Opened 6 years ago

Closed 6 years ago

#2659 closed defect (duplicate)

Problem restoring a header sequence

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

Description 

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-01-30)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-01-30)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/aiste/Downloads/5vvs.pdb

5vvs.pdb title:  
Rna pol II elongation complex [more info...]  
  
Chain information for 5vvs.pdb #1  
---  
Chain | Description  
A | DNA-directed RNA polymerase II subunit RPB1  
B | DNA-directed RNA polymerase II subunit RPB2  
C | DNA-directed RNA polymerase II subunit RPB3  
D | DNA-directed RNA polymerase II subunit RPB4  
E | DNA-directed RNA polymerases I, II, and III subunit RPABC1  
F | DNA-directed RNA polymerases I, II, and III subunit RPABC2  
G | DNA-directed RNA polymerase II subunit RPB7  
H | DNA-directed RNA polymerases I, II, and III subunit RPABC3  
I | DNA-directed RNA polymerase II subunit RPB9  
J | DNA-directed RNA polymerases I, II, and III subunit RPABC5  
K | DNA-directed RNA polymerase II subunit RPB11  
L | DNA-directed RNA polymerases I, II, and III subunit RPABC4  
N | DNA (NTS)  
R | RNA  
T | DNA (TS)  
  
Non-standard residues in 5vvs.pdb #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> set bgColor white

> hide #!1.2 models

> hide #!1.1 models

Missing or invalid "atoms" argument: invalid atoms specifier  

> sequence chain #1/R

Alignment identifier is 1.R  

Missing or invalid "atoms" argument: invalid atoms specifier  

Missing or invalid "atoms" argument: invalid atoms specifier  

> sequence chain #1/T

Alignment identifier is 1.T  

> select /T:1-38

763 atoms, 848 bonds selected  

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete sel

> select /R:1-10

220 atoms, 246 bonds selected  

> sequence chain #1/T

Chains must have same sequence  

Chains must have same sequence  

> sequence chain #1/N

Alignment identifier is 1.N  

> delete sel

> sequence chain #1/T

Chains must have same sequence  

Chains must have same sequence  

> sequence chain #1/R

Alignment identifier is 1.R  

> delete sel

> sequence chain #1/N

Chains must have same sequence  

Chains must have same sequence  

> sequence chain #1/R

Chains must have same sequence  

Chains must have same sequence  

> sequence chain #1/T

Chains must have same sequence  

Chains must have same sequence  

> sequence chain #1/L

Alignment identifier is 1.L  

> show selAtoms ribbons

> hide selAtoms

> lighting simple

> lighting shadows true

> lighting soft

> lighting full

> set silhouettes true

> save /Users/aiste/Desktop/image3.png supersample 3

> save /Users/aiste/Desktop/image4.png supersample 3

> show selAtoms surfaces

> set silhouettes false

> set silhouettes true

> save /Users/aiste/Desktop/image5.png supersample 3

> lighting full

> hide selAtoms surfaces

> hide selAtoms

> show selAtoms ribbons

> show selAtoms surfaces

> surface transparency 80

> save /Users/aiste/Desktop/image6.png supersample 3

> set silhouettes false

> save /Users/aiste/Desktop/image7.png supersample 3

> close #1

> open /Users/aiste/Downloads/blockedtSH2_surfaceX.pdb

Chain information for blockedtSH2_surfaceX.pdb #1  
---  
Chain | Description  
| No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
  

> hide #!1.1 models

> delete sel

> delete sel

sequence chain

Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  

Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  

> sequence chain #1/A

Alignment identifier is 1.A  

> sequence chain #1/G

Alignment identifier is 1.G  

> sequence chain #1/E

Alignment identifier is 1.E  

> sequence chain #1/A

Alignment identifier is 1.A  

> sequence chain #1/B

Alignment identifier is 1.B  

> delete sel

> delete sel

> delete sel

> delete sel

sequence chain

Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  

Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  

> open /Users/aiste/Downloads/coral8.pdb

Summary of feedback from opening /Users/aiste/Downloads/coral8.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Project description:  
  
