- ChimeraX-users - RBVI Mailing Lists

ChimeraX troubleshooting
by Joseph Chamieh 17 Jun '20

17 Jun '20

Dear ChimeraX developers, First I would like to thank you for your wonderful job. I was looking for a software able to modelize my peptide in 3D and do all the calculations on it and I found ChimeraX yesterday, I downloaded and installed the software and directly found it as the best answer for my problems, however it worked in the morning and after a restarting of my laptop on midday, I was not able to start the software, so I uninstalled/reinstalled, I restarted again but since then I could not find the solution, I use an HP laptop Win 10 64 bit, I attached the dxdiag summary. I would appreciate it if you could help me find the solution. Best regards Joseph _____________________________________________________________________ Joseph Chamieh, PhD, HDR Institut des Biomolécules Max Mousseron, UMR CNRS 5247, Université de Montpellier, Place Eugène Bataillon, case courrier 1706, F-34095 Montpellier Cedex 5, France Phone: +33 4 67 14 39 20 Fax: +33 4 67 63 10 46 <http://www.dsbc.univ-montp2.fr/recherche_en.html> http://www.dsbc.univ-montp2.fr/recherche_en.html <http://orcid.org/0000-0003-4209-1337> http://orcid.org/0000-0003-4209-1337 ______________________________________________________________________

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Re: [chimerax-users] ChimeraX markers to IMOD model
by Tom Goddard 17 Jun '20

17 Jun '20

Hi Joe, I made ChimeraX able to read IMOD model files (same as in Chimera), in the current ChimeraX daily build. This does not help with your problem of marking particles for subtomogram averaging. As I added IMOD model reading I looked at whether ChimeraX could write such a file. The file has Fortran binary records and while I could write a file that ChimeraX would read, I am not sure whether IMOD or any other software would read it because the file has lots of information and I don't know what is required and what is optional. Tom > On Jun 17, 2020, at 7:35 AM, Atherton, Joseph <joseph.atherton(a)kcl.ac.uk> wrote: > > Thanks Tom > > Dr Joe Atherton > Lecturer in Cryo-electron Microscopy > Randall Centre for Cell and Molecular Biophysics > King's College London, UK > Email: joseph.atherton(a)kcl.ac.uk <mailto:joseph.atherton@kcl.ac.uk> > Tel: (+44) 0207 836 5454 > https://kclpure.kcl.ac.uk/portal/joseph.atherton.html <https://kclpure.kcl.ac.uk/portal/joseph.atherton.html> > From: Tom Goddard <goddard(a)sonic.net> > Sent: 16 June 2020 17:54 > To: Atherton, Joseph <joseph.atherton(a)kcl.ac.uk> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] ChimeraX markers to IMOD model > > Hi Joe, > > Neither Chimera nor ChimeraX can write IMOD model files. (Chimera can read those files but that is not available in ChimeraX yet.) So I don't know how you could get ChimeraX markers (which are written as an XML .cmm file) into an IMOD model. > > Tom > > >> On Jun 16, 2020, at 7:04 AM, Atherton, Joseph <joseph.atherton(a)kcl.ac.uk <mailto:joseph.atherton@kcl.ac.uk>> wrote: >> >> Hi, >> >> I'd like to use the markers function in ChimeraX to make an IMOD 'model' for use in PEET for subtomogram averaging. ChimeraX's 'planes' function makes it a convenient program for doing this. Is such an export/conversion possible? >> >> All the best, >> Joe >> >> Dr Joe Atherton >> Lecturer in Cryo-electron Microscopy >> Randall Centre for Cell and Molecular Biophysics >> King's College London, UK >> Email: joseph.atherton(a)kcl.ac.uk <mailto:joseph.atherton@kcl.ac.uk> >> Tel: (+44) 0207 836 5454 >> https://kclpure.kcl.ac.uk/portal/joseph.atherton.html <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fkclpure.k…>_______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl…>

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ChimeraX markers to IMOD model
by Atherton, Joseph 16 Jun '20

16 Jun '20

Hi, I'd like to use the markers function in ChimeraX to make an IMOD 'model' for use in PEET for subtomogram averaging. ChimeraX's 'planes' function makes it a convenient program for doing this. Is such an export/conversion possible? All the best, Joe Dr Joe Atherton Lecturer in Cryo-electron Microscopy Randall Centre for Cell and Molecular Biophysics King's College London, UK Email: joseph.atherton(a)kcl.ac.uk Tel: (+44) 0207 836 5454 https://kclpure.kcl.ac.uk/portal/joseph.atherton.html

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Re: [chimerax-users] ChimeraX does not start after installation
by Tom Goddard 15 Jun '20

