id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
4117	Chimera documentation mistakenly used with ChimeraX	aalikhanip@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Windows-7-6.1.7601-SP1
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Dear Chimera Team
Thank you for your helpful software.
While working with the ChimeraX program, I encountered two important problems. First, I can't find the Ramachandran map section. Secondly, there is no option to reduce the energy level in the tool section under structure editing. Even typing a minimize command has no effect. 
The point is that as you can see in the picture, there are only four options in the models window, but I saw in the trainings, there should be many other options. 
I look forward for your reply. 
Kind regards  

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""C:\Users\AAlikhani\Desktop\Drug Design-Bazi\2y6d.pdb"" format pdb

2y6d.pdb title:  
The discovery of MMP7 inhibitors exploiting A novel selectivity trigger [more
info...]  
  
Chain information for 2y6d.pdb #1  
---  
Chain | Description  
A | matrilysin  
  
Non-standard residues in 2y6d.pdb #1  
---  
CA — calcium ion  
SO4 — sulfate ion  
TQJ —
N-[(2S)-1-[4-(5-bromopyridin-2-yl)piperazin-1-yl]sulfonyl-5-pyrimidin-2-yl-
pentan-2-yl]-N-hydroxy-methanamide  
ZN — zinc ion  
  

> select /A

1377 atoms, 1308 bonds, 22 pseudobonds, 271 residues, 3 models selected  

> surface (#!1 & sel)

> coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: /A ARG 165 NH2, /A ARG 165 CZ, /A ARG 165 NH1, /A
GLY 264 O, /A GLY 264 C, and 15 other atoms  

> mlp sel

Map values for surface ""2y6d.pdb_A SES surface"": minimum -29.38, mean -4.45,
maximum 23.24  

> color bfactor sel

1377 atoms, 271 residues, 1 surfaces, atom bfactor range 7.97 to 52.6  

> ui tool show ""Model Panel""

> ui tool show ""Model Panel""

> hide #1.3 models

> show #1.3 models

> hide #1.2 models

> show #1.2 models

> hide #!1 models

> show #!1 models

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

> hide #1.3 models

> show #1.3 models

> hide #1.2 models

> show #1.2 models

> hide #1.3 models

> show #1.3 models

> ui tool show ""Model Panel""

> help help:user

> toolshed show

> ui tool show ""Command Line Interface""

> ui tool show ""Conference Call""

> volume hide

No volumes specified  

> volume style surface

No volumes specified  

> volume style mesh

No volumes specified  

> volume style image

No volumes specified  

> transparency sel 50

> volume showOutlineBox true

No volumes specified  

> volume step 1

No volumes specified  

> volume step 2

No volumes specified  

> volume planes z style image imageMode ""full region""

No volumes specified  

> volume region all imageMode ""full region""

No volumes specified  

> volume projectionMode 2d-xyz

No volumes specified  

> volume projectionMode 3d

No volumes specified  

> volume appearance initial

No volumes specified  

> ui mousemode right ""next docked""

> ui mousemode right ""next docked""

> ui mousemode right ""next docked""