Ignored bad PDB record found on line 2  
REMARK j: 75 T: 0.411E-02 Suc: 97 Eva: 797197 CPU: 0.116E+05 F: 2.4586 Pen:
1.4571  
  
Ignored bad PDB record found on line 3  
REMARK The best Chi^2 values: 1.00155  
  
Ignored bad PDB record found on line 4  
REMARK Cross: 0.00029 Center: 1.42812  
  
Ignored bad PDB record found on line 5  
REMARK Cont Penalt.: 0.00000  
  
9 messages similar to the above omitted  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
95 messages similar to the above omitted  
Ignored bad PDB record found on line 1449  
REMARK *******************************  
  
Ignored bad PDB record found on line 1450  
REMARK Evaluated from PDB file 2.pdb  
  
Ignored bad PDB record found on line 1451  
REMARK Old center positioned at 9.047 28.292 -40.031  
  
Ignored bad PDB record found on line 1452  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 1453  
REMARK New center positioned at 9.047 28.292 -40.031  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
194 messages similar to the above omitted  
Ignored bad PDB record found on line 1655  
REMARK *******************************  
  
Ignored bad PDB record found on line 1656  
REMARK Evaluated from PDB file 3.pdb  
  
Ignored bad PDB record found on line 1657  
REMARK Old center positioned at 24.230 40.969 -48.177  
  
Ignored bad PDB record found on line 1658  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 1659  
REMARK New center positioned at 24.230 40.969 -48.177  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
463 messages similar to the above omitted  
Ignored bad PDB record found on line 2130  
REMARK *******************************  
  
Ignored bad PDB record found on line 2131  
REMARK Evaluated from PDB file 4.pdb  
  
Ignored bad PDB record found on line 2132  
REMARK Old center positioned at -26.383 41.634 -20.071  
  
Ignored bad PDB record found on line 2133  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 2134  
REMARK New center positioned at -26.383 41.634 -20.071  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1332 messages similar to the above omitted  
Ignored bad PDB record found on line 5688  
REMARK *******************************  
  
Ignored bad PDB record found on line 5689  
REMARK Evaluated from PDB file 5.pdb  
  
Ignored bad PDB record found on line 5690  
REMARK Old center positioned at -28.198 23.077 8.429  
  
Ignored bad PDB record found on line 5691  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 5692  
REMARK New center positioned at -28.198 23.077 8.429  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1060 messages similar to the above omitted  
Ignored bad PDB record found on line 6760  
REMARK *******************************  
  
Ignored bad PDB record found on line 6761  
REMARK Evaluated from PDB file 6.pdb  
  
Ignored bad PDB record found on line 6762  
REMARK Old center positioned at -13.895 72.598 -36.399  
  
Ignored bad PDB record found on line 6763  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 6764  
REMARK New center positioned at -13.895 72.598 -36.399  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
237 messages similar to the above omitted  
Ignored bad PDB record found on line 7009  
REMARK *******************************  
  
Ignored bad PDB record found on line 7010  
REMARK Evaluated from PDB file domain_3PSJ.pdb  
  
Ignored bad PDB record found on line 7011  
REMARK Old center positioned at 49.673 35.982 45.003  
  
Ignored bad PDB record found on line 7012  
REMARK Rotated by Euler angles 327.825 66.437 65.120  
  
Ignored bad PDB record found on line 7013  
REMARK New center positioned at 11.599 67.625 -46.981  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1589 messages similar to the above omitted  
  
Chain information for coral8.pdb #2  
---  
Chain | Description  
| No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
  

> close #1

> close #2

> open /Users/aiste/Downloads/coral15.pdb

Summary of feedback from opening /Users/aiste/Downloads/coral15.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Project description:  
  
Ignored bad PDB record found on line 2  
REMARK j: 73 T: 0.508E-02 Suc: 92 Eva: 763417 CPU: 0.111E+05 F: 2.4641 Pen:
1.4541  
  
Ignored bad PDB record found on line 3  
REMARK The best Chi^2 values: 1.00998  
  
Ignored bad PDB record found on line 4  
REMARK Cross: 0.00032 Center: 1.42201  
  
Ignored bad PDB record found on line 5  
REMARK Cont Penalt.: 0.00000  
  
9 messages similar to the above omitted  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
95 messages similar to the above omitted  
Ignored bad PDB record found on line 1449  
REMARK *******************************  
  