15 Jun '20

Hi Józef, OpenGL provides no mechanism for an applications to choose among multiple GPUs, or even know that multiple GPUs are available. It is up to your operating system to choose the GPU. Tom > On Jun 15, 2020, at 10:59 AM, Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk> wrote: > > Hi Tom, > > Thanks. This is weird because I have recently updated to the latest NVidia drivers, which should have fixed this (and it didn't). I have been searching around based on your pointers and I suspect that Windows somehow tells ChimeraX to use the integrated graphics rather than one of the four NVidia GPUs (I guess Intel graphics is the GPU default in the Win installation) I have never checked or tried to update the driver for the integrated graphics so it might be that it is using some ancient generic driver (I just assumed that Windows would automatically directed ChimeraX to the more powerful GPU options). > I have found some instructions to force ChimeraX to use NVidia GPUs so I will try this (when I can access my workstation again). > > Best, > Józef > From: Tom Goddard <goddard(a)sonic.net> > Sent: Monday, June 15, 2020 5:46 PM > To: Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] ChimeraX does not start after installation > > Hi Józef, > > The reason ChimeraX does not start on hour Windows computer is given in the middle of this error message: > > ERROR: ChimeraX requires OpenGL graphics version 3.3. > Your computer graphics driver provided version 1.1 > > Your OpenGL graphics driver is not working. Version 1.1 is from the 1990s and is what Windows gives you when you have no working graphics driver. So the fix will be to install a working graphics driver. > > When ChimeraX does not get a usable graphics driver it is supposed to still start and present a message explaining this. I am not sure why it crashed in your case. But I see in your error message > > Windows fatal exception: code 0x80000003 > > and searching online this says you have misconfigured Windows system files. All the top hits when searching for that error look like scams telling you how to use their special utility to "fix" your system. Be cautious -- I would not suggest running any spacial "cleaner" tools as they are usually malware. > > > Tom > >> On Jun 14, 2020, at 9:54 AM, Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk <mailto:J.R.Lewandowski@warwick.ac.uk>> wrote: >> >> Hi Tom, >> >> I finally got to run ChimeraX-console with --debug (did not have access to the machine during lockdown) to see why ChimeraX does not start on my system. I am pasting the output below message. Can you give me any pointers on how to make my ChimeraX installation to work. From a cursory look it seems there is a problem with OpenGL implementation. >> Any tips would be welcome. I had latest Nvidia studio drivers, now I updated to the latest Nvidia gaming drivers and the problem with starting ChimeraX persists. >> >> Thanks, >> Józef >> >> Starting main interface >> [15380:7256:0608/122433.144:ERROR:gl_surface_wgl.cc <http://gl_surface_wgl.cc/>(391)] wglCreatePbufferARB not available. >> [15380:7256:0608/122433.144:ERROR:gl_surface_qt.cpp(200)] Requested OpenGL implementation is not supported. Implementation: 1 >> Windows fatal exception: code 0x80000003 >> >> Thread 0x000010d4 (most recent call first): >> File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 1139 in do_handshake >> File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 870 in _create >> File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 423 in wrap_socket >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1422 in connect >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 966 in send >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1026 in _send_output >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1247 in endheaders >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1298 in _send_request >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1252 in request >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1319 in do_open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1362 in https_open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 503 in _call_chain >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 543 in _open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 525 in open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 222 in urlopen >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\available.py", line 37 in load >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 444 in reload_available >> File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 870 in run >> File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 926 in _bootstrap_inner >> File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 890 in _bootstrap >> >> Thread 0x00001c4c (most recent call first): >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 879 in _populate_menus >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 458 in __init__ >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 196 in build >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 617 in init >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 895 in <module> >> File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85 in _run_code >> File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193 in _run_module_as_main >> ERROR: ChimeraX requires OpenGL graphics version 3.3. >> Your computer graphics driver provided version 1.1 >> Try updating your graphics driver. >> Traceback (most recent call last): >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\graphics.py", line 56, in event >> self._check_opengl() >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\graphics.py", line 76, in _check_opengl >> self._check_for_bad_intel_driver() >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\graphics.py", line 86, in _check_for_bad_intel_driver >> if r.opengl_vendor() == 'Intel': >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\graphics\opengl.py", line 980, in opengl_vendor >> return GL.glGetString(GL.GL_VENDOR).decode('utf-8') >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\OpenGL\platform\baseplatform.py", line 415, in __call__ >> return self( *args, **named ) >> File "src\errorchecker.pyx", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError >> OpenGL.error.GLError: GLError( >> err = 1282, >> description = b'invalid operation', >> baseOperation = glGetString, >> cArguments = (GL_VENDOR,) >> ) >> Windows fatal exception: access violation >> >> Thread 0x000010d4 (most recent call first): >> File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 929 in read >> File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 1071 in recv_into >> File "C:\Program Files\ChimeraX 1.0\bin\lib\socket.py", line 589 in readinto >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 267 in _read_status >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 306 in begin >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1344 in getresponse >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1322 in do_open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1362 in https_open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 503 in _call_chain >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 543 in _open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 525 in open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 222 in urlopen >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\available.py", line 37 in load >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 444 in reload_available >> File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 870 in run >> File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 926 in _bootstrap_inner >> File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 890 in _bootstrap >> >> Current thread 0x00001c4c (most recent call first): >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 702 in rapid_access_shown >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 203 in build >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 617 in init >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 895 in <module> >> File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85 in _run_code >> File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193 in _run_module_as_main >> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Thursday, March 12, 2020 9:37 PM >> To: Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk <mailto:J.R.Lewandowski@warwick.ac.uk>> >> Cc: chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] ChimeraX does not start after installation >> >> Hi Józef, >> >> Try starting ChimeraX from a Windows Command Prompt with the debug option >> >> "c:\Program Files\ChimeraX\bin\ChimeraX-console.exe" --debug >> >> and you will probably get a Python traceback which will give some clue as to what is going wrong. If your graphics driver is not functioning ChimeraX is supposed to show you a window with an error message, but perhaps this has not been tested on Windows. >> >> Tom >> >> >> >>> On Mar 12, 2020, at 3:17 AM, Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk <mailto:J.R.Lewandowski@warwick.ac.uk>> wrote: >>> >>> Hi, >>> >>> I am trying to get ChimeraX on a Windows 10 installation on a workstation with 4 GPUs (RTX 2080Ti). >>> The program installs just fine but when I start it, it shows the splash screen up to Loading main interface and then quits. I have tried both with the 0.92 release and the daily_build. >>> Any chance you could help with with getting it to work? >>> Browsing archives I learned that this may be down to some incompatibilities with drivers. >>> The onboard graphics is ASPEED Graphics Family with driver version 9.0.10.102 >>> The four Nvidia GeForce RTX2080Ti have driver 26.21.14.4219 installed (I updated to the latest drivers hoping it fixes it - it doesn't). >>> Any ideas or suggestions? >>> >>> Thanks, >>> Józef >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

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Re: [chimerax-users] ChimeraX does not start after installation
by Tom Goddard 15 Jun '20

