Changing SS assignment

[bssfh@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
I'm trying to correct some parts of a structure that should display as one long beta-strand but are instead showing as multiple beta-strands. Despite following instructions at https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-February/000362.html the command to redefine the secondary structure to beat strand is not resulting in the visualisation of that part of the structure changing.

Specifically, in PDB 5D0O, I'm trying to update chain A, residues 782-789 to beta-sheet using command setattr #1/A:782-789 res ss_type 2 but it is not doing anything

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5d0o format mmcif fromDatabase pdb

5d0o title:  
BamABCDE complex, outer membrane β barrel assembly machinery entire complex
[more info...]  
  
Chain information for 5d0o #1  
---  
Chain | Description  
A | Outer membrane protein assembly factor BamA  
B | Outer membrane protein assembly factor BamB  
C | Outer membrane protein assembly factor BamC  
D | Outer membrane protein assembly factor BamD  
E | Outer membrane protein assembly factor BamE  
  

> hide atoms

> hide cartoons

> show cartoons

> dssp

> extract

Unknown command: extract  

> extract

Unknown command: extract  

> new

Unknown command: new  

> set bgColor white

> set bgColor black

> copy

Unknown command: copy  

> hide

> hide #1/B-E

> hide #1/B-E target c

> hide #1/A target c

> show #1/E target c

> ui mousemode right zoom

> ui mousemode right translate

> ui mousemode right rotate

> hide not #1/E:71-97 targ c

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

> hide all not #1/E:71-97 targ c

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

> show #1/E:71-97 target c

> hide #1/E target c

> show #1/E:71-97 target c

> show alll targ c

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

> show all target c

> ui mousemode right zoom

> hide #1/B-E target c

> hide #1/A:106-118 target c

> hide #1/A-E target c

> hide #1/A:106-118 target c

> hide #1/A:106-118 target c

> show #1/A:106-118 target c

> hide #1/A:106-118 target c

> show #1/A:106-118 target a

> color

> color byattribute hetero

No known/registered attribute hetero  

> color byhetero

> lighting soft

> lighting full

> set bgColor white

> color bychain

> color byhetero

> rainbow

> coulombic

> color byhetero

> hide all target s

> lighting simple

> lighting flat

> lighting full

> lighting soft

> rainbow

> color byhetero

> style stick

Changed 22815 atom styles  

> ui tool show "Side View"

> hbonds

1048 hydrogen bonds found  

> style sphere

Changed 22815 atom styles  

> style ball

Changed 22815 atom styles  

> hide atoms

> show cartoons

> hide cartoons

> show atoms

> hide #1/A-E target c

> hide #1/A-E target a

> show #1/A:106-118 target a

> show #1/A:106-118 target c

> hide #1/A:106-118 target a

> lighting soft

> lighting full

> lighting simple

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting full

> lighting full

> lighting shadows false

> lighting shadows true

> graphics silhouettes true

> ~hbonds

> hbonds #1/A:106-118

11 hydrogen bonds found  

> set bgColor white

> lighting full

> hide all target c

> show all target c

> ~hbinds

Unknown command: ~hbinds  

> ~hbonds

> lighting flat

> show #1/B:96-109 target a

> hide all target a

> hide all target c

> show #1/B:96-109 target a

> color #1/B:96-109 & @CA purple

> ~colordef #1/B:96-109 & @CA purple

> color delete #1/B:96-109 & @CA purple

Expected fewer arguments  

> color byhetero

> color byhetero

> ~colordef #1/B:96-109 & @CA #909090

> color delete #1/B:96-109 & @CA #909090

Expected fewer arguments  

> color #1/B:96-109 & @CA #909090

> color byhetero

> color bychain

> color byhetero

> color bychain

> color byhetero

> rainbow

> color byhetero

> color #1/B:96-109 byelement

> lighting full

> color #1/B:96-109 & sideonly grey

> color #1/B:96-109 & @CA marine

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

> color #1/B:96-109 & @CA blue

> color #1/B:96-109 byatom

> color #1/B:96-109 & sideonly goldenrod

> color #1/B:96-109 & sideonly lightyellow

> color #1/B:96-109 & sideonly tan

> color view matrix

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

> view matrix

camera position:
0.031321,0.99415,0.10333,79.87,-0.54769,0.10355,-0.83025,6.9958,-0.8361,-0.03059,0.54773,59.052  
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  
  

> save

Missing or invalid "fileName" argument: Expected a file name  

> close session

> open 5d0o

5d0o title:  
BamABCDE complex, outer membrane β barrel assembly machinery entire complex
[more info...]  
  