> movie record

> turn y 2 180

> wait 180

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

C:\Program Files\ChimeraX 1.1\bin\ffmpeg.exe -r 25 -i
C:\Users\AALIKH~1\AppData\Local\Temp\chimovie_tLSx-%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\AAlikhani\Desktop\movie1.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\AALIKH~1\AppData\Local\Temp\chimovie_tLSx-%05d.ppm':  
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1021x655, 25 fps, 25 tbr, 25 tbn, 25 tbc  
[libx264 @ 000000000050c4c0] using cpu capabilities: MMX2 SSE2Fast SSSE3
SSE4.2 AVX  
[libx264 @ 000000000050c4c0] profile High, level 3.1  
[libx264 @ 000000000050c4c0] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC
codec - Copyleft 2003-2017 - http://www.videolan.org/x264.html - options:
cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1
psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0
deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=6 lookahead_threads=1
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00  
Output #0, mp4, to 'C:\Users\AAlikhani\Desktop\movie1.mp4':  
Metadata:  
encoder : Lavf57.56.101  
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1020x654, q=-1--1, 25 fps, 12800 tbn, 25 tbc  
Metadata:  
encoder : Lavc57.64.101 libx264  
Side data:  
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1  
Stream mapping:  
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))  
Press [q] to stop, [?] for help  
frame= 47 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 66 fps= 60 q=25.0 size= 299kB time=00:00:00.52 bitrate=4711.6kbits/s
speed=0.472x frame= 93 fps= 58 q=25.0 size= 753kB time=00:00:01.60
bitrate=3854.5kbits/s speed=0.998x frame= 117 fps= 56 q=25.0 size= 1171kB
time=00:00:02.56 bitrate=3747.6kbits/s speed=1.22x frame= 138 fps= 52 q=25.0
size= 1552kB time=00:00:03.40 bitrate=3739.8kbits/s speed=1.29x frame= 157
fps= 50 q=25.0 size= 1913kB time=00:00:04.16 bitrate=3766.5kbits/s speed=1.33x
frame= 163 fps= 39 q=-1.0 Lsize= 2932kB time=00:00:06.40 bitrate=3752.8kbits/s
speed=1.52x  
video:2929kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: 0.094183%  
[libx264 @ 000000000050c4c0] frame I:1 Avg QP:15.37 size: 37890  
[libx264 @ 000000000050c4c0] frame P:41 Avg QP:23.08 size: 28710  
[libx264 @ 000000000050c4c0] frame B:121 Avg QP:27.38 size: 14742  
[libx264 @ 000000000050c4c0] consecutive B-frames: 0.6% 1.2% 0.0% 98.2%  
[libx264 @ 000000000050c4c0] mb I I16..4: 46.6% 24.0% 29.4%  
[libx264 @ 000000000050c4c0] mb P I16..4: 0.8% 6.3% 14.7% P16..4: 6.5% 8.5%
6.0% 0.0% 0.0% skip:57.2%  
[libx264 @ 000000000050c4c0] mb B I16..4: 0.1% 0.4% 2.5% B16..8: 11.3% 12.0%
8.9% direct: 2.6% skip:62.3% L0:36.4% L1:39.3% BI:24.3%  
[libx264 @ 000000000050c4c0] 8x8 transform intra:24.5% inter:33.3%  
[libx264 @ 000000000050c4c0] coded y,uvDC,uvAC intra: 84.6% 67.9% 20.1% inter:
14.6% 10.0% 4.6%  
[libx264 @ 000000000050c4c0] i16 v,h,dc,p: 73% 10% 6% 11%  
[libx264 @ 000000000050c4c0] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 12% 12% 19% 10% 7%
7% 7% 11% 13%  
[libx264 @ 000000000050c4c0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 15% 16% 11% 11% 9%
9% 9% 10% 9%  
[libx264 @ 000000000050c4c0] i8c dc,h,v,p: 58% 19% 19% 5%  
[libx264 @ 000000000050c4c0] Weighted P-Frames: Y:0.0% UV:0.0%  
[libx264 @ 000000000050c4c0] ref P L0: 54.7% 21.5% 15.4% 8.4%  
[libx264 @ 000000000050c4c0] ref B L0: 93.2% 5.4% 1.5%  
[libx264 @ 000000000050c4c0] ref B L1: 97.9% 2.1%  
[libx264 @ 000000000050c4c0] kb/s:3679.51  
Exiting normally, received signal 15.  
  
An error occurred during encoding. See Reply Log for details.  
  
