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#15984 closed defect (not a bug)

User can't write into their own folder

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

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "C:\Users\2438063\Downloads\SRPK1 structure.cxs" format session

Log from Thu Sep 19 18:03:44 2024 Startup Messages  
---  
warning | QMainWidget::resizeDocks: all sizes need to be larger than 0  
  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/2438063/Downloads/5mxx.cif

Summary of feedback from opening C:/Users/2438063/Downloads/5mxx.cif  
---  
note | Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif  
  
5mxx.cif title:  
Crystal structure of human SR protein kinase 1 (SRPK1) in complex with
compound 1 [more info...]  
  
Chain information for 5mxx.cif #1  
---  
Chain | Description  
A | SRPK1  
  
Non-standard residues in 5mxx.cif #1  
---  
CA — calcium ion  
EDO — 1,2-ethanediol (ethylene glycol)  
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)  
W4A —
5-methyl-~{N}-[2-(4-methylpiperazin-1-yl)-5-(trifluoromethyl)phenyl]furan-2-carboxamide  
  

> select ::name="HOH"

216 atoms, 216 residues, 1 model selected  

> hide sel target a

> select ::name="CA"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
4 atoms, 4 residues, 1 model selected  

> hide sel atoms

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select ::name="EDO"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
48 atoms, 36 bonds, 12 residues, 1 model selected  

> hide sel atoms

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
3234 atoms, 3076 bonds, 15 pseudobonds, 595 residues, 3 models selected  

> hide sel atoms

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> hide sel cartoons

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> show sel cartoons

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> show sel atoms

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> style sel sphere

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
Changed 3234 atom styles  

> style sel ball

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
Changed 3234 atom styles  

> style sel stick

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
Changed 3234 atom styles  

> hide sel atoms

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> ui tool show "Show Sequence Viewer"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> sequence chain /A

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
Alignment identifier is 1/A  

> select clear

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select /A:80

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:80-228

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
1217 atoms, 1246 bonds, 149 residues, 1 model selected  

> select /A:80

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:80-225

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
1188 atoms, 1216 bonds, 146 residues, 1 model selected  

> ui tool show "Color Actions"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> color sel cornflower blue

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select clear

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> set bgColor white

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select /A:490

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

> select /A:490-573

676 atoms, 692 bonds, 84 residues, 1 model selected  

> color sel lime

> color sel orange

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select ::name="W4A"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
26 atoms, 28 bonds, 1 residue, 1 model selected  

> show sel atoms

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> hide sel atoms

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> close session

> open C:/Users/2438063/Downloads/fold_2024_09_19_15_46.zip

Unrecognized file suffix '.zip'  

> open
> C:/Users/2438063/Downloads/fold_2024_09_19_15_46/fold_2024_09_19_15_46_model_0.cif

Summary of feedback from opening
C:/Users/2438063/Downloads/fold_2024_09_19_15_46/fold_2024_09_19_15_46_model_0.cif  
---  
note | Fetching CCD ATP from http://ligand-expo.rcsb.org/reports/A/ATP/ATP.cif  
  
Chain information for fold_2024_09_19_15_46_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1-31

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
261 atoms, 261 bonds, 31 residues, 1 model selected  

> select /A:1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1-56

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
450 atoms, 453 bonds, 56 residues, 1 model selected  

> hide sel cartoons

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select /A:301

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:301-435

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
1035 atoms, 1044 bonds, 135 residues, 1 model selected  

> hide sel cartoons

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select ::name="ATP"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
31 atoms, 33 bonds, 1 residue, 1 model selected  

> set bgColor white

> close session

> open C:/Users/2438063/Downloads/1wbp.cif

1wbp.cif title:  
SRPK1 bound to 9mer docking motif peptide [more info...]  
  
Chain information for 1wbp.cif #1  
---  
Chain | Description | UniProt  
A | SERINE/THREONINE-PROTEIN KINASE SPRK1 | SRPK1_HUMAN  
B | MEMBRANE-ASSOCIATED GUANYLATE KINASE, WW AND PDZ DOMAIN-CONTAINING PROTEIN
1 | MAGI1_HUMAN  
  
Non-standard residues in 1wbp.cif #1  
---  
ACT — acetate ion  
ADP — adenosine-5'-diphosphate  
  

> hide atoms

> select ::name="ADP"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
27 atoms, 29 bonds, 1 residue, 1 model selected  

> show sel atoms

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> show sel atoms

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select ::name="ADP"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
27 atoms, 29 bonds, 1 residue, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:67-131

540 atoms, 555 bonds, 65 residues, 1 model selected  

> select
> /A:75-76,80-88,93-99,104-110,147-154,159-165,168-171,209-210,219-222,493-495,502-503

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
467 atoms, 473 bonds, 55 residues, 1 model selected  

> color sel cyan

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select
> /A:114-134,138-143,172-179,185-207,215-217,224-236,514-525,530-547,560-574,577-584,586-590,607-615,619-635,643-655

