Discontinuous secondary structure

[andrea.foote@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202110271145 (2021-10-27 11:45:32 UTC)
Description
Ribbons do not connect even when forced using e.g.,  "setattr #1.1:130-137 res ss_type 2". I am trying to beautify a model I have made - it depicts ribbons nicely in PyMOL but ChimeraX shows some as loops. When I use "setattr" encompassing the entire region I want modelled as a continuous beta strand, ChimeraX places several discontinuous ribbons, and i cannot seem to get them connected, even if i set the entire stretch to "type 0"/loop first and then afterwords set the region to "type 2"/sheet (see screen shots - in sequence from A-D).

Log:
UCSF ChimeraX version: 1.3.dev202110271145 (2021-10-27)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Volumes/Labs/Kelm/General/Andrea
> Foote/PyMOL:Chimera:Modeling/PurB_2018.pdb" format pdb

Chain information for PurB_2018.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> setattr :243-250 res ss_type 0

Assigning ss_type attribute to 16 items  

> setattr :243-250 res ss_type 2

Assigning ss_type attribute to 16 items  

> show seq

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

>

Incomplete command: sequence  

> sequence chain

Missing or invalid "chains" argument: empty atom specifier  

> A

Unknown command: sequence A  

> /A

Unknown command: sequence /A  

> sequence chain

Missing or invalid "chains" argument: empty atom specifier  

> sequence chain

Missing or invalid "chains" argument: empty atom specifier  

> sequence chainn

Missing or invalid "chains" argument: empty atom specifier  

> 123angle

123angle is provided by the uninstalled bundle SEQCROW versions 0.13 – 0.15  

>

Unknown command: sequence #1  

>

Unknown command: sequence #1  

> open 5fgp

5fgp title:  
Crystal structure of D. melanogaster Pur-alpha repeat I-II in complex with
DNA. [more info...]  
  
Chain information for 5fgp #2  
---  
Chain | Description | UniProt  
A | CG1507-PB, isoform B | Q9V4D9_DROME  
B | DNA |  
  
Non-standard residues in 5fgp #2  
---  
CL — chloride ion  
SO4 — sulfate ion  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #1/B

Alignment identifier is 1  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> ui tool show "Show Sequence Viewer"

> uniprot

Unknown command: uniprot  

> fetch uniprot

Unknown command: fetch uniprot  

> select #2

1443 atoms, 1352 bonds, 279 residues, 1 model selected  

> uniprot

Unknown command: uniprot  

> uniprot 5fgp

Unknown command: uniprot 5fgp  

> open uniprot

'uniprot' has no suffix  

> open uniprot 5fgp

'uniprot' has no suffix  

> open 5fgo

Summary of feedback from opening 5fgo fetched from pdb  
---  
note | Fetching compressed mmCIF 5fgo from
http://files.rcsb.org/download/5fgo.cif  
  
5fgo title:  
Crystal structure of D. melanogaster Pur-alpha repeat III. [more info...]  
  
Chain information for 5fgo #3  
---  
Chain | Description | UniProt  
A B C D E F | CG1507-PB, isoform B | Q9V4D9_DROME  
  
Non-standard residues in 5fgo #3  
---  
CL — chloride ion  
  
5fgo mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
  

> hide sel surfaces

[Repeated 1 time(s)]

> show sel cartoons

> select #3

3471 atoms, 3372 bonds, 553 residues, 1 model selected  

> hide sel surfaces

[Repeated 1 time(s)]

