id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
3434	Problem writing command history	s.a.white@…	Greg Couch	"{{{
The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Morphing or movie recording

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 6888 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2bbv format mmcif fromDatabase pdb

2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  
  
Chain information for 2bbv #1  
---  
Chain | Description  
A B C | protein (black beetle virus capsid protein)  
D E F | protein (black beetle virus capsid protein)  
N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3')  
  
Non-standard residues in 2bbv #1  
---  
CA — calcium ion  
  
2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  

> show cartoons

> hide atoms

> preset ""initial styles"" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides licorice/ovals

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset ""initial styles"" ""original look""

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset ""initial styles"" sticks

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset ""initial styles"" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset ""initial styles"" ""space-filling (chain colors)""

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset ""molecular surfaces"" ""ghostly white""

Changed 7604 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset ""overall look"" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> preset ""molecular surfaces"" ""atomic coloring (transparent)""

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\whitesa\Desktop\movie1.mp4

Movie saved to \C:Users\\...\Desktop\movie1.mp4  
  

> toolshed show

> cartoon

> hide atoms

> hide cartoons

> show cartoons

> hide surfaces

> show cartoons

> rainbow

> cartoon style xsection rectangle modeHelix default

> cartoon style coil xsection oval

> cartoon style xsection barbell modeHelix default

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 130, in invoke  
return self._func(self._name, data)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 286, in _command_started_cb  
typed=self._just_typed_command is not None)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 380, in add  
self._history.enqueue((item, typed))  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 171, in enqueue  
self.save()  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 201, in save  
self._history.save(self._queue)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
Error processing trigger ""command started"":  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
  
See log for complete Python traceback.  
  

> cartoon style modeHelix tube sides 20

> hide atoms

> view

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> close session

> open 3gbp

Summary of feedback from opening 3gbp fetched from pdb  
---  
notes | Fetching compressed mmCIF 3gbp from
http://files.rcsb.org/download/3gbp.cif  
Fetching CCD BGC from http://ligand-expo.rcsb.org/reports/B/BGC/BGC.cif  
  
3gbp title:  
Structure of the periplasmic glucose/galactose receptor of salmonella
typhimurium [more info...]  
  
Chain information for 3gbp #1  
---  
Chain | Description  
A | galactose-binding protein  
  
Non-standard residues in 3gbp #1  
---  
BGC — β-D-glucose  
CA — calcium ion  
  

> preset pub

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> ks vd

> movie record

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 130, in invoke  
return self._func(self._name, data)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 286, in _command_started_cb  
typed=self._just_typed_command is not None)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 380, in add  
self._history.enqueue((item, typed))  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 171, in enqueue  
self.save()  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 201, in save  
self._history.save(self._queue)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
Error processing trigger ""command started"":  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
  
See log for complete Python traceback.  
  

> turn y 2 180

> wait 180

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 130, in invoke  
return self._func(self._name, data)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 286, in _command_started_cb  
typed=self._just_typed_command is not None)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 380, in add  
self._history.enqueue((item, typed))  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 171, in enqueue  
self.save()  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 201, in save  
self._history.save(self._queue)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
Error processing trigger ""command started"":  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
  
See log for complete Python traceback.  
  

> movie encode C:\Users\whitesa\Desktop\movie2.mp4

Movie saved to \C:Users\\...\Desktop\movie2.mp4  
  

> hide ribbons

Drag select of 193 atoms, 182 bonds  

> hide selAtoms

> select ligand

24 atoms, 24 bonds, 1 model selected  

> style sel sphere

Changed 24 atom styles  

> show sel atoms

Drag select of 65 atoms, 7 pseudobonds, 58 bonds  

> hide sel atoms

> select clear

> turn y 25 300 rock 150

Drag select of 24 atoms  

> select sel @< 5

147 atoms, 125 bonds, 1 model selected  

> select sel @< 5

496 atoms, 451 bonds, 1 model selected  

> show sel atoms

> undo

> undo

> select sel @< 2

183 atoms, 165 bonds, 1 model selected  

> show sel atoms

> select clear

> movie record

> turn y 25 300 rock 150

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 130, in invoke  
return self._func(self._name, data)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 286, in _command_started_cb  
typed=self._just_typed_command is not None)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 380, in add  
self._history.enqueue((item, typed))  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 171, in enqueue  
self.save()  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 201, in save  
self._history.save(self._queue)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
Error processing trigger ""command started"":  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
  
See log for complete Python traceback.  
  

