Can't write command history: No space left on device

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/a7/Downloads/6bft.pdb format pdb

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  

Populating font family aliases took 1055 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
6bft.pdb title:  
Structure of bevacizumab fab mutant In complex with vegf [more info...]  
  
Chain information for 6bft.pdb #1  
---  
Chain | Description | UniProt  
A | avastin heavy chain fab fragment mutant | IGG1_HUMAN  
B | avastin light chain fab fragment mutant | Q8TCD0_HUMAN  
C | vascular endothelial growth factor A | VEGFA_HUMAN  
G | vascular endothelial growth factor A | VEGFA_HUMAN  
H | avastin heavy chain fab fragment mutant | IGG1_HUMAN  
L | avastin light chain fab fragment mutant | Q8TCD0_HUMAN  
  
Non-standard residues in 6bft.pdb #1  
---  
MES — 2-(N-morpholino)-ethanesulfonic acid  
SO4 — sulfate ion  
  

> sequence chain #1/A

Alignment identifier is 1/A  

> select /A:29

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

> select /A:28-29

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select /A:28

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

> select /A:28

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

> select /A:30

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

> select /A:30

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

> select /A:31

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

> select /A:31

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  

> swapaa interactive sel ASP rotLib Dunbrack

/A ASN 31: phi -98.9, psi -6.7 trans  
Changed 90 bond radii  

> swapaa interactive sel ASP rotLib Dunbrack

6bft.pdb #!1/A ASN 31: phi -98.9, psi -6.7 trans  
Changed 90 bond radii  

> swapaa #!1/A:31 ASP criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/A ASN 31: phi -98.9, psi -6.7 trans  
Applying ASP rotamer (chi angles: -65.8 -30.9) to 6bft.pdb #!1/A ASP 31  

> swapaa interactive sel ASP rotLib Dunbrack

6bft.pdb #!1/A ASP 31: phi -98.9, psi -6.7 trans  
Changed 90 bond radii  
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.  
[Repeated 1 time(s)]

> swapaa #!1/A:31 ASP criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/A ASP 31: phi -98.9, psi -6.7 trans  
Applying ASP rotamer (chi angles: -65.8 -30.9) to 6bft.pdb #!1/A ASP 31  

> swapaa #!1/A:31 ASP criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/A ASP 31: phi -98.9, psi -6.7 trans  
Applying ASP rotamer (chi angles: -65.8 -30.9) to 6bft.pdb #!1/A ASP 31  

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> select /A:33

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

> select /A:33

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

> select /A:32

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:32

12 atoms, 12 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel TPR rotLib Dunbrack

/A TYR 32: phi -139.9, psi 138.1 trans  
Changed 10 bond radii  

> swapaa #!1/A:32 TPR criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/A TYR 32: phi -139.9, psi 138.1 trans  
Applying PRO rotamer (chi angles: 26.7 -34.4) to 6bft.pdb #!1/A PRO 32  

> swapaa interactive sel TPR rotLib Dunbrack

/A PRO 32: phi -139.9, psi 138.1 trans  
Changed 10 bond radii  

> swapaa #!1/A:32 TPR criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/A PRO 32: phi -139.9, psi 138.1 trans  
Applying PRO rotamer (chi angles: 26.7 -34.4) to 6bft.pdb #!1/A PRO 32  

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> select /A:33

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

> select /A:33

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

> ui tool show Rotamers

> swapaa interactive sel ALA rotLib Dunbrack

> swapaa sel ALA rotLib Dunbrack

Using Dunbrack library  
Swapping /A GLY 33 to ALA  
  

> swapaa interactive sel ALA rotLib Dunbrack

> swapaa sel ALA rotLib Dunbrack

Using Dunbrack library  
Swapping /A ALA 33 to ALA  
  

> swapaa interactive sel ALA rotLib Dunbrack

> swapaa sel ALA rotLib Dunbrack

Using Dunbrack library  
Swapping /A ALA 33 to ALA  
  

> select /A:61

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

> select /A:61

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

> select /A:52

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

> select /A:52

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

> ui tool show Rotamers

> swapaa interactive sel GLY rotLib Dunbrack

> swapaa sel GLY rotLib Dunbrack

Using Dunbrack library  
Swapping /A ASN 52 to GLY  
  

> swapaa interactive sel GLY rotLib Dunbrack

> swapaa sel GLY rotLib Dunbrack

Using Dunbrack library  
Swapping /A GLY 52 to GLY  
  

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> select /A:28-32,62-65,74-76,87-91,166-168,197-199,211-214