Error during MPEG encoding:  
\-----------------------------  
Exit value: 3221225786  
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\AALIKH~1\AppData\Local\Temp\chimovie_tLSx-%05d.ppm':  
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1021x655, 25 fps, 25 tbr, 25 tbn, 25 tbc  
[libx264 @ 000000000050c4c0] using cpu capabilities: MMX2 SSE2Fast SSSE3
SSE4.2 AVX  
[libx264 @ 000000000050c4c0] profile High, level 3.1  
[libx264 @ 000000000050c4c0] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC
codec - Copyleft 2003-2017 - http://www.videolan.org/x264.html - options:
cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1
psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0
deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=6 lookahead_threads=1
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00  
Output #0, mp4, to 'C:\Users\AAlikhani\Desktop\movie1.mp4':  
Metadata:  
encoder : Lavf57.56.101  
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1020x654, q=-1--1, 25 fps, 12800 tbn, 25 tbc  
Metadata:  
encoder : Lavc57.64.101 libx264  
Side data:  
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1  
Stream mapping:  
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))  
Press [q] to stop, [?] for help  
frame= 47 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 66 fps= 60 q=25.0 size= 299kB time=00:00:00.52 bitrate=4711.6kbits/s
speed=0.472x frame= 93 fps= 58 q=25.0 size= 753kB time=00:00:01.60
bitrate=3854.5kbits/s speed=0.998x frame= 117 fps= 56 q=25.0 size= 1171kB
time=00:00:02.56 bitrate=3747.6kbits/s speed=1.22x frame= 138 fps= 52 q=25.0
size= 1552kB time=00:00:03.40 bitrate=3739.8kbits/s speed=1.29x frame= 157
fps= 50 q=25.0 size= 1913kB time=00:00:04.16 bitrate=3766.5kbits/s speed=1.33x
frame= 163 fps= 39 q=-1.0 Lsize= 2932kB time=00:00:06.40 bitrate=3752.8kbits/s
speed=1.52x  
video:2929kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: 0.094183%  
[libx264 @ 000000000050c4c0] frame I:1 Avg QP:15.37 size: 37890  
[libx264 @ 000000000050c4c0] frame P:41 Avg QP:23.08 size: 28710  
[libx264 @ 000000000050c4c0] frame B:121 Avg QP:27.38 size: 14742  
[libx264 @ 000000000050c4c0] consecutive B-frames: 0.6% 1.2% 0.0% 98.2%  
[libx264 @ 000000000050c4c0] mb I I16..4: 46.6% 24.0% 29.4%  
[libx264 @ 000000000050c4c0] mb P I16..4: 0.8% 6.3% 14.7% P16..4: 6.5% 8.5%
6.0% 0.0% 0.0% skip:57.2%  
[libx264 @ 000000000050c4c0] mb B I16..4: 0.1% 0.4% 2.5% B16..8: 11.3% 12.0%
8.9% direct: 2.6% skip:62.3% L0:36.4% L1:39.3% BI:24.3%  
[libx264 @ 000000000050c4c0] 8x8 transform intra:24.5% inter:33.3%  
[libx264 @ 000000000050c4c0] coded y,uvDC,uvAC intra: 84.6% 67.9% 20.1% inter:
14.6% 10.0% 4.6%  
[libx264 @ 000000000050c4c0] i16 v,h,dc,p: 73% 10% 6% 11%  
[libx264 @ 000000000050c4c0] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 12% 12% 19% 10% 7%
7% 7% 11% 13%  
[libx264 @ 000000000050c4c0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 15% 16% 11% 11% 9%
9% 9% 10% 9%  
[libx264 @ 000000000050c4c0] i8c dc,h,v,p: 58% 19% 19% 5%  
[libx264 @ 000000000050c4c0] Weighted P-Frames: Y:0.0% UV:0.0%  
[libx264 @ 000000000050c4c0] ref P L0: 54.7% 21.5% 15.4% 8.4%  
[libx264 @ 000000000050c4c0] ref B L0: 93.2% 5.4% 1.5%  
[libx264 @ 000000000050c4c0] ref B L1: 97.9% 2.1%  
[libx264 @ 000000000050c4c0] kb/s:3679.51  
Exiting normally, received signal 15.  
  
\-----------------------------  
  

> movie record

> turn y 2 180

> wait 180

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

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

> color sel bychain

> color sel bychain

> rainbow sel

Alignment identifier is 1/A  

> interfaces sel & ~solvent

0 buried areas:  

> interfaces sel & ~solvent

0 buried areas:  

> ui tool show Clashes

> clashes

4 clashes  

> select /A

1377 atoms, 1308 bonds, 26 pseudobonds, 271 residues, 4 models selected  

> surface hidePatches (#!1 & sel)

> clashes

4 clashes  

> clashes

4 clashes  

> clashes

4 clashes  

> select clear

> clashes

4 clashes  

> clashes

4 clashes  

> clashes

4 clashes  

> ui tool show Clashes

> clashes

4 clashes  

> clashes

4 clashes  

> select /A

1377 atoms, 1308 bonds, 26 pseudobonds, 271 residues, 4 models selected  

> color (#!1 & sel) light gray

> select /A

1377 atoms, 1308 bonds, 26 pseudobonds, 271 residues, 4 models selected  

> select clear

Illegal clashes 'color' attribute value (Color([1.0, 0.17254902, 0.5019608,
1.0])), leaving attribute unchanged  

> ui tool show Clashes

> clashes

4 clashes  

> clashes

4 clashes  

> preset ""overall look"" interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> open http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup

Opened http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup  

> surface cap mesh true

> surface cap mesh false

> preset ""overall look"" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> preset ""overall look"" interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> ui tool show Updates

> ui tool show ""Build Structure""

> toolshed show

> help help:user

> ui tool show Toolbar

> ui tool show Distances

> ui tool show ""Conference Call""

> minimize

Unknown command: minimize  

> minimize

Unknown command: minimize  

> minimize

Unknown command: minimize  

> ui tool show ""Model Panel""




OpenGL version: 3.3.0 NVIDIA 391.35
OpenGL renderer: GeForce GT 440/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 7 Ultimate  (Build 7601)
Memory: 8,570,281,984
MaxProcessMemory: 8,589,934,464
CPU: 4 Intel(R) Core(TM) i5-2320 CPU @ 3.00GHz""
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1
File attachment: Untitled.png

}}}

[attachment:""Untitled.png""]
"	defect	closed	normal		Documentation		not a bug						all	ChimeraX