- ChimeraX-users - RBVI Mailing Lists

"Rapid Access"
by Eric Pettersen 07 Apr '17

07 Apr '17

Hi all, In the latest builds, your file history will be shown in the main graphics area if there are no models open (e.g. usually at startup). Otherwise, you can hide/show the file list with the lightning bolt icon at the lower right of the main window. —Eric Eric Pettersen UCSF Computer Graphics Lab

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color zones in cryoem density map
by Jonas Barandun 05 Apr '17

05 Apr '17

Dear chimeraX users/developers Is there an easy way to color a cryoem density map based on individual subunits (from a pdb file) - similar to the color zone functionality in chimera? Thanks a lot Best Jonas

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Chimera for 4D imaging analysis
by John Daum 05 Apr '17

05 Apr '17

Ladies and Gents, I recently heard a talk at Janelia Research Campus's "Frontiers in Imaging Science" given by Dyche Mullins, an investigator at USCF. He heaped praise upon Chimera/ChimeraX and indicated that it had been adapted for working with 4D light microscopy images that might be quite useful for quantifying and or viewing objects in 3D space over time by surface rendering and other cool "tricks". I'm writing to inquire if Chimera, ChimeraX, or another version (perhaps currently unavailble for download from the UCSF Chimera website) will help me with my problem (analyzing, viewing, 4D data)? Thank you, John Daum Laboratory Manager, Gorbsky Lab, Bell 216 Cell Cycle and Cancer Biology Oklahoma Medical Research Foundation 825 N. E. 13th Street Oklahoma City, OK 73104 daumj(a)omrf.org Voice: 405-271-2037 Fax: 405-271-7312

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ChimeraX announce list?
by Steffen Graether 05 Apr '17

05 Apr '17

I realize that traffic is very low on the Chimerax-users list, but is there any thought about adding an announce list so that we could follow announcements on new releases as development progresses? Steffen

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chimeraX and nice dcv
by Beck, Florian 03 Apr '17

03 Apr '17

Hi, did anyone use chimerX with nice dcv remote visualisation ? I tried it and I got the following error: Could not connect to DCVD [13619:13619:0403/144451:FATAL:zygote_host_impl_linux.cc(182)] Check failed: ReceiveFixedMessage(fds[0], kZygoteBootMessage, sizeof(kZygoteBootMessage), &boot_pid). #0 0x2ada6e6ec00e <unknown> #1 0x2ada6e6ff0ce <unknown> #2 0x2ada6ec92e33 <unknown> #3 0x2ada6ec91b2b <unknown> #4 0x2ada6ec920ce <unknown> #5 0x2ada6ed09a69 <unknown> #6 0x2ada6eb13373 <unknown> #7 0x2ada6d5b1d32 <unknown> #8 0x2ada6d5b2f45 <unknown> #9 0x2ada6d555345 QtWebEngineCore::BrowserContextAdapter::BrowserContextAdapter() #10 0x2ada6cc8b75a QWebEngineProfile::QWebEngineProfile() #11 0x2ada6ca4cfc9 sipQWebEngineProfile::sipQWebEngineProfile() #12 0x2ada6ca4d1aa init_type_QWebEngineProfile #13 0x2ada6be5061b sipSimpleWrapper_init #14 0x2ada01ad1e83 type_call #15 0x2ada01a613fb _PyObject_FastCallDict #16 0x2ada01b51ae8 call_function #17 0x2ada01b5757a _PyEval_EvalFrameDefault #18 0x2ada01b5199a _PyEval_EvalCodeWithName #19 0x2ada01b5a7b8 _PyFunction_FastCallDict #20 0x2ada01a614fe _PyObject_FastCallDict #21 0x2ada01a61602 _PyObject_Call_Prepend #22 0x2ada01a6129a PyObject_Call #23 0x2ada01b56ffb _PyEval_EvalFrameDefault #24 0x2ada01b5199a _PyEval_EvalCodeWithName #25 0x2ada01b51c37 call_function #26 0x2ada01b570d1 _PyEval_EvalFrameDefault #27 0x2ada01b5199a _PyEval_EvalCodeWithName #28 0x2ada01b5a848 _PyFunction_FastCallDict #29 0x2ada01a614fe _PyObject_FastCallDict #30 0x2ada01a61602 _PyObject_Call_Prepend #31 0x2ada01a6129a PyObject_Call #32 0x2ada01ad96e9 slot_tp_init #33 0x2ada01ad1e83 type_call #34 0x2ada01a613fb _PyObject_FastCallDict #35 0x2ada01b51ae8 call_function #36 0x2ada01b5757a _PyEval_EvalFrameDefault #37 0x2ada01b50ff0 _PyFunction_FastCall #38 0x2ada01b5a9e0 _PyFunction_FastCallDict #39 0x2ada01a614fe _PyObject_FastCallDict #40 0x2ada01a61602 _PyObject_Call_Prepend #41 0x2ada01a6129a PyObject_Call #42 0x2ada01ad96e9 slot_tp_init #43 0x2ada01ad1e83 type_call #44 0x2ada01a6129a PyObject_Call #45 0x2ada01b56ffb _PyEval_EvalFrameDefault #46 0x2ada01b5199a _PyEval_EvalCodeWithName #47 0x2ada01b51c37 call_function #48 0x2ada01b570d1 _PyEval_EvalFrameDefault #49 0x2ada01b5199a _PyEval_EvalCodeWithName #50 0x2ada01b51c37 call_function #51 0x2ada01b570d1 _PyEval_EvalFrameDefault #52 0x2ada01b5199a _PyEval_EvalCodeWithName #53 0x2ada01b51f5f PyEval_EvalCodeEx #54 0x2ada01a92dae function_call #55 0x2ada01a6129a PyObject_Call #56 0x2ada01b56ffb _PyEval_EvalFrameDefault #57 0x2ada01b5199a _PyEval_EvalCodeWithName #58 0x2ada01b51c37 call_function #59 0x2ada01b5757a _PyEval_EvalFrameDefault #60 0x2ada01b50ff0 _PyFunction_FastCall #61 0x2ada01b51efd call_function Fatal Python error: Aborted Current thread 0x00002ada01821600 (most recent call first): File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/core/ui/widgets/htmlview.py", line 70 in __init__ File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/core/ui/widgets/htmlview.py", line 164 in __init__ File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/log/tool.py", line 124 in __init__ File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/log/tool.py", line 172 in __init__ File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/core/tools.py", line 181 in get_singleton File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/log/cmd.py", line 19 in get_singleton File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/log/__init__.py", line 30 in start_tool File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/core/toolshed/__init__.py", line 2051 in start_tool File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/core/tools.py", line 387 in start_tools File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/chimerax/core/tools.py", line 364 in autostart File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/ChimeraX_main.py", line 454 in init File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/site-packages/ChimeraX_main.py", line 643 in <module> File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/runpy.py", line 85 in _run_code File "/fs/gpfs03/lv06/pool/pool-bmapps/hpcl5S12/app/install/CHIMERAX/0.1-alpha1/chimerax/lib/python3.6/runpy.py", line 193 in _run_module_as_main Aborted (core dumped) best Florian