Ignored bad PDB record found on line 1450  
REMARK Evaluated from PDB file 2.pdb  
  
Ignored bad PDB record found on line 1451  
REMARK Old center positioned at 9.047 28.292 -40.031  
  
Ignored bad PDB record found on line 1452  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 1453  
REMARK New center positioned at 9.047 28.292 -40.031  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
194 messages similar to the above omitted  
Ignored bad PDB record found on line 1655  
REMARK *******************************  
  
Ignored bad PDB record found on line 1656  
REMARK Evaluated from PDB file 3.pdb  
  
Ignored bad PDB record found on line 1657  
REMARK Old center positioned at 24.230 40.969 -48.177  
  
Ignored bad PDB record found on line 1658  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 1659  
REMARK New center positioned at 24.230 40.969 -48.177  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
463 messages similar to the above omitted  
Ignored bad PDB record found on line 2130  
REMARK *******************************  
  
Ignored bad PDB record found on line 2131  
REMARK Evaluated from PDB file 4.pdb  
  
Ignored bad PDB record found on line 2132  
REMARK Old center positioned at -26.383 41.634 -20.071  
  
Ignored bad PDB record found on line 2133  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 2134  
REMARK New center positioned at -26.383 41.634 -20.071  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1332 messages similar to the above omitted  
Ignored bad PDB record found on line 5688  
REMARK *******************************  
  
Ignored bad PDB record found on line 5689  
REMARK Evaluated from PDB file 5.pdb  
  
Ignored bad PDB record found on line 5690  
REMARK Old center positioned at -28.198 23.077 8.429  
  
Ignored bad PDB record found on line 5691  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 5692  
REMARK New center positioned at -28.198 23.077 8.429  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1060 messages similar to the above omitted  
Ignored bad PDB record found on line 6760  
REMARK *******************************  
  
Ignored bad PDB record found on line 6761  
REMARK Evaluated from PDB file 6.pdb  
  
Ignored bad PDB record found on line 6762  
REMARK Old center positioned at -13.895 72.598 -36.399  
  
Ignored bad PDB record found on line 6763  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 6764  
REMARK New center positioned at -13.895 72.598 -36.399  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
237 messages similar to the above omitted  
Ignored bad PDB record found on line 7009  
REMARK *******************************  
  
Ignored bad PDB record found on line 7010  
REMARK Evaluated from PDB file domain_3PSJ.pdb  
  
Ignored bad PDB record found on line 7011  
REMARK Old center positioned at 49.673 35.982 45.003  
  
Ignored bad PDB record found on line 7012  
REMARK Rotated by Euler angles 321.941 80.316 72.675  
  
Ignored bad PDB record found on line 7013  
REMARK New center positioned at 8.440 67.158 -47.297  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1589 messages similar to the above omitted  
  
Chain information for coral15.pdb #1  
---  
Chain | Description  
| No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
  

> close #1

> open /Users/aiste/Downloads/coral10.pdb

Summary of feedback from opening /Users/aiste/Downloads/coral10.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Project description:  
  
Ignored bad PDB record found on line 2  
REMARK j: 81 T: 0.218E-02 Suc: 60 Eva: 895882 CPU: 0.129E+05 F: 2.5318 Pen:
1.5215  
  
Ignored bad PDB record found on line 3  
REMARK The best Chi^2 values: 1.01028  
  
Ignored bad PDB record found on line 4  
REMARK Cross: 0.00027 Center: 1.49467  
  
Ignored bad PDB record found on line 5  
REMARK Cont Penalt.: 0.00000  
  
9 messages similar to the above omitted  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
95 messages similar to the above omitted  
Ignored bad PDB record found on line 1449  
REMARK *******************************  
  
Ignored bad PDB record found on line 1450  
REMARK Evaluated from PDB file 2.pdb  
  
Ignored bad PDB record found on line 1451  
REMARK Old center positioned at 9.047 28.292 -40.031  
  