202 atoms, 199 bonds, 27 residues, 1 model selected  

> select /A:31

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

> select /A:31

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

> select /A:28-32,62-65,74-76,87-91,166-168,197-199,211-214

202 atoms, 199 bonds, 27 residues, 1 model selected  

> select /A:32

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

> select /A:32

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

> select /A:28-32,62-65,74-76,87-91,166-168,197-199,211-214

202 atoms, 199 bonds, 27 residues, 1 model selected  

> select /A:32

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

> select /A:32

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

> ui tool show Rotamers

> swapaa interactive sel TRP rotLib Dunbrack

/A PRO 32: phi -139.9, psi 138.1 trans  
Changed 468 bond radii  

> swapaa #!1/A:32 TRP criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/A PRO 32: phi -139.9, psi 138.1 trans  
Applying TRP rotamer (chi angles: -63.5 88.5) to 6bft.pdb #!1/A TRP 32  

> swapaa interactive sel TRP rotLib Dunbrack

/A TRP 32: phi -139.9, psi 138.1 trans  
Changed 468 bond radii  

> swapaa #!1/A:32 TRP criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/A TRP 32: phi -139.9, psi 138.1 trans  
Applying TRP rotamer (chi angles: -63.5 88.5) to 6bft.pdb #!1/A TRP 32  

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> select /A:117

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

> select /A:117

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

> select /A:109-110

23 atoms, 24 bonds, 2 residues, 1 model selected  

> select /A:109-110

23 atoms, 24 bonds, 2 residues, 1 model selected  

> select /A:109

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:109

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:102

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:102

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:99

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:99

12 atoms, 12 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel TRP rotLib Dunbrack

/A TYR 99: phi -71.5, psi 158.9 trans  
Changed 468 bond radii  
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.  
[Repeated 1 time(s)]

> swapaa #!1/A:99 TRP criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/A TYR 99: phi -71.5, psi 158.9 trans  
Applying TRP rotamer (chi angles: -67.7 99.6) to 6bft.pdb #!1/A TRP 99  

> swapaa interactive sel TRP rotLib Dunbrack

/A TRP 99: phi -71.5, psi 158.9 trans  
Changed 468 bond radii  

> swapaa #!1/A:99 TRP criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/A TRP 99: phi -71.5, psi 158.9 trans  
Applying TRP rotamer (chi angles: -67.7 99.6) to 6bft.pdb #!1/A TRP 99  

> select /A:102

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:102

12 atoms, 12 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel PHE rotLib Dunbrack

/A TYR 102: phi -96.4, psi 158.2 trans  
Changed 162 bond radii  

> swapaa #!1/A:102 PHE criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/A TYR 102: phi -96.4, psi 158.2 trans  
Applying PHE rotamer (chi angles: -66.9 92.4) to 6bft.pdb #!1/A PHE 102  

> select /A:104-105

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select /A:104-105

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select /A:104

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

> select /A:104

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

> ui tool show Rotamers

> swapaa interactive sel ASN rotLib Dunbrack

/A GLY 104: phi -92.1, psi -99.7 trans  
Changed 180 bond radii  

> swapaa #!1/A:104 ASN criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/A GLY 104: phi -92.1, psi -99.7 trans  
Applying ASN rotamer (chi angles: -71.2 -24.5) to 6bft.pdb #!1/A ASN 104  

> swapaa interactive sel ASN rotLib Dunbrack

/A ASN 104: phi -92.1, psi -99.7 trans  
Changed 180 bond radii  

> swapaa #!1/A:104 ASN criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/A ASN 104: phi -92.1, psi -99.7 trans  
Applying ASN rotamer (chi angles: -71.2 -24.5) to 6bft.pdb #!1/A ASN 104  