15 Jun '20

Hi Józef, The reason ChimeraX does not start on hour Windows computer is given in the middle of this error message: ERROR: ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.1 Your OpenGL graphics driver is not working. Version 1.1 is from the 1990s and is what Windows gives you when you have no working graphics driver. So the fix will be to install a working graphics driver. When ChimeraX does not get a usable graphics driver it is supposed to still start and present a message explaining this. I am not sure why it crashed in your case. But I see in your error message Windows fatal exception: code 0x80000003 and searching online this says you have misconfigured Windows system files. All the top hits when searching for that error look like scams telling you how to use their special utility to "fix" your system. Be cautious -- I would not suggest running any spacial "cleaner" tools as they are usually malware. Tom > On Jun 14, 2020, at 9:54 AM, Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk> wrote: > > Hi Tom, > > I finally got to run ChimeraX-console with --debug (did not have access to the machine during lockdown) to see why ChimeraX does not start on my system. I am pasting the output below message. Can you give me any pointers on how to make my ChimeraX installation to work. From a cursory look it seems there is a problem with OpenGL implementation. > Any tips would be welcome. I had latest Nvidia studio drivers, now I updated to the latest Nvidia gaming drivers and the problem with starting ChimeraX persists. > > Thanks, > Józef > > Starting main interface > [15380:7256:0608/122433.144:ERROR:gl_surface_wgl.cc <http://gl_surface_wgl.cc/>(391)] wglCreatePbufferARB not available. > [15380:7256:0608/122433.144:ERROR:gl_surface_qt.cpp(200)] Requested OpenGL implementation is not supported. Implementation: 1 > Windows fatal exception: code 0x80000003 > > Thread 0x000010d4 (most recent call first): > File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 1139 in do_handshake > File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 870 in _create > File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 423 in wrap_socket > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1422 in connect > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 966 in send > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1026 in _send_output > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1247 in endheaders > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1298 in _send_request > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1252 in request > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1319 in do_open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1362 in https_open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 503 in _call_chain > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 543 in _open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 525 in open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 222 in urlopen > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\available.py", line 37 in load > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 444 in reload_available > File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 870 in run > File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 926 in _bootstrap_inner > File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 890 in _bootstrap > > Thread 0x00001c4c (most recent call first): > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 879 in _populate_menus > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 458 in __init__ > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 196 in build > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 617 in init > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 895 in <module> > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85 in _run_code > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193 in _run_module_as_main > ERROR: ChimeraX requires OpenGL graphics version 3.3. > Your computer graphics driver provided version 1.1 > Try updating your graphics driver. > Traceback (most recent call last): > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\graphics.py", line 56, in event > self._check_opengl() > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\graphics.py", line 76, in _check_opengl > self._check_for_bad_intel_driver() > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\graphics.py", line 86, in _check_for_bad_intel_driver > if r.opengl_vendor() == 'Intel': > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\graphics\opengl.py", line 980, in opengl_vendor > return GL.glGetString(GL.GL_VENDOR).decode('utf-8') > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\OpenGL\platform\baseplatform.py", line 415, in __call__ > return self( *args, **named ) > File "src\errorchecker.pyx", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError > OpenGL.error.GLError: GLError( > err = 1282, > description = b'invalid operation', > baseOperation = glGetString, > cArguments = (GL_VENDOR,) > ) > Windows fatal exception: access violation > > Thread 0x000010d4 (most recent call first): > File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 929 in read > File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 1071 in recv_into > File "C:\Program Files\ChimeraX 1.0\bin\lib\socket.py", line 589 in readinto > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 267 in _read_status > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 306 in begin > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1344 in getresponse > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1322 in do_open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1362 in https_open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 503 in _call_chain > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 543 in _open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 525 in open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 222 in urlopen > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\available.py", line 37 in load > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 444 in reload_available > File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 870 in run > File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 926 in _bootstrap_inner > File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 890 in _bootstrap > > Current thread 0x00001c4c (most recent call first): > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 702 in rapid_access_shown > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 203 in build > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 617 in init > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 895 in <module> > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85 in _run_code > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193 in _run_module_as_main > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, March 12, 2020 9:37 PM > To: Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] ChimeraX does not start after installation > > Hi Józef, > > Try starting ChimeraX from a Windows Command Prompt with the debug option > > "c:\Program Files\ChimeraX\bin\ChimeraX-console.exe" --debug > > and you will probably get a Python traceback which will give some clue as to what is going wrong. If your graphics driver is not functioning ChimeraX is supposed to show you a window with an error message, but perhaps this has not been tested on Windows. > > Tom > > > >> On Mar 12, 2020, at 3:17 AM, Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk <mailto:J.R.Lewandowski@warwick.ac.uk>> wrote: >> >> Hi, >> >> I am trying to get ChimeraX on a Windows 10 installation on a workstation with 4 GPUs (RTX 2080Ti). >> The program installs just fine but when I start it, it shows the splash screen up to Loading main interface and then quits. I have tried both with the 0.92 release and the daily_build. >> Any chance you could help with with getting it to work? >> Browsing archives I learned that this may be down to some incompatibilities with drivers. >> The onboard graphics is ASPEED Graphics Family with driver version 9.0.10.102 >> The four Nvidia GeForce RTX2080Ti have driver 26.21.14.4219 installed (I updated to the latest drivers hoping it fixes it - it doesn't). >> Any ideas or suggestions? >> >> Thanks, >> Józef >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

1 0

Support
by greene＠chem.ucsb.edu 15 Jun '20

15 Jun '20

Hello, I am using the new ChimeraX, and it is great thus far! One issue I have come across is that if I want to display sidechains that are directly adjacent a connective line links the alpha carbons that I can't seem to get rid of. Tried lots of little workarounds, but can't seem to get it to go away (see attached picture). Is this just a bug I will have to deal with or is there a workaround? Brandon Greene *Assistant Professor * *Department of Chemistry and Biochemistry* *University of California Santa Barbara*

2 1

cut-through session color
by Steve Chou 15 Jun '20

15 Jun '20

Dear ChimeraX developers and users, Is it possible to define the color surface cut-through sessions? Thanks in advance! Steve -- Steve Chou

2 2

Cupy dependency for ChimeraX bundle
by Arthur Ecoffet 09 Jun '20

09 Jun '20

Hi, I am currently trying to develop a bundle for ChimeraX and the methods implemented can both run on GPU (using Cupy with a Cuda dependency) or on CPU. I am wondering how to deal with this "pseudo-dependency" with cupy, since it is not necessary to run the code but it is more computationally efficient. If a Cupy dependency is written in the "bundle_info.xml" file, will it create errors for computers without Nvidia Cuda installed ? Is there any way for users to install supplemental package by hand directly in chimeraX python as it was possible with Chimera ? Or is the only solution to add by hand a dependency line in the xml file ? Thanks, Arthur

3 2

Volume series
by Kotaro TANAKA 09 Jun '20

09 Jun '20

Hi, I'm trying to create a morphing movie of a series of 3D maps. For that purpose, if I understand correctly, I need a volume series (vseries) of those maps, and according to the documentation (https://www.rbvi.ucsf.edu/chimerax/docs/user/trajectories.html#vseries) I should obtain a volume series simply by opening the maps at once in a file opening dialogue. I attached a screen shot of the Models panel after opening my maps, and my question is, are those maps already consisting a volume series? vseries commands fail with 'No volume series specified' I would appreciate your comments, thank you Best regards, Kotaro

4 7

Deleting regions of whole protein
by Anas Hussain 08 Jun '20

08 Jun '20

Hello, I am currently working on a projectpertaining to the Corona Virus. I was wondering if there is anyway I could delete parts of awhole protein using the ChimeraX software. Thank you, Dr. Anas Hussain.