Chain information for 5d0o #1  
---  
Chain | Description  
A | Outer membrane protein assembly factor BamA  
B | Outer membrane protein assembly factor BamB  
C | Outer membrane protein assembly factor BamC  
D | Outer membrane protein assembly factor BamD  
E | Outer membrane protein assembly factor BamE  
  

> hide #1/A-E target ac

> set bgColor white

> lighting full

> show #1/B:96-109 target a

> view matrix camera
> 0.031321,0.99415,0.10333,79.87,-0.54769,0.10355,-0.83025,6.9958,-0.8361,-0.03059,0.54773,59.052

> view matrix camera
> 0.031321,0.99415,0.10333,79.87,-0.54769,0.10355,-0.83025,6.9958,-0.8361,-0.03059,0.54773,59.052

> style #1/B:96-109 sphere

Changed 212 atom styles  

> color #1/B:96-109 byelement

> save "/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic
> Biology (2018-22)/Presentations and
> Reports/Biochemist_article/Figure1_secondary_structure/loop_atoms.png" width
> 2000 height 2000 supersample 10 transparentBackground true

> view matrix camera
> 0.031321,0.99415,0.10333,79.87,-0.54769,0.10355,-0.83025,6.9958,-0.8361,-0.03059,0.54773,59.052

> style #1/B:96-109 ball

Changed 212 atom styles  

> color #1/B:96-109 & sideonly tan

> view matrix camera
> 0.031321,0.99415,0.10333,79.87,-0.54769,0.10355,-0.83025,6.9958,-0.8361,-0.03059,0.54773,59.052

> view matrix camera
> 0.031321,0.99415,0.10333,79.87,-0.54769,0.10355,-0.83025,6.9958,-0.8361,-0.03059,0.54773,59.052

> style #1/B:96-109 ball

Changed 212 atom styles  

> color #1/B:96-109 & sideonly tan

> save "/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic
> Biology (2018-22)/Presentations and
> Reports/Biochemist_article/Figure1_secondary_structure/loop_ballandstick.png"
> width 2000 height 2000 supersample 10 transparentBackground true

> color #1/B:96-109 & @CA purple

> save "/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic
> Biology (2018-22)/Presentations and
> Reports/Biochemist_article/Figure1_secondary_structure/loop_ballandstick_REFFORTRACE.png"
> width 2000 height 2000 supersample 10 transparentBackground true

> hide #1/B:96-109 target a

> show #1/B:96-109 target c

> save "/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic
> Biology (2018-22)/Presentations and
> Reports/Biochemist_article/Figure1_secondary_structure/loop_cartoon.png"
> width 2000 height 2000 supersample 10 transparentBackground true

> hide #1/B:96-109 target a

> show #1/B:97-109 target c

> show #1/B:97-109 target c

> hide #1/B:96-109 target c

> show #1/B:97-109 target c

> color byelement

> select down

Nothing selected  

> show #1/B:97-109 target a

> hide #1/B:97-109 target c

> hide #1/B:97-109 target a

> show #1/B:97-109 target c

> color byelement target c

> color blue target c

> color sandybrown target c

> hide #1/B:96-109 target a

> show #1/B:97-109 target c

> color color sandybrown target c

> save "/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic
> Biology (2018-22)/Presentations and
> Reports/Biochemist_article/Figure1_secondary_structure/loop_cartoon.png"
> width 2000 height 2000 supersample 10 transparentBackground true

> hide #1/A-E target ac

> show #1/A:106-118 target a

> show #1/A:106-118 target a

> view #1/A:106-118 targ a

Expected an integer >= 1 or a keyword  

> view #1/A:106-118

> view matrix

camera position:
0.52141,-0.38813,0.75993,81.649,0.81177,-0.048872,-0.58194,-4.0523,0.26301,0.9203,0.28959,49.247  
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  
  

> show #1/A:106-118 target a

> style #1/A:106-118 sphere

Changed 197 atom styles  

> color #1/A:106-118 byelement

> save "/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic
> Biology (2018-22)/Presentations and
> Reports/Biochemist_article/Figure1_secondary_structure/helix_atoms.png"
> width 2000 height 2000 supersample 10 transparentBackground true

