Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#4117 closed defect (not a bug)

Chimera documentation mistakenly used with ChimeraX

Reported by: aalikhanip@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Documentation Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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

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Change History (4)

by aalikhanip@…, 5 years ago

Attachment: Untitled.png​ added

Added by email2trac

comment:1 by Tom Goddard, 5 years ago

Component: Unassigned → Documentation
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Chimera documentation mistakenly used with ChimeraX

You are talking about features described in the Chimera documentation but you are using a different program ChimeraX that does not have those features. You should install Chimera 1.15, not ChimeraX. Our newer ChimeraX program does not have as many features and also is not supported on Windows 7 (although it may work).

comment:2 by Tom Goddard, 5 years ago

Resolution: → not a bug
Status: assigned → closed

in reply to:  4 comment:3 by aalikhanip@…, 5 years ago 

Thank you for the clarification.

---------------------
Mahdi AAlikhani

Ph.D. Candidate of Medical Biotechnology

Golestan Uni. of Medical Sciences (GoUMS)

aalikhani@goums.ac.ir

Mobile: +98 919 030 7341

On Fri, Jan 8, 2021, 4:31 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:
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