2 1

mesh grid sampling
by Steve Chou 08 Jun '20

08 Jun '20

Dear ChimeraX developers and users, I'm trying to display a map as mesh in ChimeraX, but the grid sampling is too sparse. *volume #1 style mesh level 0.02 step 1 color blue* Is there a way to increase the grid sampling, so that the chicken wires look denser? Thanks in advance! Steve -- Steve Chou

2 2

developing bundles autocompletion
by Daniel Esteban Palma Igor 06 Jun '20

06 Jun '20

Hi, normally I use spyder for writing python code, is there a way to have autocompletion of functions and modules when developing a bundle for ChimeraX? Any other tips for development is well received. Regards, Daniel Palma Igor

2 3

2D and 3D objects
by Jazzar, Rodolphe 04 Jun '20

04 Jun '20

Hi, First of all, this is a great program, and I am barely using it to full extent of its possibilities. I am currently interested in combining a 3D object (a molecule.pdb) and a 2D object/plane/image (as a .png or any other). The idea being that I want to show a slice of an ELF plot, with the 3D molecule embedded through the 2D plot. Good news is that I can import both objects (.pdb and .png). However I face a size issue with the 2D object, which is considerably bigger than the 3D one. Would you know if I can size down a 2D object, or enlarge a 3D one respectively. All in all would you know if chimeraX can generate something like the picture attached by combining a 2D and a 3D object. Thanks for your time, Cheers, Rodolphe [cid:D31DAF51-91B8-4F78-94B3-4C0FCD9C860E] Dr. Rodolphe Jazzar, CNRS Research Associate - (French National Centre for Scientific Research) UCSD-UMI 3555 ORCID : 0000-0002-4156-7826 Office: (858)-534-5315 Mobile: 858-337-2228 University of California, San Diego, 5213 Pacific Hall, Department of Chemistry, 9500 Gilman Dr, # 0343, La Jolla, CA 92093-0343 http://bertrandgroup.ucsd.edu<http://bertrandgroup.ucsd.edu/> https://northamerica.cnrs.fr<https://northamerica.cnrs.fr/> http://www.cnrs.fr/en/cnrs [cid:image001.png@01CFDE12.00855770]

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Re: [chimerax-users] ChimeraX cross links
by Elaine Meng 04 Jun '20

04 Jun '20

> On Jun 4, 2020, at 1:25 AM, Dina Schneidman <duhovka(a)gmail.com> wrote: > > Hi, > We are getting addicted to the ChimeraX graphics, amazing! > I couldn't find how to add cross-links on top of the structure. What would be the best way to do this? > Also, is there a way to color different cross-link types in distinct colors? > Thanks and stay safe! > Dina Hi Dina, Glad you like it, and I certainly hope you and your family are staying safe too! As I understand it there are two ways for atomic structures with crosslinks to be shown in ChimeraX: (1) some integrative modeling structures include such crosslinks. If you download the "cif" from the PDB IHM site <https://pdb-dev.wwpdb.org/> and then change its filename suffix to "ihm" instead, then you can open it in ChimeraX. If the IHM model has crosslinks, they should show up somewhere in the model hierarchy of that data, which you can explore in the Models panel. An example of one with crosslinks is the BBSome: <https://pdb-dev.wwpdb.org/entry.html?PDBDEV_00000018> (2) or if you just have any atomic structure already in ChimeraX and you want to add crosslinks, you can read in pseudobond file (filename.pb), which is just a series of atom-pair specifications in plain text. You can also include color, radius, number of dashes. The file description is the bottom section of this page: <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html> Also, you can change colors, number of dashes, and radius of any pseudobonds already in the structure or previously added, just using the commands "color" "style" and "size"; see the links in the top section of the pseudobonds page. There is a chimerax mailing list CC-d here for questions (unless they contain private data). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Installation of ChimeraX in Centos 7
by Gaya Yadav 01 Jun '20

01 Jun '20

?Dear Sir/Madam, I am trying to install Chimera X in the Centos 7 in my local directory. I installed it by converting it chimerax-rc.cpio?. But I cannot launch it, it was showing error about the openGL. Is that because of the openGL or it is not installed properly? Here is the error: WARNING: QXcbConnection: XCB error: 145 (Unknown), sequence: 178, resource id: 0, major code: 139 (Unknown), minor code: 20 NOTE: available bundle cache has not been initialized yet ERROR: ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4 Try updating your graphics driver. WARNING: The X11 connection broke: No error (code 0) XIO: fatal IO error 0 (Success) on X server "localhost:12.0" after 668 requests (668 known processed) with 0 events remaining. ? Thanks Gaya

2 2

Source Code
by Dario Eltzner 29 May '20

29 May '20

Hello, I was interested in reading the ChimeraX source code but found only this site https://www.cgl.ucsf.edu/chimerax/docs/devel/conventions.html which references a git repo that is password protected. Is the source code not freely available? Best Wishes Dario Eltzner

2 2

Re: [chimerax-users] 3D stereo lighting is not the same as mono
by Tom Goddard 27 May '20