> show sel cartoons

> hide sel atoms

> align #2 toAtoms #3

Unequal number of atoms to pair, 1443 and 3471  

> show #3 target m

> align #2/AB toAtoms #3

Unequal number of atoms to pair, 0 and 3471  

> align #2.1-2 toAtoms #3

Unequal number of atoms to pair, 0 and 3471  

> align 2.1-2 and 3

Missing or invalid "atoms" argument: invalid atoms specifier  

> align #2 toAtoms #3.1-2

Unequal number of atoms to pair, 1443 and 0  

> align #2 toAtoms #3.1

Unequal number of atoms to pair, 1443 and 0  

> ~select #3

Nothing selected  

> select #3

3471 atoms, 3372 bonds, 553 residues, 1 model selected  

> view #3 clip false

> sym #3

5fgo mmCIF Assemblies  
---  
1| author_and_software_defined_assembly| 1 copy of chains A,B  
2| author_and_software_defined_assembly| 1 copy of chains C,D  
3| author_and_software_defined_assembly| 1 copy of chains E,F  
  

> log metadata #3

Metadata for 5fgo #3  
---  
Title | Crystal structure of D. melanogaster Pur-alpha repeat III.  
Citation | Weber, J., Bao, H., Hartlmuller, C., Wang, Z., Windhager, A.,
Janowski, R., Madl, T., Jin, P., Niessing, D. (2016). Structural basis of
nucleic-acid recognition and double-strand unwinding by the essential neuronal
protein Pur-alpha. Elife, 5. PMID: 26744780. DOI: 10.7554/eLife.11297  
Non-standard residue | CL — chloride ion  
Gene source | Drosophila melanogaster (fruit fly)  
Experimental method | X-ray diffraction  
Resolution | 2.6Å  
  
> log chains #3

Chain information for 5fgo #3  
---  
Chain | Description | UniProt  
A B C D E F | CG1507-PB, isoform B | Q9V4D9_DROME  
  

> align #2/A toAtoms #3.1

Unequal number of atoms to pair, 1274 and 0  

> align #2 toAtoms #3

Unequal number of atoms to pair, 1443 and 3471  

> align #2 toAtoms #3/AB

Unequal number of atoms to pair, 1443 and 0  

> align #2 toAtoms #3/A-B

Unequal number of atoms to pair, 1443 and 1154  

> ~select #3

Nothing selected  

> hide #2 models

> hide #3 models

> color byattribute chain

No known/registered attribute chain  

> split chains

Split PurB_2018.pdb (#1) into 2 models  
Split 5fgp (#2) into 2 models  
Split 5fgo (#3) into 6 models  
Chain information for PurB_2018.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for PurB_2018.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 5fgp A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 5fgp B #2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 5fgo A #3.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 5fgo B #3.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 5fgo C #3.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 5fgo D #3.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 5fgo E #3.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 5fgo F #3.6  
---  
Chain | Description  
F | No description available  
  

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

> color #1.1 #dba945

> color #1.1 #db876a

> color #1.2 #7fdba2

> color #1.2 #94b2db

> color #1.2 #639edb

> color #1.1 #e3abdd

> color #1.1 #c666e3

> color #1.1 #e35dd3

> color #1.1 #d5e388

> color #1.1 #d3e36c

> ui mousemode right select

> select clear

> select #1.2/B:42

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #1.2/B:88

15 atoms, 13 bonds, 2 residues, 1 model selected  

> select clear

> select #1.2/B:42

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1.2/B:89

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1.2/B:43

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #1.2/B:88

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select clear

[Repeated 6 time(s)]