> hbonds #1/A:106-118

11 hydrogen bonds found  

> style #1/A:106-118 ball

Changed 197 atom styles  

> hbonds #1/A:106-118 & mainchain

10 hydrogen bonds found  

> ~hbonds

> hbonds #1/A:106-118 & mainchain

10 hydrogen bonds found  

> view matrix camera
> 0.52141,-0.38813,0.75993,81.649,0.81177,-0.048872,-0.58194,-4.0523,0.26301,0.9203,0.28959,49.247

> save "/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic
> Biology (2018-22)/Presentations and
> Reports/Biochemist_article/Figure1_secondary_structure/helix_ballandstick.png"
> width 2000 height 2000 supersample 10 transparentBackground true

> hide #1/A:106-118 target a

> show #1/A:106-118 target c

> color #1/A:106-118 lightcoral

> save "/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic
> Biology (2018-22)/Presentations and
> Reports/Biochemist_article/Figure1_secondary_structure/helix_cartoon.png"
> width 2000 height 2000 supersample 10 transparentBackground true

> hide #1/A-E target ac

> show #1/E:71-97 target a

> show #1/E:71-97 target a

> view #1/E:71-97

> show #1/E:71-97 target c

> hide #1/E:71-97 target a

> view matrix

camera position:
0.51706,0.65489,0.55114,148,-0.793,0.12414,0.59645,107.24,0.32219,-0.74544,0.58353,157.21  
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  
  

> show #1/E:71-97 target a

> view matrix camera
> 0.51706,0.65489,0.55114,148,-0.793,0.12414,0.59645,107.24,0.32219,-0.74544,0.58353,157.21

> hide #1/A-E target ac

> show #1/E:71-97 target a

> view matrix camera
> 0.51706,0.65489,0.55114,148,-0.793,0.12414,0.59645,107.24,0.32219,-0.74544,0.58353,157.21

> show #1/E:71-97 target a

> style #1/E:71-97 sphere

Changed 436 atom styles  

> save "/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic
> Biology (2018-22)/Presentations and
> Reports/Biochemist_article/Figure1_secondary_structure/sheet_atoms.png"
> width 2000 height 2000 supersample 10 transparentBackground true

> hbonds #1/E:71-97

31 hydrogen bonds found  

> style #1/E:71-97 ball

Changed 436 atom styles  

> hide #1/E:71-97 target a

> show #1/E:71-97 target c

> hide #1/E:71-97 target c

> show #1/E:76-91 target c

> hide #1/A-E target ac

> show #1/E:71-97 target a

> view matrix camera
> 0.51706,0.65489,0.55114,148,-0.793,0.12414,0.59645,107.24,0.32219,-0.74544,0.58353,157.21

> show #1/E:71-97 target a

> style #1/E:71-97 sphere

Changed 436 atom styles  

> hbonds #1/E:71-97

31 hydrogen bonds found  

> style #1/E:71-97 ball

Changed 436 atom styles  

> view matrix camera
> 0.51706,0.65489,0.55114,148,-0.793,0.12414,0.59645,107.24,0.32219,-0.74544,0.58353,157.21

> view #1/E:71-97

> save "/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic
> Biology (2018-22)/Presentations and
> Reports/Biochemist_article/Figure1_secondary_structure/sheet_ballandsticks.png"
> width 2000 height 2000 supersample 10 transparentBackground true

> hide #1/E:71-97 target a

> show #1/E:71-97 target c

> save "/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic
> Biology (2018-22)/Presentations and
> Reports/Biochemist_article/Figure1_secondary_structure/sheet_cartoon.png"
> width 2000 height 2000 supersample 10 transparentBackground true

> close session

> open 5d0o format mmcif fromDatabase pdb

5d0o title:  
BamABCDE complex, outer membrane β barrel assembly machinery entire complex
[more info...]  
  
Chain information for 5d0o #1  
---  
Chain | Description  
A | Outer membrane protein assembly factor BamA  
B | Outer membrane protein assembly factor BamB  
C | Outer membrane protein assembly factor BamC  
D | Outer membrane protein assembly factor BamD  
E | Outer membrane protein assembly factor BamE  
  

> hide #1 target a

> show #1 target c

> color #1,4/A rgb(0.252,0.680,1.000)

> color #1,4/B rgb(0.000,0.831,0.321)

> color #1,4/C rgb(1.000,0.861,0.137)

> color #1,4/D rgb(1.000,0.400,0.100)

> color #1,4/E rgb(0.780,0.000,0.400)