27 May '20

Try "camera sbs" and see if shadows look right. If they do look ok, but stereo does not then it will require some debugging with a stereo system that reproduces the problem and I am not able to test that until quarantine is over. Tom > On May 26, 2020, at 10:01 AM, Kenneth Satyshur <kenneth.satyshur(a)wisc.edu> wrote: > > Thanks. I will check out the versions as they come out. Hopefully this can be fixed. I can try a VR and see what is up with the display if anything. > kas > > > Kenneth A. Satyshur, M.S., Ph.D. > Senior Scientist, > Department of Bacteriology: College of Ag and Life Sciences; > Departments of Bio Molecular Chemistry, > Neuroscience, Oncology, and Carbone Cancer Center: > School of Medicine and Public Health; > and the School of Pharmacy > University of Wisconsin-Madison > Madison, Wisconsin, 53706 > 608-215-5207 > From: Tom Goddard <goddard(a)sonic.net> > Sent: Tuesday, May 26, 2020 11:48 AM > To: Kenneth Satyshur <kenneth.satyshur(a)wisc.edu> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] 3D stereo lighting is not the same as mono > > I made a bug report for this > > https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/3315 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/3315> > > I am not able to test stereo, don't have a computer that can do it. For me other two eye modes like VR and SBS (side-by-side) have correct shadows. The problem may be a graphics driver bug effecting shadow calculation. Or it might be a bug in ChimeraX in how OpenGL quad-buffering are used. > > Tom > > >> On May 23, 2020, at 4:39 PM, Kenneth Satyshur <kenneth.satyshur(a)wisc.edu <mailto:kenneth.satyshur@wisc.edu>> wrote: >> >> I am using version 1.0 in Centos7 with Nvidia 3D glasses and K4000 video card. I do all my work in 3D stereo. Especially density fitting. I noticed that the lighting is different in mono vs stereo mode. When i go to stereo mode with >> >> camera stereo >> >> the image is in stereo but the "full" lighting is on and the image is very dark with shadows. If I switch to 'simple' it is bright and has weak shadowing. Switching to 'soft' the image is flat black and can only be seen with white background but contains no atoms. I think this is a bug. >> But a Great improvement in rendering of images. >> thanks >> kas >> p.s. old chimera does stereo very well on my system >> Linux kenworkathome 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux >> >> >> Kenneth A. Satyshur, M.S., Ph.D. >> Senior Scientist, >> Department of Bacteriology: College of Ag and Life Sciences; >> Departments of Bio Molecular Chemistry, >> Neuroscience, Oncology, and Carbone Cancer Center: >> School of Medicine and Public Health; >> and the School of Pharmacy >> University of Wisconsin-Madison >> Madison, Wisconsin, 53706 >> 608-215-5207 >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

2 3

3D stereo lighting is not the same as mono
by Kenneth Satyshur 26 May '20

26 May '20

I am using version 1.0 in Centos7 with Nvidia 3D glasses and K4000 video card. I do all my work in 3D stereo. Especially density fitting. I noticed that the lighting is different in mono vs stereo mode. When i go to stereo mode with camera stereo the image is in stereo but the "full" lighting is on and the image is very dark with shadows. If I switch to 'simple' it is bright and has weak shadowing. Switching to 'soft' the image is flat black and can only be seen with white background but contains no atoms. I think this is a bug. But a Great improvement in rendering of images. thanks kas p.s. old chimera does stereo very well on my system Linux kenworkathome 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, Department of Bacteriology: College of Ag and Life Sciences; Departments of Bio Molecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center: School of Medicine and Public Health; and the School of Pharmacy University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207

2 1

Recreating views
by Martin Montgomery 22 May '20

22 May '20

Hi, I have a session file that contains everything I need to make figures for a paper. With pymol, I saved the get_view matrix in a text file for each view which meant that with one session file I could easily recreate the views if I needed to go back and tweak a figure. In ChimeraX, the closest way that I found to replicate this was to use named views. Am happy to supply a session file if it helps also happy to be educated if there is a better way of doing this, especially as now the ChimeraX session files can get rather large. Cheers MGM Martin G Montgomery Senior Scientist ATP Synthase Group MRC Mitochondrial Biology Unit University of Cambridge The Keith Peters Building Cambridge Biomedical Campus Hills Road Cambridge Great Britain CB2 0XY www.mrc-mbu.cam.ac.uk <http://www.mrc-mbu.cam.ac.uk/>

5 6

Save/restore scene?
by Oliver Clarke 20 May '20

20 May '20

Hi ChimeraX-ers, Is there currently an equivalent of the "scene" command from Chimera? It was super helpful to be able to quickly switch between different (and often complex) representations of a molecule. I know the view command for saving and restoring orientations, and the "name" command for saving selections, but I can't find an equivalent of scene. I'm guessing it's not yet implemented, but count me as one vote for porting it over after 1.0 is out the door, it was super helpful in Chimera! Cheers Oli

2 1

Feature suggestion - show color code in picker?
by Oliver Clarke 20 May '20

20 May '20

Hi, I love the color editor in ChimeraX, it is much nicer than the one in Chimera and is super useful! One minor suggestion - would it be possible to add a dynamically updated label showing in the editor the current color code? This sometimes shows up in the log but not always, and it is useful to have easily copy-able for use in scripts and aliases. Cheers Oli

3 4

Cartoon smooth loops chimX
by Dominik Hrebík 19 May '20

19 May '20

Hi all! Is there any possibility to smooth loops in cartoon representation in ChimeraX? I can't find it in the user guide. Something similar to pymol's cartoon_smooth_loops,1: https://pymolwiki.org/index.php/Cartoon_smooth_loops Best, Dominik -- ################################## Dominik Hrebik Laboratory of Structural Virology CEITEC, Masaryk University Kamenice 5 / A35 Brno, 625 00, Czech Republic Phone: +420 549 49 7764 <%2B420%20549%2049%207756> ##################################

2 1

Focus in ChimeraX
by Luca Pellegrini 18 May '20

18 May '20

Hi, What is the ChimeraX equivalent to the Focus command in Chimera? I have selected a portion of a structure, and would like to bring it into focus without dragging it into view. Also Focus would automatically set the selection as the pivot point. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA lp212(a)cam.ac.uk

3 2

Turntable rotation
by Scott, Brandon L. 16 May '20

16 May '20

I would like to create an animation where the camera is spun around at a constant azimuthal angle so the object appears to spin on a tabletop. Currently, when I use roll, when it spins to the backside I see underneath the model rather than remaining on top. Any help is greatly appreciated. -Brandon ____________________ Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor SDSMT, Nanoscience and Nanoengineering