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Re: [chimerax-users] Tubes
by Tom Goddard 03 Apr '17

03 Apr '17

Hi Martin, That is odd, I didn’t know the helix cylinder diameters varied in ChimeraX. I don’t know the algorithm or how to change the diameter. Maybe Conrad (who wrote the code) or Elaine will know. There is a chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list that you can ask such questions on. Tom > On Apr 3, 2017, at 10:40 AM, Martin Moncrieffe wrote: > > Hi Tom, > > When displaying helices as tubes, can one set the radius of the tubes? I’ve noticed that depending on the structure, the tube diameter is scaled scaled differently even though the docs state that w/h/x-secton do not apply in tube mode. I’m sure you guys have some fancy algorithm to do so. > > Anyway, I really like what you’re all doing so far. > > Best. > > __martin > >

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Hello everyone
by Bagaruwa Danjuma 28 Mar '17

28 Mar '17

Please I tried several times to download ChimeraX but I kept receiving the following message: Not Found The requested URL /chimerax/download.html was not found on this server. ------------------------------ Apache/2.4.6 (CentOS) Server at www.cgl.ucsf.edu Port 443 What do I do to get it downloaded. Thank you very much. Abubakar

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ChimeraX Alpha release
by Eric Pettersen 28 Mar '17

28 Mar '17

Hi all, We have released an alpha version of ChimeraX. While it still lacks many features, it has enough useful new and fun features that you might want to take it out for a spin even if it doesn’t prove ready to be your day-to-day workhorse yet. Hope you like it! Home page: http://www.cgl.ucsf.edu/chimerax/ <http://www.cgl.ucsf.edu/chimerax/> Download page: http://www.cgl.ucsf.edu/chimerax/download.html <http://www.cgl.ucsf.edu/chimerax/download.html> —Eric Eric Pettersen UCSF Computer Graphics Lab

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Opening X3D?
by Aaron Lewis 28 Feb '17

28 Feb '17

Dear x-users, I've tried to open x3d files using recent Mac and Linux dailies, but without any success. This would be useful as a way to view maps colored in Chimera 1 & Segger. I take it from docs/user/commands/open.html that the following usage should be supported: open ~/Desktop/color.x3d format x3d but I only get the error below. Any suggestions would be welcome. Aaron -- Traceback (most recent call last): File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/tool.py", line 158, in execute cmd.run(cmd_text) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2257, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/open.py", line 108, in open models = session.models.open(paths, format=format, name=name, **kw) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/models.py", line 351, in open session, filenames, format=format, name=name, **kw) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 368, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 298, in open_data open_func = fmt.open_func AttributeError: 'NoneType' object has no attribute 'open_func'

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application does not work
by Mikhail G 02 Feb '17

02 Feb '17

Dear sir/madam: I downloaded and installed chimerax 01 at windows 7 (Norton antivirus). It was installed OK, however when i try running a program it blinks and quits. What to do? i reinstalled it 2 times. MG

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