> wait 300

> movie encode C:\Users\whitesa/Desktop/movie2.mp4

C:\Program Files\ChimeraX 1.0\bin\ffmpeg.exe -r 25 -i
C:\Users\whitesa\AppData\Local\Temp\chimovie_ZZMj-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 C:\Users\whitesa/Desktop/movie2.mp4  
stdout:  
  
stderr:  
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers  
built with gcc 6.3.0 (GCC)  
configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2
--enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-
fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass
--enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-
libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-
libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-
libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-
libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264
--enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-
lzma --enable-zlib  
libavutil 55. 34.101 / 55. 34.101  
libavcodec 57. 64.101 / 57. 64.101  
libavformat 57. 56.101 / 57. 56.101  
libavdevice 57. 1.100 / 57. 1.100  
libavfilter 6. 65.100 / 6. 65.100  
libswscale 4. 2.100 / 4. 2.100  
libswresample 2. 3.100 / 2. 3.100  
libpostproc 54. 1.100 / 54. 1.100  
Input #0, image2, from
'C:\Users\whitesa\AppData\Local\Temp\chimovie_ZZMj-%05d.ppm':  
Duration: 00:00:12.00, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1340x785, 25 tbr, 25 tbn, 25 tbc  
C:\Users\whitesa/Desktop/movie2.mp4: Permission denied  
  
An error occurred during encoding. See Reply Log for details.  
  
Error during MPEG encoding:  
\-----------------------------  
Exit value: 1  
Error message:  
stdout:  
  
stderr:  
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers  
built with gcc 6.3.0 (GCC)  
configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2
--enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-
fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass
--enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-
libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-
libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-
libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-
libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264
--enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-
lzma --enable-zlib  
libavutil 55. 34.101 / 55. 34.101  
libavcodec 57. 64.101 / 57. 64.101  
libavformat 57. 56.101 / 57. 56.101  
libavdevice 57. 1.100 / 57. 1.100  
libavfilter 6. 65.100 / 6. 65.100  
libswscale 4. 2.100 / 4. 2.100  
libswresample 2. 3.100 / 2. 3.100  
libpostproc 54. 1.100 / 54. 1.100  
Input #0, image2, from
'C:\Users\whitesa\AppData\Local\Temp\chimovie_ZZMj-%05d.ppm':  
Duration: 00:00:12.00, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1340x785, 25 tbr, 25 tbn, 25 tbc  
C:\Users\whitesa/Desktop/movie2.mp4: Permission denied  
  
\-----------------------------  
  

> view

> movie record

> turn y 25 300 rock 150

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 130, in invoke  
return self._func(self._name, data)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 286, in _command_started_cb  
typed=self._just_typed_command is not None)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 380, in add  
self._history.enqueue((item, typed))  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 171, in enqueue  
self.save()  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 201, in save  
self._history.save(self._queue)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
Error processing trigger ""command started"":  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
  
See log for complete Python traceback.  
  

> wait 300

> movie encode C:\Users\whitesa/Desktop/movie2.mp4

Movie saved to C:\Users\whitesa/Desktop/movie2.mp4  
  

> movie record

> turn y 25 300 rock 150

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 130, in invoke  
return self._func(self._name, data)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 286, in _command_started_cb  
typed=self._just_typed_command is not None)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 380, in add  
self._history.enqueue((item, typed))  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 171, in enqueue  
self.save()  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 201, in save  
self._history.save(self._queue)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
Error processing trigger ""command started"":  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
  
See log for complete Python traceback.  
  