3 4

Re: [chimerax-users] transition from Chimera
by Tom Goddard 15 May '20

15 May '20

Hi Jerome, Putting that "open instructions,html" in your startup preferences is a nice way to show an HTML interface that could have links that execute commands in ChimeraX. I had not thought of that use. Tom > On May 15, 2020, at 1:37 AM, MUTTERER Jerome (IBMP) <jerome.mutterer(a)ibmp-cnrs.unistra.fr> wrote: > > Hi Tom, > Thank you very much for your answers. > I didn't try the drag and drop emulation approach, but I confirm the "remotecontrol rest" option at startup works nicely. > I added the following 2 lines to the Favorites>Settings...>Startup tab > > remote rest start port xxxxx > open instructions.html > > and it makes it easy to operate. > Thanks a lot! > > Jerome > > > De: "Tom Goddard" <goddard(a)sonic.net> > À: "MUTTERER Jerome, IBMP" <jerome.mutterer(a)ibmp-cnrs.unistra.fr> > Cc: chimerax-users(a)cgl.ucsf.edu > Envoyé: Mardi 12 Mai 2020 20:14:39 > Objet: Re: [chimerax-users] transition from Chimera > > Hi Jerome, > > We don't have the chimerax --send option to open files in an already running ChimeraX, although we plan on adding it. > > I have two ideas for how to do this in current ChimeraX. One is to use the remotecontrol command to tell ChimeraX to accept commands via http. In ChimeraX I enable this with command > > remote rest start port 58123 > > Then http requests can run commands in ChimeraX. The http url can be entered in a web browser or from a script. From a script you could use curl or wget programs, for example, > > curl http://localhost:58123/run?command=open+/Users/goddard/Downloads/ChimeraX/P… <http://localhost:58123/run?command=open+/Users/goddard/Downloads/ChimeraX/P…>.cif > > You could make ChimeraX alway enable http requests by putting the "remote..." command in ChimeraX Settings/Preferences under the Startup tab "Execute these commands at startup". > > The other idea I have is simpler but did not work in my test. ChimeraX accepts files dragged and dropped on the application. On macOS (and probably Linux and Windows) I should be able to run a shell command that says drop this file on ChimeraX. On Mac the shell command looks like > > % open -a /Applications/ChimeraX.app ~/Downloads/ChimeraX/PDB/1a0m.cif > > That worked for starting ChimeraX and showing the first file. But when I run it again to open a different it merely raised ChimeraX and did not open the new file. That is a bug. I've made a bug report for it. I don't know the equivalent commands on Linux and Windows and whether the would work. > > Tom > > > On May 12, 2020, at 1:50 AM, Jerome Mutterer <jerome.mutterer(a)ibmp-cnrs.unistra.fr <mailto:jerome.mutterer@ibmp-cnrs.unistra.fr>> wrote: > > Dear all, > I'm trying to transition from Chimera to ChimeraX, but my workflow relies on passing scripts to an open, with GUI, instance of Chimera using --send > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send> > > I see that this is not described here: > https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html <https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html> > > Is that still available somehow in ChimeraX? > Thanks for any input. > Sincerely, > Jerome. > > -- > Jerome Mutterer > CNRS - Institut de biologie moléculaire des plantes > 12, rue du Général Zimmer > 67084 Strasbourg Cedex > www.ibmp.cnrs.fr <http://www.ibmp.cnrs.fr/> > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

1 0

Stuck on one XML-RPC command
by Mungo Carstairs (Staff) 14 May '20

14 May '20

Any XML-RPC fans who can help me with this please? This label command works in the PyMOL command line: label 4zho//A/36/CA 4zho//B/36/CA, "hello world" How do I format an equivalent XML-RPC request? I've tried <methodCall> <methodName>label</methodName> <params> <parameter> <value>4zho//A/36/CA 4zho//B/36/CA</value> </parameter> <parameter> <value>"hello world"</value> </parameter> </params> </methodCall> but get back a fault response XML message with <class 'SyntaxError'>:invalid syntax (<string>, line 1) I have also tried encoding the " as %22, or omitting the quotes, same result. Any ideas please? Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

1 0

Stereo and VR support
by Gökhan Tolun 14 May '20

14 May '20

Hi, Would it be possible to make the graphics window undockable, too, Like the other ones? This would allow the use of stereo monitors with SBS and tb support, which does not work currently with menus, etc. surrounding the graphics window. Also, will you implement DTI stereo as in Chimera? By the way, if theres a way of making ISOLDE work in VR, thatd be great! Thanks, Gökhan

3 3

pyqtchart
by Anthony James Schaefer 14 May '20

14 May '20

Hello, I'm interesting in using pyqtchart (https://pypi.org/project/PyQtChart/) as an alternative to matplotlib for some plots in my bundle (I like the default style better, it resizes better - small things like that). If I list pyqtchart as a dependency in my bundle_info.xml like ... <Dependencies> <Dependency name="pyqtchart"/> </Dependencies> ... a new version of PyQt5 gets installed in the directory where bundles get installed. The QChart module from pyqtchart gets installed in this new PyQt5 package. I can't use the QChart module because it's not in the PyQt5 that ChimeraX uses. Is there anything I can do with my bundle to get it to install a usable pyqtchart? Thanks, Tony

2 3

wrong version in download
by Christine Gee 13 May '20

13 May '20

Dear ChimeraX I downloaded what was supposed to be chimeraX 0.5 from your site, and 0.1 instead. I have an older mac with an older OS (10.11.6) and would like the last version that was developed for it. Can you please let me know where I can download 0.5? Also does it work with isolde? Regards Christine Dr Christine Gee Research Specialist Kuriyan Lab HHMI/Molecular and Cell Biology/QB3 527 Stanley Hall MC 3220 University of California, Berkeley Berkeley, CA 94720-3220 Lab Phone: 510 643 0164 Cell: 510 230 7891 Email: christinelgee(a)berkeley.edu <mailto:christinelgee@berkeley.edu>