Ignored bad PDB record found on line 1452  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 1453  
REMARK New center positioned at 9.047 28.292 -40.031  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
194 messages similar to the above omitted  
Ignored bad PDB record found on line 1655  
REMARK *******************************  
  
Ignored bad PDB record found on line 1656  
REMARK Evaluated from PDB file 3.pdb  
  
Ignored bad PDB record found on line 1657  
REMARK Old center positioned at 24.230 40.969 -48.177  
  
Ignored bad PDB record found on line 1658  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 1659  
REMARK New center positioned at 24.230 40.969 -48.177  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
463 messages similar to the above omitted  
Ignored bad PDB record found on line 2130  
REMARK *******************************  
  
Ignored bad PDB record found on line 2131  
REMARK Evaluated from PDB file 4.pdb  
  
Ignored bad PDB record found on line 2132  
REMARK Old center positioned at -26.383 41.634 -20.071  
  
Ignored bad PDB record found on line 2133  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 2134  
REMARK New center positioned at -26.383 41.634 -20.071  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1332 messages similar to the above omitted  
Ignored bad PDB record found on line 5688  
REMARK *******************************  
  
Ignored bad PDB record found on line 5689  
REMARK Evaluated from PDB file 5.pdb  
  
Ignored bad PDB record found on line 5690  
REMARK Old center positioned at -28.198 23.077 8.429  
  
Ignored bad PDB record found on line 5691  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 5692  
REMARK New center positioned at -28.198 23.077 8.429  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1060 messages similar to the above omitted  
Ignored bad PDB record found on line 6760  
REMARK *******************************  
  
Ignored bad PDB record found on line 6761  
REMARK Evaluated from PDB file 6.pdb  
  
Ignored bad PDB record found on line 6762  
REMARK Old center positioned at -13.895 72.598 -36.399  
  
Ignored bad PDB record found on line 6763  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 6764  
REMARK New center positioned at -13.895 72.598 -36.399  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
237 messages similar to the above omitted  
Ignored bad PDB record found on line 7009  
REMARK *******************************  
  
Ignored bad PDB record found on line 7010  
REMARK Evaluated from PDB file domain_3PSJ.pdb  
  
Ignored bad PDB record found on line 7011  
REMARK Old center positioned at 49.673 35.982 45.003  
  
Ignored bad PDB record found on line 7012  
REMARK Rotated by Euler angles 265.761 150.485 331.506  
  
Ignored bad PDB record found on line 7013  
REMARK New center positioned at -49.975 74.102 -18.061  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1589 messages similar to the above omitted  
  
Chain information for coral10.pdb #1  
---  
Chain | Description  
| No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
  

sequence chain

Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  

Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  

> sequence chain #1/G

Alignment identifier is 1.G  

> close #1

> open /Users/aiste/Downloads/blockedtSH2_surface.pdb

Chain information for blockedtSH2_surface.pdb #1  
---  
Chain | Description  
| No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
  

sequence chain

Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  

Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> show selAtoms ribbons

> hide selAtoms

> show selAtoms surfaces

> lighting full

> lighting soft

> set silhouettes true

> sequence chain #1/G

Alignment identifier is 1.G  

> save /Users/aiste/Desktop/image8.png supersample 3

> surface transparency 80

> select #1.8

1578 atoms selected  

> show selAtoms ribbons

> sequence chain #1/G

Destroying pre-existing alignment with identifier 1.G  
Alignment identifier is 1.G  

> hide selAtoms surfaces

> ~select #1.8

Nothing selected  

> select #1.8

1578 atoms selected  

> ~select #1.8

Nothing selected  

> lighting full

> hide selAtoms surfaces

> show selAtoms surfaces

> surface transparency 80

> save /Users/aiste/Desktop/image9.png supersample 3

> lighting full

> surface transparency 0

> lighting full

> lighting full

> lighting soft

> lighting full

> lighting soft

> save session /Users/aiste/Desktop/spt6_alldomais_minusflex.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

> close #1

> open 5VKO format mmCIF fromDatabase pdb

5vko title:  
SPT6 tSH2-RPB1 1468-1500 pT1471, pS1493 [more info...]  
  