> select #1.2/B:44

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1.2/B:88

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #1.2/B:65

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

72 atoms, 73 bonds, 8 residues, 1 model selected  

> select up

2390 atoms, 2433 bonds, 324 residues, 1 model selected  

> select down

72 atoms, 73 bonds, 8 residues, 1 model selected  

> select down

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

72 atoms, 73 bonds, 8 residues, 1 model selected  

> select add #1.2/B:68

76 atoms, 76 bonds, 9 residues, 1 model selected  

> select up

148 atoms, 149 bonds, 18 residues, 1 model selected  

> select #1.2/B:78

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select clear

> select #1.2/B:46

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

277 atoms, 281 bonds, 46 residues, 1 model selected  

> select down

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select down

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select down

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

277 atoms, 281 bonds, 46 residues, 1 model selected  

> select down

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #1.2/B:47

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select up

316 atoms, 320 bonds, 51 residues, 1 model selected  

> select down

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select up

316 atoms, 320 bonds, 51 residues, 1 model selected  

> select down

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select add #1.2/B:51

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select up

316 atoms, 320 bonds, 51 residues, 1 model selected  

> select down

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select clear

> select #1.2/B:47

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

39 atoms, 38 bonds, 5 residues, 1 model selected  

> select #1.2/B:52

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1.2/B:47

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

39 atoms, 38 bonds, 5 residues, 1 model selected  

> select add #1.2/B:52

47 atoms, 45 bonds, 6 residues, 1 model selected  

> select up

92 atoms, 91 bonds, 11 residues, 1 model selected  

> select add #1.2/B:58

103 atoms, 102 bonds, 12 residues, 1 model selected  

> select up

164 atoms, 165 bonds, 19 residues, 1 model selected  

> select up

2390 atoms, 2433 bonds, 324 residues, 1 model selected  

> select down

164 atoms, 165 bonds, 19 residues, 1 model selected  

> select subtract #1.2/B:65

156 atoms, 158 bonds, 18 residues, 1 model selected  

> select add #1.2/B:65

164 atoms, 165 bonds, 19 residues, 1 model selected  

> select add #1.2/B:66

169 atoms, 169 bonds, 20 residues, 1 model selected  

> select up

178 atoms, 179 bonds, 21 residues, 1 model selected  

> select add #1.2/B:68

182 atoms, 182 bonds, 22 residues, 1 model selected  

> select up

254 atoms, 256 bonds, 31 residues, 1 model selected  

> select add #1.2/B:78

259 atoms, 260 bonds, 32 residues, 1 model selected  

> select up

267 atoms, 269 bonds, 34 residues, 1 model selected  

> select add #1.2/B:81

273 atoms, 274 bonds, 35 residues, 1 model selected  

> select up

328 atoms, 330 bonds, 42 residues, 1 model selected  

> select add #1.2/B:89

336 atoms, 337 bonds, 43 residues, 1 model selected  

> select up

478 atoms, 484 bonds, 61 residues, 1 model selected  

> select add #1.2/B:46

486 atoms, 491 bonds, 62 residues, 1 model selected  

> select add #1.2/B:45

495 atoms, 499 bonds, 63 residues, 1 model selected  

> select add #1.2/B:44

504 atoms, 507 bonds, 64 residues, 1 model selected  

> select add #1.2/B:43

511 atoms, 513 bonds, 65 residues, 1 model selected  

> select add #1.2/B:42

520 atoms, 521 bonds, 66 residues, 1 model selected  

> select add #1.2/B:108

529 atoms, 529 bonds, 67 residues, 1 model selected  

> select add #1.2/B:109

537 atoms, 536 bonds, 68 residues, 1 model selected  

> create II sele

Unknown command: create II sele  
Drag select of 84 residues  
Drag select of 24 residues  