> dssp

> view #1

> view #1 pad 1.5

> view #1 pad -3

> view #1 pad -2

> view #1 pad -1

> view #1 pad

Missing "pad" keyword's argument  

> view #1

> view #1 -0.5

Expected an integer >= 1 or a keyword  

> view #1 -1

Missing or invalid "frames" argument: Must be greater than or equal to 1  

> view #1pad -0.5

Expected an objects specifier or a view name or a keyword  

> view #1 pad -0.5

> view matrix

camera position:
0.6561,0.41151,-0.63261,-191.57,0.75425,-0.38572,0.53135,238.21,-0.025355,-0.82576,-0.56345,-189.83  
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  
  

> view #1 pad -0.5

> view matrix camera
> 0.6561,0.41151,-0.63261,-191.57,0.75425,-0.38572,0.53135,238.21,-0.025355,-0.82576,-0.56345,-189.83

> save "/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic
> Biology (2018-22)/Presentations and
> Reports/Biochemist_article/Figure2_BAM_complex_architecture/5d0o_FRONT.png"
> width 2000 height 2000 supersample 10 transparentBackground true

> save "/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic
> Biology (2018-22)/Presentations and
> Reports/Biochemist_article/Figure2_BAM_complex_architecture/5d0o_FRONT.png"
> width 2000 height 2000 supersample 10 transparentBackground true

> setattr #1/A:782-789 ss_type 2

Missing or invalid "attrValue" argument: Expected an integer, a number, true
or false, or a text string  

> setattr #1/A:782-789 res ss_type 2

Assigning ss_type attribute to 8 items  

> setattr #1/A:782-789 res ss_type 2

Assigning ss_type attribute to 8 items  

> setattr #1/A:782-789 res ss_type 2

Assigning ss_type attribute to 8 items  

> lighting simple

> setattr #1/A:767-777 res ss_type 2

Assigning ss_type attribute to 11 items  

> dssp

> is_strand

Unknown command: is_strand  

> setattr

Missing or invalid "target" argument: Expected a text string  

> setattr #1/A:784-787 res ss_type 2

Assigning ss_type attribute to 4 items  

> setattr #1/A:784-788 res ss_type 2

Assigning ss_type attribute to 5 items  

> setattr #1/A:803-806 residue ss_type 2

Assigning ss_type attribute to 4 items  

> setattr #1/A:782-789 residue ss_type 2

Assigning ss_type attribute to 8 items  

> setattr #1/A:784-788 res ss_type 0

Assigning ss_type attribute to 5 items  

> setattr #1/A:782-789 residue ss_type 2

Assigning ss_type attribute to 8 items  

> setattr #1/A:630-632 residue ss_type 2

Assigning ss_type attribute to 3 items  

> hide atoms

> show cartoons

> hide cartoons

> show atoms

> hide atoms

> show cartoons

> open 5ayw

Summary of feedback from opening 5ayw fetched from pdb  
---  
note | Fetching compressed mmCIF 5ayw from
http://files.rcsb.org/download/5ayw.cif  
  
5ayw title:  
Structure of a membrane complex [more info...]  
  
Chain information for 5ayw #2  
---  
Chain | Description  
A | Outer membrane protein assembly factor BamA  
B | Outer membrane protein assembly factor BamB  
C | Outer membrane protein assembly factor BamC  
D | Outer membrane protein assembly factor BamD  
E | Outer membrane protein assembly factor BamE  
  

> view #2

> hide atoms

> show cartoons




OpenGL version: 4.1 ATI-2.11.25
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,1
      Processor Name: Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1554.120.19.0.0 (iBridge: 18.16.14663.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G9216)
      Kernel Version: Darwin 18.7.0
      Time since boot: 11:17

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 555X:

      Chipset Model: Radeon Pro 555X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00e3
      ROM Revision: 113-C980AL-075
      VBIOS Version: 113-C97501P-005
      EFI Driver Version: 01.A1.075
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
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[Eric Pettersen]

Hi Samuel,

Unfortunately that mail message does not mention that there is also an 'ss_id' attribute that is used to distinguish between directly adjacent secondary structure elements that should be depicted separately. So the stretch of residues you are trying to treat as a single strand have three different ss_ids (33, 0 [the coil], and 34), which you could see directly with the command "label /A:782-789 residues attribute ss_id". So if you assigned all those residues ss_id 33 (in addition to the ss_type assignment), then you would get the effect desired, e.g.:

setattr /a:782-789 r ss_id 33

--Eric

Eric Pettersen
UCSF Computer Graphics Lab