2 1

Manual segmentation in ChimeraX
by Pattana Jaroenlak (Michael) 13 May '20

13 May '20

Hello, I saw the twitter post from ChimeraX on segmentation of EM serial images ( https://twitter.com/ucsfchimerax/status/1260425173238415360?s=12) It was very beautiful. I have serial section EM images. I am wondering that can I do manual segmentation on ChimeraX? Some cellular features on my images can not be picked up by thresholding or watersheding. Thank you PJ -- *Pattana (Michael) Jaroenlak, PhD* Bhabha & Ekiert Labs Skirball Institute of Biomolecular Medicine New York University School of Medicine *Email: pattana.jaroenlak(a)nyulangone.org <pattana.jaroenlak(a)nyumc.org>, p.jaroenlak(a)gmail.com <p.jaroenlak(a)gmail.com>*

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Renaming chain IDs
by Fahrenkamp, Dirk 12 May '20

12 May '20

Hi ChimeraX team. I am happily using chimeraX along with ISOLDE for modelling. Lately, I am running into issues with complexes having too many chains to be handled by the standard .pdb format which is why I am using .cif now. Is there a smooth way/command to rename chain IDs and change _entity.pdbx_description _struct_asym.entity_id accordingly? Thanks! Kind regards, Dirk -- Dr. rer. nat. Dirk Fahrenkamp UKE Hamburg Zentrum für experimentelle Medizin Institut für Struktur- und Systembiologie/ CSSB Centre for Structural Systems Biology c/o Deutsches Elektronen-Synchrotron DESY Notkestraße 85, Building 15 3.OG D-22607 Hamburg Telefon:+49 (0) 40 8998-87657 Dirk.Fahrenkamp(a)cssb-Hamburg.de www.cssb-hamburg.de

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transition from Chimera
by Jerome Mutterer 12 May '20

12 May '20

Dear all, I'm trying to transition from Chimera to ChimeraX, but my workflow relies on passing scripts to an open, with GUI, instance of Chimera using --send https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send I see that this is not described here: https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html Is that still available somehow in ChimeraX? Thanks for any input. Sincerely, Jerome. -- Jerome Mutterer CNRS - Institut de biologie moléculaire des plantes 12, rue du Général Zimmer 67084 Strasbourg Cedex www.ibmp.cnrs.fr

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Map "Blobs" tool - Generate objects?
by Christophe Leterrier 12 May '20

12 May '20

Hi, I started using ChimeraX for visualization and quantification of 3D microscopy images. The "blob" tool is particularly impressive to semi-automatically segment objects of interest and measure their characteristics. However, I could not find a way to generate an independent object from the picked blobs. This makes the quantification process unreproducible as it is not possible to store the blobs in the session or automatically measure all the picked blobs. Am I wrong in the intent of the tool, or is there a way to do this? Thank you, -- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France

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ChimeraX on Twitter
by Tom Goddard 09 May '20

09 May '20

For ChimeraX news, tips, tricks and special features meet us on Twitter @UCSFChimeraX. https://twitter.com/UCSFChimeraX <https://twitter.com/UCSFChimeraX> Tom, Eric, Elaine, Greg, Conrad, Scooter, Tom -- the UCSF ChimeraX team.

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How to display crystal packing?
by Guillaume Gaullier 08 May '20

08 May '20

Hello, Today I was trying to display a crystal packing from a PDB entry in ChimeraX, but could not find how to do this. I read the documentation for the sym command https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html ; but either I didn’t get it, or this is not the adequate command for what I am trying to do. What I want to do is the equivalent of PyMOL’s "Action / generate / symmetry mates / +/- one unit cell and within… Å", which is different from the biological assembly the sym command can generate from the PDB annotation. When working with crystallographic data, ISOLDE displays molecules related to the working model by crystallographic symmetry, so displaying the crystal packing seems doable in ChimeraX. Or is it one of ISOLDE’s additions? It would be wonderful if someone could help me with this (it is one of the last few things I need on a regular basis, that I still don’t know how to do in ChimeraX). Thank you in advance, Guillaume

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preview ChimeraX 1.0!
by Elaine Meng 07 May '20

07 May '20

The ChimeraX 1.0 (!!) release candidate is now available: <http://www.rbvi.ucsf.edu/chimerax/download.html> Please, please try it out and report any issues that you find, as we plan to make the production release by the end of the month. To report issues, use the ChimeraX menu: Help... Report a Bug <http://www.rbvi.ucsf.edu/chimerax/docs/contact.html> For what's new, see the Change Log: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Problems with making movie in chimerax
by Nandish Kumar Khanra 07 May '20

07 May '20

Hello all, I want to make a movie of a multi-domain protein between two functional states using Chimerax. One domain undergoes drastic conformational change while there is virtually no structural change in another domain. I did the following steps to make the movie. * Aligned two models using matchmaker, mm #1 to #2 pair ss ss false * make morph morph #1,2 frames 100 play false cartesian true * make movie movie record size 1000,1000 coordset #3 wait 100 movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true The stationary domain of two functional states aligned perfectly after structural alignment, but I do see motions in that domain in the movie. Am I doing anything wrong? Is there a way to overcome this? Thanks, Nandish

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Script to color zone a map according to the underlying model
by Caroline Stone 07 May '20

07 May '20

Dear All, As an exercise in scripting, I am trying to write a script to imitate the appearance a published figure (from Toropova et al 2017). I would like to display a semi-transparent map which has been color zoned to match the underlying model in surface view. ChimeraX does everything in the script apart from the last two commands, in which I color zone the map, and then make it transparent. I don't get any errors in the log to give me a clue what to change. If I omit these last two commands from the script and then make them manually from the command line after the script is finished, it works. Is there something I can change that would allow me to include the final two commands in the script? Any pointers would be much appreciated. # ChimeraX script to imitate dynein 2 tail Toropova et al 2017 figure style # Adds custom colours to the ChimeraX session # Open model and set camera view and model rotation open 6RLB windowsize 775 775 view matrix camera -0.30533,0.56038,0.76991,623.53,0.82837,-0.24247,0.50499,467.83,0.46967,0.79195,-0.39016,-7.3434 models #1,1,0,0,0,0,1,0,0,0,0,1,0 # Work with model representation surface #1 set bgColor white lighting soft graphics silhouettes true # Define custom colours color name midblue #6b80b5 color name midgreen #a0c497 color name midyellow #f9ef87 color name midtomato #f97054 color name midmagenta #a4449b # Recolour model using custom colours defined above select #1/A; color sel midblue select #1/B; color sel skyblue select #1/C; color sel midtomato select #1/D; color sel midmagenta select #1/E/F; color sel midgreen select #1/G/H; color sel lightpink select #1/I-N; color sel midyellow select clear # Open map and modify color and transparency open emdb:4918 volume #2 step 1 volume #2 level 0.0172 surface dust #2 size 10 color zone #2 near #1 distance 15 volume #2 transparency 0.75 Best wishes, Caroline

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Silhouettes cause fill
by Daniel Asarnow 06 May '20

06 May '20

Hi, Is there any way to avoid this effect where silhouettes lead to an apparent flood fill? The helix in the upper left of this clip shows what I mean: [image: image.png] I was able to work around it a bit by making the silhouettes thinner than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1. Thanks and best, -da

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Re: [chimerax-users] Chimera X -showing electrostatic potential
by Elaine Meng 06 May '20

06 May '20

Dear Yi Shi, The structure is nice work, and worth showing off! We are fine so far... I hope you are well too. To color a surface by electrostatic potential in ChimeraX, currently you need to use a separate program to generate the electrostatic potential map, for example the APBS web server or the DelPhi web server mentioned/linked to the Chimera tutorial here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#es…> After you generate the map (e.g. a .dx file, .phi file, or .cube file) <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume> ... then you can open it in ChimeraX and use it for coloring the protein molecular surface with the ChimeraX "color electrostatic" command: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map> If you open a .cube file it will automatically show as isosurfaces. However, you can hide the isosurfaces such as by clicking the "eye" icon in the Volume Viewer panel, and then carry on with using the coloring command as mentioned above. Of course, you need to open the protein structure and then display the protein's molecular surface first, e.g. with the "surface" command, Actions menu, or Molecule Display icon. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 5, 2020, at 7:14 PM, Yi Shi <yi.shi(a)pitt.edu> wrote: > > Dear Elaine, > > Hope this finds you, your family and colleagues safe and well. > > We have a question about Chimera X software that you and your colleagues developed. Do you know how to show the electrostatic potential using Chimera X? Do we need some external software to do this? > > BTW, the software that you developed was amazing that we really enjoy it. And thanks a million for using our Nup84 hybrid structure for the cover of your paper in Protein Science. Absolutely beautiful work! > > Thanks in advance. > Yi > > Yi Shi Ph.D. > Assistant Professor > Department of Cell Biology > Program for Integrative Systems Biology > Pitt/ CMU Program in Computational Biology > University of Pittsburgh School of Medicine > BST3 9049 > 3500 5th Avenue > Pittsburgh PA 15213 > 412-383-3242 (office) > 412-383-3243 (lab) > www.shi-lab.org

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Scroll threshold step size
by Daniel Asarnow 04 May '20

04 May '20

Hi, Is it possible to adjust the step size when using alt + scrollwheel to change the contour level? I'd like to make it coarser for RSI reasons. Thanks, -da

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ubuntu 20.04
by Hua tiger 03 May '20

03 May '20

Please create a download and install package for ubuntu 20.04 Thank you very much. John

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Chimera-Animation equivalent utility/command
by Ray Y.-R. Wang 01 May '20

01 May '20

Dear all, I have been searching for the equivalent function in ChimeraX for the Animation functionality (under Tools/Utilities) in Chimera, where we can save many checkpoints as "scenes" in one Chimera session. I am wondering whether there's a command-line equivalent thing in ChimeraX I can adapt. Thanks so much! Best, Ray

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Missing segments
by Daniel Asarnow 01 May '20

01 May '20

Hi all, When I save a CIF from ChimeraX, the missing segment pseudobonds are replaced by real (super unphysical) bonds. Can I do something about it, or is this a bug? Thanks and best, -da

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morph movie with secondary structure and dssp
by Joel Meyerson 30 Apr '20

30 Apr '20

Hi, I am making a morph between two PDB models representing two states of the same protein, and the overall secondary structure does not change much between the models. However, there is a region where the secondary structure does change. I would like to capture the secondary structure change in the morph and have a couple questions. 1. It seems the morph uses the secondary structure from PDB #1. Is there a way to use the two different secondary structure headers from the two PDBs to define the secondary structure endpoints on the morph? 2. If the above is not possible, is there a way to restrict DSSP to update only the region of interest (i.e. a residue range), and not change secondary structure throughout the molecule? Thanks, Joel

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addh and phenix
by Daniel Asarnow 24 Apr '20

24 Apr '20

Hi, Seems like with NAG glycans the addh result is incompatible with phenix real space refinement. It's easy enough to fix by deleting HD2 - the offending hydrogen - manually. I was wondering if anyone had an opinion about this, before I report a phenix bug. Error looks like: Number of atoms with unknown nonbonded energy type symbols: 5 "ATOM 2629 HD2 ASN A 362 .*. H " (4 more similar lines). Best, -da

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How to hide dashed lines?
by Steve Chou 24 Apr '20

24 Apr '20

Dear ChimeraX developers and users, I see a dashed line between an ion and a side chain when I display the side chain. Is there a way to hide the dashed line, either in command line or GUI? How to select all the atoms in residues (e.g., /A:10-100) except n, c, and o atoms? Many thanks, Steve -- Steve Chou

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displaying ribbon and tube simultaneously
by Joel Meyerson 23 Apr '20

23 Apr '20

Hi, I would like to display a model as a ribbon, but then specify a single helix to show as a tube. So far I’ve only been able to show the model either entirely as a ribbon, or entirely as tubes. Is there syntax I can use to blend the two helix styles? Thanks, Joel

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Molecular Docking problem
by Estela Fernandes e Silva 23 Apr '20

23 Apr '20

Dears, Good night! I'm starting to use SwissDock to investigate new drugs. I'm having trouble viewing “the best result” through Chimera for Web (the browser cannot be configured) In the option “Download your predictions file” I can open all the ligands through ChimeraX (my computer's desktop) at the same time. But I would like to see only one ligand at a time. Would it be possible? Best regards Estela

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deleting sidechain in ChimeraX
by Joel Meyerson 22 Apr '20

22 Apr '20

Hi, What is the command or sequence of commands which can be used to delete the sidechain on an amino acid or range of amino acids? I reviewed the ChimeraX atom spec page but could not find a way to do this. Thanks, Joel

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