> select clear

Drag select of 11 residues  
Drag select of 12 residues  

> select up

531 atoms, 538 bonds, 77 residues, 1 model selected  
Drag select of 37 residues  

> select subtract #1.1/A:19

321 atoms, 535 bonds, 39 residues, 1 model selected  

> select subtract #1.1/A:20

314 atoms, 528 bonds, 38 residues, 1 model selected  

> select subtract #1.1/A:40

305 atoms, 520 bonds, 37 residues, 1 model selected  

> select subtract #1.1/A:41

296 atoms, 512 bonds, 36 residues, 1 model selected  

> select add #1.1/A:78

301 atoms, 516 bonds, 37 residues, 1 model selected  

> select up

515 atoms, 517 bonds, 78 residues, 1 model selected  

> select down

301 atoms, 516 bonds, 37 residues, 1 model selected  

> select add #1.1/A:79

305 atoms, 519 bonds, 38 residues, 1 model selected  

> select add #1.1/A:80

309 atoms, 522 bonds, 39 residues, 1 model selected  

> select add #1.1/A:81

315 atoms, 527 bonds, 40 residues, 1 model selected  

> select up

529 atoms, 531 bonds, 81 residues, 1 model selected  

> select down

315 atoms, 527 bonds, 40 residues, 1 model selected  

> select add #1.1/A:82

324 atoms, 535 bonds, 41 residues, 1 model selected  

> select up

538 atoms, 540 bonds, 82 residues, 1 model selected  

> select down

324 atoms, 535 bonds, 41 residues, 1 model selected  
Drag select of 4 residues  

> select add #1.1/A:82

349 atoms, 535 bonds, 44 residues, 1 model selected  

> select add #1.1/A:86

356 atoms, 541 bonds, 45 residues, 1 model selected  

> select add #1.1/A:87

364 atoms, 548 bonds, 46 residues, 1 model selected  

> select add #1.1/A:88

370 atoms, 553 bonds, 47 residues, 1 model selected  

> show target m

[Repeated 1 time(s)]

> hide target m

> show #!1 models

> show #1.1 models

> hide #!1 models

> show #!1 models

Drag select of 5 residues  

> select add #1.1/A:88

393 atoms, 553 bonds, 51 residues, 1 model selected  

> select add #1.1/A:108

402 atoms, 561 bonds, 52 residues, 1 model selected  

> select clear

> ui tool show "Blast Protein"

> ui tool show "Model Loops"

> ui tool show "Modeller Comparative"

> ui tool show "Show Sequence Viewer"

> sequence chain #2.1/A

Alignment identifier is 2.1/A  

> select #2.1/A:41

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2.1/A:41-52

98 atoms, 97 bonds, 12 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1.1/A

Alignment identifier is 1.1/A  

> select #1.1/A:2

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1.1/A:2-5

25 atoms, 24 bonds, 4 residues, 1 model selected  

> select #1.1/A:2-5,9-17

73 atoms, 71 bonds, 13 residues, 1 model selected  

> select #1.1/A:2-5,9-17,23-33

143 atoms, 143 bonds, 24 residues, 1 model selected  

> select clear

> select #1.1/A:19-20

11 atoms, 11 bonds, 2 residues, 1 model selected  

> select #1.1/A:19-24

39 atoms, 40 bonds, 6 residues, 1 model selected  

> select #1.1/A:28

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1.1/A:28-36

43 atoms, 42 bonds, 9 residues, 1 model selected  

> select clear

[Repeated 2 time(s)]

> select #1.1/A:155

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1.1/A:155-164

91 atoms, 91 bonds, 10 residues, 1 model selected  

> select #1.1/A:19-24

39 atoms, 40 bonds, 6 residues, 1 model selected  

> select #1.1/A:27-28

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #1.1/A:27-32

34 atoms, 34 bonds, 6 residues, 1 model selected  

> select #1.1/A:38

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1.1/A:38-44

51 atoms, 50 bonds, 7 residues, 1 model selected  

> select #1.1/A:27-32

34 atoms, 34 bonds, 6 residues, 1 model selected  

> select #1.1/A:19-24

39 atoms, 40 bonds, 6 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1.1/A

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

> select #1.1/A:10

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1.1/A:10-16

35 atoms, 34 bonds, 7 residues, 1 model selected  

> select #1.1/A:22-23

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1.1/A:22-32

70 atoms, 72 bonds, 11 residues, 1 model selected  

> select #1.1/A:10-16

35 atoms, 34 bonds, 7 residues, 1 model selected  

> select #1.1/A:22-32

70 atoms, 72 bonds, 11 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #1.1/A:117-118