> select /A:106

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

> select /A:106

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

> select /A:105

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

> select /A:105

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

> select /A:106

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

> select /A:106

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

> ui tool show Rotamers

> swapaa interactive sel ALA rotLib Dunbrack

> swapaa sel ALA rotLib Dunbrack

Using Dunbrack library  
Swapping /A SER 106 to ALA  
  

> swapaa interactive sel ALA rotLib Dunbrack

> swapaa sel ALA rotLib Dunbrack

Using Dunbrack library  
Swapping /A ALA 106 to ALA  
  

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> sequence chain #1/B

Alignment identifier is 1/B  

> select /B:51

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

> select /B:51

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

> select /A:55

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

> select /A:55

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

> select /A:59

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

> select /A:59

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

> ui tool show Rotamers

> swapaa interactive sel LYS rotLib Dunbrack

/A THR 59: phi -139.9, psi 121.5 trans  
Changed 438 bond radii  

> swapaa #!1/A:59 LYS criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/A THR 59: phi -139.9, psi 121.5 trans  
Applying LYS rotamer (chi angles: -176.8 177.3 179.4 -180.0) to 6bft.pdb #!1/A
LYS 59  

> swapaa interactive sel LYS rotLib Dunbrack

/A LYS 59: phi -139.9, psi 121.5 trans  
Changed 438 bond radii  

> swapaa #!1/A:59 LYS criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/A LYS 59: phi -139.9, psi 121.5 trans  
Applying LYS rotamer (chi angles: -176.8 177.3 179.4 -180.0) to 6bft.pdb #!1/A
LYS 59  

> select /B:65

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

> select /B:65

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

> select /A:123

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

> select /A:123

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

> select /A:105

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

> select /A:105

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

> ui tool show Rotamers

> swapaa interactive sel THR rotLib Dunbrack

/A SER 105: phi -90.8, psi 167.0 trans  
Changed 12 bond radii  

> swapaa #!1/A:105 THR criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/A SER 105: phi -90.8, psi 167.0 trans  
Applying THR rotamer (chi angles: 63.7) to 6bft.pdb #!1/A THR 105  

> swapaa interactive sel THR rotLib Dunbrack

/A THR 105: phi -90.8, psi 167.0 trans  
Changed 12 bond radii  
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.  

> swapaa #!1/A:105 THR criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/A THR 105: phi -90.8, psi 167.0 trans  
Applying THR rotamer (chi angles: 63.7) to 6bft.pdb #!1/A THR 105  

> swapaa interactive sel THR rotLib Dunbrack

/A THR 105: phi -90.8, psi 167.0 trans  
Changed 12 bond radii  
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.  

> swapaa interactive sel THR rotLib Dunbrack

6bft.pdb #!1/A THR 105: phi -90.8, psi 167.0 trans  
Changed 12 bond radii  

> swapaa #!1/A:105 THR criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/A THR 105: phi -90.8, psi 167.0 trans  
Applying THR rotamer (chi angles: 63.7) to 6bft.pdb #!1/A THR 105  

> select /A:105-106

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
12 atoms, 11 bonds, 2 residues, 1 model selected  

> select /A:105-106

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
12 atoms, 11 bonds, 2 residues, 1 model selected  

> select /A:106

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /A:106

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
5 atoms, 4 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  

> swapaa interactive sel SER rotLib Dunbrack

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
/A ALA 106: phi -79.8, psi 131.0 trans  
Changed 9 bond radii  

> swapaa #!1/A:106 SER criteria 1 rotLib Dunbrack

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
Using Dunbrack library  
6bft.pdb #!1/A ALA 106: phi -79.8, psi 131.0 trans  
Applying SER rotamer (chi angles: 175.1) to 6bft.pdb #!1/A SER 106  

> swapaa interactive sel SER rotLib Dunbrack

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
/A SER 106: phi -79.8, psi 131.0 trans  
Changed 9 bond radii  

> swapaa #!1/A:106 SER criteria 1 rotLib Dunbrack retain false

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
Using Dunbrack library  
6bft.pdb #!1/A SER 106: phi -79.8, psi 131.0 trans  
Applying SER rotamer (chi angles: 175.1) to 6bft.pdb #!1/A SER 106  

> sequence chain #1/A

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> select /A:31-33,52,59,99,102,104-105

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
80 atoms, 79 bonds, 9 residues, 1 model selected  