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
1370 atoms, 1384 bonds, 171 residues, 1 model selected  

> color sel orange

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> ui tool show "Color Actions"

> color sel gold

> select /A:67-131

540 atoms, 555 bonds, 65 residues, 1 model selected  

> select
> /A:114-134,138-143,172-179,185-207,215-217,224-236,514-525,530-547,560-574,577-584,586-590,607-615,619-635,643-655

1370 atoms, 1384 bonds, 171 residues, 1 model selected  

> select clear

> select /A:138

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

> select /A:138-143

51 atoms, 51 bonds, 6 residues, 1 model selected  

> select /A:185-186

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

> select /A:185-207

183 atoms, 186 bonds, 23 residues, 1 model selected  

> select /A:607

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

> select /A:607-615

72 atoms, 72 bonds, 9 residues, 1 model selected  

> select /A:597-598

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:597-608

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
101 atoms, 104 bonds, 12 residues, 1 model selected  

> select
> /A:114-134,138-143,172-179,185-207,215-217,224-236,514-525,530-547,560-574,577-584,586-590,607-615,619-635,643-655

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
1370 atoms, 1384 bonds, 171 residues, 1 model selected  

> select /A:615

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:603-615

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
110 atoms, 113 bonds, 13 residues, 1 model selected  

> select /A:561

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:561

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:561

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:548-561

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
123 atoms, 127 bonds, 14 residues, 1 model selected  

> select clear

> select /A:209-237

235 atoms, 237 bonds, 29 residues, 1 model selected  

> select /A:213

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

> select /A:213-217

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
41 atoms, 41 bonds, 5 residues, 1 model selected  

> select /A:213-217

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
41 atoms, 41 bonds, 5 residues, 1 model selected  

> select /A:213-217

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
41 atoms, 41 bonds, 5 residues, 1 model selected  

> color sel lime

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select /A:218

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:218

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
8 atoms, 7 bonds, 1 residue, 1 model selected  

> select
> /A:114-134,138-143,172-179,185-207,215-217,224-236,514-525,530-547,560-574,577-584,586-590,607-615,619-635,643-655

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
1370 atoms, 1384 bonds, 171 residues, 1 model selected  

> select
> /A:114-134,138-143,172-179,185-207,215-217,224-236,514-525,530-547,560-574,577-584,586-590,607-615,619-635,643-655

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
1370 atoms, 1384 bonds, 171 residues, 1 model selected  

> select /A:213-215

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
25 atoms, 24 bonds, 3 residues, 1 model selected  

> select /A:213-215

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
25 atoms, 24 bonds, 3 residues, 1 model selected  

> select /A:213-216

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
32 atoms, 32 bonds, 4 residues, 1 model selected  

> select /A:213-216

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
32 atoms, 32 bonds, 4 residues, 1 model selected  

> select /A:216

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:216

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:213-214

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:213-214

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:213-214

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.40668.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
16 atoms, 15 bonds, 2 residues, 1 model selected  

> save "C:/Users/2438063/Downloads/SRPK1 structure.cxs"

——— End of log from Thu Sep 19 18:03:44 2024 ———

opened ChimeraX session  

> select /A:213

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

> select /A:213-215

25 atoms, 24 bonds, 3 residues, 1 model selected  

> select clear

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select /A:213-215

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
25 atoms, 24 bonds, 3 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> sequence chain /A

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
Alignment identifier is 1/A  

> select clear

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select /A:507

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
10 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:507-510

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
37 atoms, 38 bonds, 4 residues, 1 model selected  

> select /A:507-509

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
28 atoms, 29 bonds, 3 residues, 1 model selected  

> select /A:507-509

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
28 atoms, 29 bonds, 3 residues, 1 model selected  

> select /A:509-510

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:509-511

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
24 atoms, 23 bonds, 3 residues, 1 model selected  

> select /A:507-510

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
37 atoms, 38 bonds, 4 residues, 1 model selected  

> select /A:507-510

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
37 atoms, 38 bonds, 4 residues, 1 model selected  

> select /A:507-510

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
37 atoms, 38 bonds, 4 residues, 1 model selected  

> select /A:507-510

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
37 atoms, 38 bonds, 4 residues, 1 model selected  

> color sel hot pink

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select clear

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select
> /A:114-134,138-143,172-179,185-207,215-217,224-236,514-525,530-547,560-574,577-584,586-590,607-615,619-635,643-655

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2438063\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36736.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
1370 atoms, 1384 bonds, 171 residues, 1 model selected  




OpenGL version: 3.3.0 - Build 31.0.101.2121
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP EliteBook 830 G6
OS: Microsoft Windows 10 Education (Build 19045)
Memory: 16,976,740,352
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8365U CPU @ 1.60GHz
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    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
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 13 months ago

Component:	Unassigned → Input/Output
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → User can't write into their own folder

comment:2 by Eric Pettersen, 13 months ago

Resolution:	→ not a bug
Status:	accepted → closed

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