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #1.1/A:117-127

64 atoms, 64 bonds, 11 residues, 1 model selected  

> select #1.1/A:10

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1.1/A:10-11

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select clear

> select #1.1/A:166

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1.1/A:166-168

12 atoms, 11 bonds, 3 residues, 1 model selected  

> select #1.1/A:10-16

35 atoms, 34 bonds, 7 residues, 1 model selected  

> set bgColor white

> color #1.1 #75bee6

> color #1.1 #70a9ff

> show sel surfaces

> select clear

> show #!1.1 surfaces

> transparency #1.1#!1 100

> graphics silhouettes true

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

[Repeated 1 time(s)]

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> select #1.1/A:15@O

1 atom, 1 residue, 1 model selected  

> select clear

> hide #1.1.1 models

> show #1.1.1 models

> graphics silhouettes true

> hide #!1.1 models

> show #!1.1 models

> select #1.1.1

2390 atoms, 324 residues, 1 model selected  

> ~select #1.1.1

1 model selected  

> select #1.1

2390 atoms, 2433 bonds, 324 residues, 1 model selected  

> ~select #1.1.1

2433 bonds, 2 models selected  

> graphics silhouettes false

> select #1.1.1

2390 atoms, 324 residues, 1 model selected  

> select #1.1

2390 atoms, 2433 bonds, 324 residues, 1 model selected  

> ~select #1.1

1 model selected  

> select #1.1.1

2390 atoms, 324 residues, 1 model selected  

> graphics silhouettes true

> select clear

> lighting flat

> lighting full

> lighting soft

> select #1.1.1

2390 atoms, 324 residues, 1 model selected  

> select #1.1

2390 atoms, 2433 bonds, 324 residues, 1 model selected  

> graphics silhouettes false

> ~select #1.1

1 model selected  

> graphics silhouettes true

> graphics silhouettes false

> select #1.1.1

2390 atoms, 324 residues, 1 model selected  

> graphics silhouettes true

> ~select #1.1.1

1 model selected  

> select #1.1.1

2390 atoms, 324 residues, 1 model selected  

> show #1.1.1 target m

> hide #1.1.1 target m

[Repeated 1 time(s)]