Chain information for 5vko #1  
---  
Chain | Description  
A | Transcription elongation factor SPT6  
B | DNA-directed RNA polymerase II subunit RPB1  
  
Non-standard residues in 5vko #1  
---  
IPA — isopropyl alcohol (2-propanol)  
  
  

> delete sel

> delete sel

> sequence chain #1/B

Alignment identifier is 1.B  

> delete sel

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting full

> lighting flat

> lighting flat

> lighting full

> set silhouettes false

> set silhouettes true

> lighting soft

> lighting soft

> lighting shadows true intensity 0.5

> lighting full

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting simple

> lighting soft

> lighting soft

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting simple

> open 5VKO format mmCIF fromDatabase pdb

5vko title:  
SPT6 tSH2-RPB1 1468-1500 pT1471, pS1493 [more info...]  
  
Chain information for 5vko #2  
---  
Chain | Description  
A | Transcription elongation factor SPT6  
B | DNA-directed RNA polymerase II subunit RPB1  
  
Non-standard residues in 5vko #2  
---  
IPA — isopropyl alcohol (2-propanol)  
  
  

> close #1

> close

> open 5VKO format mmCIF fromDatabase pdb

5vko title:  
SPT6 tSH2-RPB1 1468-1500 pT1471, pS1493 [more info...]  
  
Chain information for 5vko #1  
---  
Chain | Description  
A | Transcription elongation factor SPT6  
B | DNA-directed RNA polymerase II subunit RPB1  
  
Non-standard residues in 5vko #1  
---  
IPA — isopropyl alcohol (2-propanol)  
  
  

> delete sel

> delete sel

> sequence chain #1/B

Alignment identifier is 1.B  

> delete sel

> sequence chain #1/A

Alignment identifier is 1.A  

> split sel

Chain information for 5vko A #1.1  
---  
Chain | Description  
A | No description available  
  
Split 5vko (#1) into 2 models  

> sequence chain #1.1/A

Alignment identifier is 1.1.A  

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1.1.A  
Alignment identifier is 1.1.A  

> color sel black

> close #1

> open 5VKO format mmCIF fromDatabase pdb

5vko title:  
SPT6 tSH2-RPB1 1468-1500 pT1471, pS1493 [more info...]  
  
Chain information for 5vko #1  
---  
Chain | Description  
A | Transcription elongation factor SPT6  
B | DNA-directed RNA polymerase II subunit RPB1  
  
Non-standard residues in 5vko #1  
---  
IPA — isopropyl alcohol (2-propanol)  
  
  

> delete sel

> sequence chain #1/B

Alignment identifier is 1.B  

> delete sel

> sequence chain #1/A

Alignment identifier is 1.A  

> color sel dark green

> set silhouettes false

> set silhouettes true

> lighting simple

> lighting full

> lighting full

> lighting soft

> lighting soft

> lighting full

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

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

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

> color blueviolet

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

> color plum

> color medium purple

> color purple

> color medium purple

> color sel light blue

> show selAtoms surfaces

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

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

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

> surface transparency 80

> hide selAtoms surfaces

> view cofr false

> save /Users/aiste/Desktop/image10.png supersample 3

> lighting flat

> lighting full

> set silhouettes false

> set silhouettes true

> open /Users/aiste/Desktop/spt6_alldomais_minusflex.cxs format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 594, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 590, in restore_snapshot  
inst.seq_canvas.restore_state(session, data['seq canvas'])  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1120, in restore_state  
headers.append(header_class.session_restore(session, self.sv, header_state))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/headers/header_sequence.py", line 164, in
session_restore  
inst = HeaderSequence(alignment)  
TypeError: __init__() missing 1 required positional argument:
'refresh_callback'  
  
opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 229, in _actually_resize  
self._reformat()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1027, in _reformat  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1602, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2244, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2194, in _layout_line  
font=self._label_font(line))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2134, in _label_font  
if self.has_associated_structures(line):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2072, in
has_associated_structures  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2072, in <listcomp>  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon HD - FirePro D700 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Sessions
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Problem restoring a header sequence

comment:2 by Eric Pettersen, 6 years ago

Resolution: → duplicate
Status: accepted → closed
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