> wait 300

> movie encode C:\Users\whitesa/Desktop/movie2.mp4

Movie saved to C:\Users\whitesa/Desktop/movie2.mp4  
  

> ui tool show ""Command Line Interface""

> movie record

> turn y 25 300 rock 150

> wait 300

> movie encode C:\Users\whitesa/Desktop/movie3.mp4

Movie saved to C:\Users\whitesa/Desktop/movie3.mp4  
  

> preset interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> open 3gbp fromDatabase eds

Summary of feedback from opening 3gbp fetched from eds  
---  
note | Fetching map 3gbp from
http://www.ebi.ac.uk/pdbe/coordinates/files/3gbp.ccp4  
  
Opened 3gbp.ccp4, grid size 97,68,86, pixel 0.787,0.777,0.802, shown at level
1.02, step 1, values float32  

> volume #2 level 0.5

> surface zone #2 nearAtoms ligand distance 8

> style ligand ball

Changed 24 atom styles  

> resfit #1 map #2

> volume #2 level 0.45

> volume #2 level 0.4

> close #2

> preset original

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> view

> open 2fw0

Summary of feedback from opening 2fw0 fetched from pdb  
---  
warning | Unable to fetch template for 'NA': might have incorrect bonds  
notes | Fetching compressed mmCIF 2fw0 from
http://files.rcsb.org/download/2fw0.cif  
Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif  
Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif  
Fetching CCD CIT from http://ligand-expo.rcsb.org/reports/C/CIT/CIT.cif  
Fetching CCD MLA from http://ligand-expo.rcsb.org/reports/M/MLA/MLA.cif  
  
2fw0 title:  
Apo Open Form of Glucose/Galactose Binding Protein [more info...]  
  
Chain information for 2fw0 #2  
---  
Chain | Description  
A | D-galactose-binding periplasmic protein  
  
Non-standard residues in 2fw0 #2  
---  
CA — calcium ion  
CIT — citric acid  
MLA — malonic acid (dicarboxylic acid C3; propanediolic acid;
methanedicarboxylic acid)  
NA — sodium ion  
  

> view

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3gbp, chain A (#1) with 2fw0, chain A (#2), sequence alignment
score = 1483.7  
RMSD between 150 pruned atom pairs is 0.439 angstroms; (across all 304 pairs:
6.811)  
  

> view

> morph #1,2

Computed 21 frame morph #3  

> coordset #3 1,21

> coordset #3 1,21

> wait 21

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 130, in invoke  
return self._func(self._name, data)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 286, in _command_started_cb  
typed=self._just_typed_command is not None)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 380, in add  
self._history.enqueue((item, typed))  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 171, in enqueue  
self.save()  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 201, in save  
self._history.save(self._queue)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
Error processing trigger ""command started"":  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
  
See log for complete Python traceback.  
  

> coordset #3 21,1

> coordset #3 1,21

> wait 21

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 130, in invoke  
return self._func(self._name, data)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 286, in _command_started_cb  
typed=self._just_typed_command is not None)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py"", line 380, in add  
self._history.enqueue((item, typed))  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 171, in enqueue  
self.save()  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 201, in save  
self._history.save(self._queue)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\history.py"", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
Error processing trigger ""command started"":  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.tmp' ->
'C:\\\Users\\\whitesa\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
File ""C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\safesave.py"", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
  
See log for complete Python traceback.  
  

> coordset #3 21,1




OpenGL version: 3.3.0 - Build 26.20.100.6888
OpenGL renderer: Intel(R) HD Graphics 620
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Latitude 5480
OS: Microsoft Windows 10 Enterprise (Build 18363)
Memory: 17,056,178,176
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-7600U CPU @ 2.80GHz""
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

}}}
"	defect	assigned	normal		Input/Output				Tom Goddard Eric Pettersen				all	ChimeraX