> select /B:94

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /B:94

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
7 atoms, 6 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  

> swapaa interactive sel ILE rotLib Dunbrack

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
/B VAL 94: phi -76.1, psi 148.4 trans  
Changed 45 bond radii  

> swapaa #!1/B:94 ILE criteria 1 rotLib Dunbrack

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
Using Dunbrack library  
6bft.pdb #!1/B VAL 94: phi -76.1, psi 148.4 trans  
Applying ILE rotamer (chi angles: 62.6 170.5) to 6bft.pdb #!1/B ILE 94  

> swapaa interactive sel ILE rotLib Dunbrack

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
/B ILE 94: phi -76.1, psi 148.4 trans  
Changed 45 bond radii  

> swapaa #!1/B:94 ILE criteria 1 rotLib Dunbrack retain false

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
Using Dunbrack library  
6bft.pdb #!1/B ILE 94: phi -76.1, psi 148.4 trans  
Applying ILE rotamer (chi angles: 62.6 170.5) to 6bft.pdb #!1/B ILE 94  

> sequence chain #1/B

Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  

> sequence chain #1/L

Alignment identifier is 1/L  

> select /L:94

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

> select /L:94

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

> ui tool show Rotamers

> swapaa interactive sel ILE rotLib Dunbrack

/L VAL 94: phi -76.1, psi 143.1 trans  
Changed 45 bond radii  

> swapaa #!1/L:94 ILE criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/L VAL 94: phi -76.1, psi 143.1 trans  
Applying ILE rotamer (chi angles: -64.0 169.5) to 6bft.pdb #!1/L ILE 94  

> swapaa interactive sel ILE rotLib Dunbrack

/L ILE 94: phi -76.1, psi 143.1 trans  
Changed 45 bond radii  

> swapaa #!1/L:94 ILE criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/L ILE 94: phi -76.1, psi 143.1 trans  
Applying ILE rotamer (chi angles: -64.0 169.5) to 6bft.pdb #!1/L ILE 94  

> sequence chain #1/H

Alignment identifier is 1/H  

> select /H:31

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

> select /H:31

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

> ui tool show Rotamers

> swapaa interactive sel ASP rotLib Dunbrack

/H ASN 31: phi -90.0, psi -10.0 trans  
Changed 90 bond radii  

> swapaa #!1/H:31 ASP criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/H ASN 31: phi -90.0, psi -10.0 trans  
Applying ASP rotamer (chi angles: -66.9 -27.4) to 6bft.pdb #!1/H ASP 31  

> swapaa interactive sel ASP rotLib Dunbrack

/H ASP 31: phi -90.0, psi -10.0 trans  
Changed 90 bond radii  
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.  
[Repeated 4 time(s)]

> swapaa #!1/H:31 ASP criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/H ASP 31: phi -90.0, psi -10.0 trans  
Applying ASP rotamer (chi angles: -66.9 -27.4) to 6bft.pdb #!1/H ASP 31  

> swapaa interactive sel ASP rotLib Dunbrack

/H ASP 31: phi -90.0, psi -10.0 trans  
Changed 90 bond radii  

> swapaa #!1/H:31 ASP criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/H ASP 31: phi -90.0, psi -10.0 trans  
Applying ASP rotamer (chi angles: -66.9 -27.4) to 6bft.pdb #!1/H ASP 31  

> select /H:32

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /H:32

12 atoms, 12 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel TRP rotLib Dunbrack

/H TYR 32: phi -133.5, psi 132.7 trans  
Changed 468 bond radii  

> swapaa #!1/H:32 TRP criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/H TYR 32: phi -133.5, psi 132.7 trans  
Applying TRP rotamer (chi angles: -65.3 88.7) to 6bft.pdb #!1/H TRP 32  

> swapaa interactive sel TRP rotLib Dunbrack

/H TRP 32: phi -133.5, psi 132.7 trans  
Changed 468 bond radii  
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.  

> swapaa #!1/H:32 TRP criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/H TRP 32: phi -133.5, psi 132.7 trans  
Applying TRP rotamer (chi angles: -65.3 88.7) to 6bft.pdb #!1/H TRP 32  

> swapaa interactive sel TRP rotLib Dunbrack

/H TRP 32: phi -133.5, psi 132.7 trans  
Changed 468 bond radii  
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.  
[Repeated 2 time(s)]

> swapaa #!1/H:32 TRP criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/H TRP 32: phi -133.5, psi 132.7 trans  
Applying TRP rotamer (chi angles: -65.3 88.7) to 6bft.pdb #!1/H TRP 32  

> swapaa interactive sel TRP rotLib Dunbrack

/H TRP 32: phi -133.5, psi 132.7 trans  
Changed 468 bond radii  

> swapaa #!1/H:32 TRP criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/H TRP 32: phi -133.5, psi 132.7 trans  
Applying TRP rotamer (chi angles: -65.3 88.7) to 6bft.pdb #!1/H TRP 32  

> select /H:33-34

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

> select /H:33-34

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

> select /H:33

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

> select /H:33

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

> ui tool show Rotamers

> swapaa interactive sel ALA rotLib Dunbrack

> swapaa sel ALA rotLib Dunbrack

Using Dunbrack library  
Swapping /H GLY 33 to ALA  
  

> swapaa interactive sel ALA rotLib Dunbrack

> swapaa sel ALA rotLib Dunbrack

Using Dunbrack library  
Swapping /H ALA 33 to ALA  
  

> swapaa interactive sel ALA rotLib Dunbrack

> swapaa sel ALA rotLib Dunbrack

Using Dunbrack library  
Swapping /H ALA 33 to ALA  
  

> swapaa interactive sel ALA rotLib Dunbrack

> swapaa sel ALA rotLib Dunbrack

Using Dunbrack library  
Swapping /H ALA 33 to ALA  
  

> swapaa interactive sel ALA rotLib Dunbrack

> swapaa sel ALA rotLib Dunbrack

Using Dunbrack library  
Swapping /H ALA 33 to ALA  
  

> swapaa interactive sel ALA rotLib Dunbrack

> swapaa sel ALA rotLib Dunbrack

Using Dunbrack library  
Swapping /H ALA 33 to ALA  
  

> sequence chain #1/H

Destroying pre-existing alignment with identifier 1/H  
Alignment identifier is 1/H  

> sequence chain #1/H

Destroying pre-existing alignment with identifier 1/H  
Alignment identifier is 1/H  

> select /H:52

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

> select /H:52

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

> ui tool show Rotamers

> swapaa interactive sel GLY rotLib Dunbrack

> swapaa sel GLY rotLib Dunbrack

Using Dunbrack library  
Swapping /H ASN 52 to GLY  
  

> swapaa interactive sel GLY rotLib Dunbrack

> swapaa sel GLY rotLib Dunbrack

Using Dunbrack library  
Swapping /H GLY 52 to GLY  
  

> swapaa interactive sel GLY rotLib Dunbrack

> swapaa sel GLY rotLib Dunbrack

Using Dunbrack library  
Swapping /H GLY 52 to GLY  
  

> swapaa interactive sel GLY rotLib Dunbrack

> swapaa sel GLY rotLib Dunbrack

Using Dunbrack library  
Swapping /H GLY 52 to GLY  
  

> swapaa interactive sel GLY rotLib Dunbrack

> swapaa sel GLY rotLib Dunbrack

Using Dunbrack library  
Swapping /H GLY 52 to GLY  
  

> select /H:52-53

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /H:52-53

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /H:52

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

> select /H:52

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

> ui tool show Rotamers

> swapaa interactive sel GLY rotLib Dunbrack

> swapaa sel GLY rotLib Dunbrack

Using Dunbrack library  
Swapping /H GLY 52 to GLY  
  

> select /H:59

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

> select /H:59

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

> ui tool show Rotamers

> swapaa interactive sel LYS rotLib Dunbrack

/H THR 59: phi -138.3, psi 121.5 trans  
Changed 438 bond radii  

> swapaa #!1/H:59 LYS criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/H THR 59: phi -138.3, psi 121.5 trans  
Applying LYS rotamer (chi angles: -176.8 177.3 179.4 -180.0) to 6bft.pdb #!1/H
LYS 59  

> swapaa interactive sel LYS rotLib Dunbrack

/H LYS 59: phi -138.3, psi 121.5 trans  
Changed 438 bond radii  

> swapaa #!1/H:59 LYS criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/H LYS 59: phi -138.3, psi 121.5 trans  
Applying LYS rotamer (chi angles: -176.8 177.3 179.4 -180.0) to 6bft.pdb #!1/H
LYS 59  

> select /H:99

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /H:99

12 atoms, 12 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel TRP rotLib Dunbrack

/H TYR 99: phi -74.1, psi 164.1 trans  
Changed 468 bond radii  

> swapaa #!1/H:99 TRP criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/H TYR 99: phi -74.1, psi 164.1 trans  
Applying TRP rotamer (chi angles: -67.7 99.6) to 6bft.pdb #!1/H TRP 99  

> swapaa interactive sel TRP rotLib Dunbrack

/H TRP 99: phi -74.1, psi 164.1 trans  
Changed 468 bond radii  

> swapaa #!1/H:99 TRP criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/H TRP 99: phi -74.1, psi 164.1 trans  
Applying TRP rotamer (chi angles: -67.7 99.6) to 6bft.pdb #!1/H TRP 99  

> select /H:102

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /H:102

12 atoms, 12 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel PHE rotLib Dunbrack

/H TYR 102: phi -100.6, psi 155.0 trans  
Changed 162 bond radii  

> swapaa #!1/H:102 PHE criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/H TYR 102: phi -100.6, psi 155.0 trans  
Applying PHE rotamer (chi angles: -66.9 92.4) to 6bft.pdb #!1/H PHE 102  

> swapaa interactive sel PHE rotLib Dunbrack

/H PHE 102: phi -100.6, psi 155.0 trans  
Changed 162 bond radii  
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.  
[Repeated 4 time(s)]

> swapaa #!1/H:102 PHE criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/H PHE 102: phi -100.6, psi 155.0 trans  
Applying PHE rotamer (chi angles: -66.9 92.4) to 6bft.pdb #!1/H PHE 102  

> select /H:104

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

> select /H:104

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

> ui tool show Rotamers

> swapaa interactive sel ASN rotLib Dunbrack

/H GLY 104: phi 90.1, psi -58.9 trans  
Changed 180 bond radii  

> swapaa #!1/H:104 ASN criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/H GLY 104: phi 90.1, psi -58.9 trans  
Applying ASN rotamer (chi angles: -68.0 -29.5) to 6bft.pdb #!1/H ASN 104  

> swapaa interactive sel ASN rotLib Dunbrack

/H ASN 104: phi 90.1, psi -58.9 trans  
Changed 180 bond radii  

> swapaa #!1/H:104 ASN criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/H ASN 104: phi 90.1, psi -58.9 trans  
Applying ASN rotamer (chi angles: -68.0 -29.5) to 6bft.pdb #!1/H ASN 104  

> select /H:105

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

> ui tool show Rotamers

> swapaa interactive sel THR rotLib Dunbrack

/H SER 105: phi -149.8, psi 161.6 trans  
Changed 12 bond radii  
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.  
[Repeated 2 time(s)]

> swapaa #!1/H:105 THR criteria 1 rotLib Dunbrack

Using Dunbrack library  
6bft.pdb #!1/H SER 105: phi -149.8, psi 161.6 trans  
Applying THR rotamer (chi angles: -172.1) to 6bft.pdb #!1/H THR 105  

> swapaa interactive sel THR rotLib Dunbrack

/H THR 105: phi -149.8, psi 161.6 trans  
Changed 12 bond radii  

> swapaa #!1/H:105 THR criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6bft.pdb #!1/H THR 105: phi -149.8, psi 161.6 trans  
Applying THR rotamer (chi angles: -172.1) to 6bft.pdb #!1/H THR 105  

> sequence chain #1/H

Traceback (most recent call last):  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Users/a7/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
Destroying pre-existing alignment with identifier 1/H  
Alignment identifier is 1/H  

> save /Users/a7/Desktop/edit2.pdb relModel #1

> toolshed show




OpenGL version: 4.1 INTEL-16.1.7
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 429.120.4.0.0
      SMC Version (system): 2.43f11

Software:

    System Software Overview:

      System Version: macOS 11.1 (20C69)
      Kernel Version: Darwin 20.2.0
      Time since boot: 3:19

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0