> show #1.1.1 target m

> hide #!1.1 models

> show #!1.1 models

> select #1.1

2390 atoms, 2433 bonds, 324 residues, 1 model selected  

> ~select #1.1.1

2433 bonds, 2 models selected  

> select #1.1

2390 atoms, 2433 bonds, 324 residues, 1 model selected  

> hide #1.1.1 target m

> show #1.1.1 models

> hide #!1.1 target m

> show #!1.1 target m

> tube helices

Unknown command: tube helices  

> cylinders

Unknown command: cylinders  

> ~surface

> surface

> ~cartoon

> cartoon

> select 1.1:1-210

Expected an objects specifier or a keyword  

> select #1.1:1-210

1530 atoms, 1554 bonds, 210 residues, 1 model selected  

> sticks

Unknown command: sticks  

> spheres

Unknown command: spheres  

> ~surface

> surface and sele

Expected an atoms specifier or a keyword  

> surface sele

Expected an atoms specifier or a keyword  

> ~select

Nothing selected  

> ~select

Nothing selected  

> select

9694 atoms, 9590 bonds, 1480 residues, 13 models selected  

> select up

9694 atoms, 9590 bonds, 1480 residues, 23 models selected  

> select down

13 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select down

3 models selected  

> select down

3 models selected  

> select down

3 models selected  

> select down

3 models selected  

> select down

3 models selected  

> select down

3 models selected  

> select down

3 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select up

3 models selected  

> select #2

1443 atoms, 1352 bonds, 279 residues, 3 models selected  

> select #1

4780 atoms, 4866 bonds, 648 residues, 3 models selected  

> ~select #1.2

2390 atoms, 2433 bonds, 324 residues, 4 models selected  

> select clear

> select #1.1/A:197

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1.1/A:201

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1.1/A:200

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 219 residues  

> select clear

> help

> show #!2.1 models

> show #!2.2 models

> show #!3 models

> hide #!2 models

> hide #!2.1 models

> hide #!2.2 models

> select #1.1/A:230

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #1.1/A:232

16 atoms, 15 bonds, 2 residues, 2 models selected  

> select add #1.1/A:231

24 atoms, 22 bonds, 3 residues, 2 models selected  

> select add #1.1/A:233

33 atoms, 30 bonds, 4 residues, 2 models selected  

> select add #1.1/A:234

37 atoms, 33 bonds, 5 residues, 2 models selected  

> select add #1.1/A:235

44 atoms, 39 bonds, 6 residues, 2 models selected  

> select add #1.1/A:236

50 atoms, 44 bonds, 7 residues, 2 models selected  

> select up

230 atoms, 234 bonds, 36 residues, 2 models selected  

> select up

2390 atoms, 2433 bonds, 324 residues, 2 models selected  

> select up

2390 atoms, 2433 bonds, 324 residues, 2 models selected  

> select up

4780 atoms, 4866 bonds, 648 residues, 3 models selected  

> select down

2390 atoms, 2433 bonds, 324 residues, 3 models selected  

> select down

1 model selected  

> select down

230 atoms, 234 bonds, 36 residues, 1 model selected  

> select down

50 atoms, 44 bonds, 7 residues, 2 models selected  

> select down

50 atoms, 44 bonds, 7 residues, 2 models selected  

> select down

50 atoms, 44 bonds, 7 residues, 2 models selected  

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!3.1 models

> show #!3.2 models

> show #!3.3 models

> show #!3.4 models

> show #!3.5 models

> show #!3.6 models

> hide #!3.3 models

> hide #!3.4 models

> hide #!3.5 models

> hide #!3.6 models

> hide #!3.1 models

> hide #!3 models

> show #!3 models

> hide #!1.1 models

> hide #1.1.1 models

> select #3.2/B:200

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3.2/B:192

8 atoms, 7 bonds, 1 residue, 1 model selected  

> setattr #3.2:192-200 res ss_type 2

Assigning ss_type attribute to 9 items  

> hide #!3 models

> hide #!3.2 models

> show #1.1.1 models

> hide #1.1.1 models

> select #1.1/A:133

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select clear

> select #1.1/A:130

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select add #1.1/A:131

13 atoms, 11 bonds, 2 residues, 2 models selected  

> select add #1.1/A:132

22 atoms, 19 bonds, 3 residues, 2 models selected  

> select add #1.1/A:133

28 atoms, 24 bonds, 4 residues, 2 models selected  

> select add #1.1/A:134

37 atoms, 32 bonds, 5 residues, 2 models selected  

> select add #1.1/A:135

48 atoms, 43 bonds, 6 residues, 2 models selected  

> select add #1.1/A:136

56 atoms, 50 bonds, 7 residues, 2 models selected  

> select add #1.1/A:137

63 atoms, 56 bonds, 8 residues, 2 models selected  

> setattr #1.1:130-137 res ss_type 2

Assigning ss_type attribute to 8 items  

> setattr #1.1:130-137 res ss_type 0

Assigning ss_type attribute to 8 items  

> setattr #1.1:130-137 res ss_type 2

Assigning ss_type attribute to 8 items  




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      Kernel Version: Darwin 20.3.0
      Time since boot: 1 day 8 minutes

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      Type: GPU
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      Revision ID: 0x0009
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PyQt5 5.15.2, Qt 5.15.2
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File attachment: Screen Shot 2021-10-28 at 1.36.09 PM.png

Screen Shot 2021-10-28 at 1.36.09 PM.png​

[andrea.foote@…]

Added by email2trac

[Eric Pettersen]

Hi Andrea,

In order to handle the case where a structure has adjacent helices with no intervening non-helix residue, there is also an 'ss_id' attribute to mark what secondary structure element a residue belongs to, and there will always be a short coil depiction between residues with differing ss_ids. So to get the effect you want to achieve you also have to assign the same ss_id to all those residues. I would suggest assigning an ss_id that isn't likely to already be used, such as 101, 102, etc.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab