June 2020 - ChimeraX-users - RBVI Mailing Lists

selection modes
by Philipp Milkereit 17 Jun '20

17 Jun '20

Dear all, is there a way to add user-defined selectors or named selections (command: name) to the current selection by choosing them from the Menu:Select or in the Basic Actions window? Changing to Menu_Mode:Add in Menu:Select seems not to have any effect on that. I think in Chimera1 named selections still could be added to the current selection using the "append" selection mode. At the moment adding named selections to the current selection works for me in ChimeraX just with the command line "select add" command. Many thanks for your help, Philipp Milkereit

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Re: [chimerax-users] ChimeraX troubleshooting
by Tom Goddard 17 Jun '20

17 Jun '20

Hi Joseph, Ok, it is complaining about a ChimeraX preference file C:\Users\Joseph\AppData\Local\UCSF\ChimeraX\ui-1 that saves your last ChimeraX window size (which is used when you start ChimeraX the next time), and saves any tools you added to the Favorites menu. It is supposed to be a text file but yours somehow contains all binary 0. Could you send us that ui-1 file, then delete it, and hopefully ChimeraX will start if there are no other problems. I will open a bug report and we will look at how this happened and probably put in some code so that if a preference file is unreadable ChimeraX will still start and just warn you about the corrupted file. You will get an email about that bug report and it would help if you could reply to that email with the ui-1 file as an attachment to help us debug the problem. Tom > On Jun 17, 2020, at 2:03 PM, Joseph Chamieh <joseph.chamieh(a)umontpellier.fr> wrote: > > Dear Tom > Thank you for your answer, this is the result of what you asked for: > > C:\>"C:\Program Files\ChimeraX 1.0\bin\ChimeraX-console.exe" --debug > C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\win32\lib\pywintypes.py:2: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses > import imp, sys, os > Traceback (most recent call last): > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193, in _run_module_as_main > "__main__", mod_spec) > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85, in _run_code > exec(code, run_globals) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 895, in <module> > exit_code = init(sys.argv) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 502, in init > sess.ui = ui_class(sess) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 110, in __init__ > self.settings = UI_Settings(session, "ui") > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\settings.py", line 165, in __init__ > ConfigFile.__init__(self, session, tool_name, version=version) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\configfile.py", line 289, in __init__ > self._config.read(self._filename, encoding='utf-8') > File "C:\Program Files\ChimeraX 1.0\bin\lib\configparser.py", line 696, in read > self._read(fp, filename) > File "C:\Program Files\ChimeraX 1.0\bin\lib\configparser.py", line 1079, in _read > raise MissingSectionHeaderError(fpname, lineno, line) > configparser.MissingSectionHeaderError: File contains no section headers. > file: 'C:\\Users\\Joseph\\AppData\\Local\\UCSF\\ChimeraX\\ui-1', line: 1 > '\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00' > > I remain at your disposal for any further information > 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> > ______________________________________________________________________ > > De : Tom Goddard [mailto:goddard@sonic.net] > Envoyé : Wednesday, June 17, 2020 7:01 PM > À : Joseph Chamieh <joseph.chamieh(a)umontpellier.fr> > Cc : chimerax-users(a)cgl.ucsf.edu > Objet : Re: [chimerax-users] ChimeraX troubleshooting > > Hi Joseph, > > To see why ChimeraX is failing to start on Windows, run it from a Windows Command Prompt as follows (two dashes in --debug) > > "C:\Program Files\ChimeraX 1.0\bin\ChimeraX-console.exe" --debug > > and send us the error message this gives. > > Tom > > > >> On Jun 17, 2020, at 1:51 AM, Joseph Chamieh <joseph.chamieh(a)umontpellier.fr <mailto:joseph.chamieh@umontpellier.fr>> wrote: >> >> 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> >> ______________________________________________________________________ >> >> <DxDiag.txt>_______________________________________________ >> 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>

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maximized on startup
by Anthony James Schaefer 17 Jun '20

17 Jun '20

Hello, Would it be possible to add an option for the ChimeraX app to be maximized on startup? I've got the window size set to 'last used' and I almost always maximize ChimeraX. With this combo, ChimeraX starts out the size of my screen, but not maximized. Thanks, Tony

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operation (rotation and translation) marix relative to the original PDB
by Steve Chou 17 Jun '20

17 Jun '20

Dear ChimeraX developers and users, After we load a 3D molecule [model (pdb) or map (mrc)] into ChimeraX, we turn (rotate) and move (translate) the molecule to find out a nice orientation to print the image. How to write out and read in the operation/manipulation matrix (rotation matrix, 3x3; translation vector, 3x1; or their combination, 4x4) relative to the original orientation/coordinates in ChimeraX? Many thanks in advance! Steve -- Steve Chou

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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>

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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*

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