name="THRA"::name="TRPA"::name="TYRA"::name="U10"::name="VALA"::name="ZMP"::name="ZN"

9698 atoms, 9516 bonds, 440 pseudobonds, 718 residues, 8 models selected  

> setattr sel a thickness 0.5

Assigning thickness attribute to 9698 items  
Not creating attribute 'thickness'; use 'create true' to override  

> select clear

> select #2

66587 atoms, 68159 bonds, 110 pseudobonds, 8178 residues, 2 models selected  

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select clear

> select
> ::name="3PE"::name="ALAA"::name="ARGA"::name="ASNA"::name="ASPA"::name="ATP"::name="CDL"::name="CYSA"::name="FES"::name="FMN"::name="GLNA"::name="GLUA"::name="GLYA"::name="HISA"::name="ILEA"::name="K"::name="LEUA"::name="LYSA"::name="META"::name="NDP"::name="PC1"::name="PHEA"::name="PROA"::name="SERA"::name="SF4"::name="THRA"::name="TRPA"::name="TYRA"::name="U10"::name="VALA"::name="ZMP"::name="ZN"

9698 atoms, 9516 bonds, 440 pseudobonds, 718 residues, 8 models selected  

> select clear

> hide atoms

> hide #!1 models

> hide #2 surfaces

> show #2/7 surfaces

> show #2 cartoons

> hide #2 cartoons

> show #2/7 cartoons

> show #2/7 atoms

> sequence chain #2/7

Alignment identifier is 2/7  

> hide #2 cartoons

> hide #2 atoms

> show #2/A7 cartoons

> sequence chain #2/A7

Chains must have same sequence  

> sequence chain #1/7

Alignment identifier is 1/7  

> hide #!2 models

> show #!4 models

> show #!3 models

> show #4 surfaces

> transparency #4 100

> select
> ::name="3PE"::name="ALAA"::name="ARGA"::name="ASNA"::name="ASPA"::name="ATP"::name="CDL"::name="CYSA"::name="FES"::name="FMN"::name="GLNA"::name="GLUA"::name="GLYA"::name="HISA"::name="ILEA"::name="K"::name="LEUA"::name="LYSA"::name="META"::name="NDP"::name="PC1"::name="PHEA"::name="PROA"::name="SERA"::name="SF4"::name="THRA"::name="TRPA"::name="TYRA"::name="U10"::name="VALA"::name="ZMP"::name="ZN"

9698 atoms, 9516 bonds, 440 pseudobonds, 718 residues, 8 models selected  

> show sel atoms

> sequence chain #4/A8

Chains must have same sequence  

> sequence chain #4/8

Alignment identifier is 4/8  

> help help:contact.html




OpenGL version: 4.1 NVIDIA-14.0.32 355.11.11.10.10.143
OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine
OpenGL vendor: NVIDIA CorporationHardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac14,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 432.60.3.0.0
      SMC Version (system): 2.17f7

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1615)
      Kernel Version: Darwin 19.6.0
      Time since boot: 44 days 3:11

Graphics/Displays:

    NVIDIA GeForce GT 750M:

      Chipset Model: NVIDIA GeForce GT 750M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 1 GB
      Vendor: NVIDIA (0x10de)
      Device ID: 0x0fe9
      Revision ID: 0x00a2
      ROM Revision: 3762
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        HP VH240a:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: 6CM1160B4N  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    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: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    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: 5.0.9
    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: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 3 years ago

Component: Unassigned → Input/Output
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → PDB two-letter chain ID sometimes not recognized if TER missing

comment:2 by pett, 11 months ago

Description: modified (diff)
Resolution: → fixed
Status: accepted → closed

Now if the chain ID changes between consecutive records, the code just pretends that the TER card was there.

Fix in the next build, but not release candidate since I'm not 100% sure that there aren't other ramifications to the change (though I don't *think* there are).

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