- ChimeraX-users - RBVI Mailing Lists

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

2 2

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

2 1

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

2 2

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

2 1

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 > >

3 2

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

2 2

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

1 0

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'

2 3

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

2 1

Porting Chimera 1 extensions to ChimeraX
by Tom Goddard 12 Jan '17

12 Jan '17

Hi Matt, We don’t have a guide to porting Chimera 1 extensions to ChimeraX yet. We have not yet even made an alpha release of ChimeraX, and have just one outside developer who is writing a new extension rather than porting an old one. We will be providing info on porting extensions in the future. A major ChimeraX goal is to improve support for extension developers. Here are some basics about porting. 1) Chimera 1 uses the Tk window tookit for dialogs, menus, buttons, … while ChimeraX uses the Qt toolkit. 2) All attributes of molecules and maps are accessible from Python in both Chimera 1 and ChimeraX. 3) Methods for density maps are mostly identical in Chimera 1 and ChimeraX. 4) Methods for molecules, atoms, residues are mostly the same but with some changes (e.g. alt locs are different, chain ids can be longer than 1 character …) 5) To get better performance operating on large numbers of atoms there are new numpy array based methods to change atom attributes. 6) The packaging of an extension is different. Chimera 1 uses a ChimeraExtension.py file. ChimeraX uses Python wheels and a online distribution site called Tool Shed, https://cxtoolshed.rbvi.ucsf.edu <https://cxtoolshed.rbvi.ucsf.edu/>, and ChimeraX menu Tools / General / Toolshed allows one click installs of any tools. 7) Chimera 1 did not provide programming API documentation, while ChimeraX has API documentation http://www.rbvi.ucsf.edu/chimerax/docs/devel/index.html <http://www.rbvi.ucsf.edu/chimerax/docs/devel/index.html> 8) Chimera 1 used Python 2, ChimeraX uses Python 3. Python 3 import statements and print statements are different and integer divide produces a float, but mostly it is the same. Most Chimera 1 extensions have a graphical user interface in Python / Tk that is often a lot of the code. Now we use Python / Qt because support for Tk is poor. Qt is totally different so all graphical user interface will have to be rewritten. Tom > On Jan 12, 2017, at 11:51 AM, Dougherty, Matthew T wrote: > > Hi Tom, > > Are there any guidelines, docs or examples as to converting extensions into chimeraX? > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ================================================= > =================================================

1 0

Re: [chimerax-users] obj export ? other 3d format ?
by Tom Goddard 04 Jan '17

04 Jan '17

Hi Giorgio, Thanks for the explanation. So Maya and Cinema4d can’t directly read Collada with vertex colors and preserve the coloring? Chimera uses vertex colors instead of textures for multicolor surfaces. Can your meshlab file conversion process work with the X3D output from Chimera and ChimeraX? I know X3D is not very well supported. What advantage do you see in using ChimeraX instead of Chimera for this model export? ChimeraX has completely reliable surface calculation where Chimera fails for large molecules. There is a semi-secret Chimera option to the surface command “grid 0.5” that makes Chimera use the reliable surface calculation from ChimeraX but the resulting surface is not associated with the atoms that generated it so copying colors from the atoms is more difficult (need to use the Chimera Color Zone tool). ChimeraX has nice ambient occlusion lighting that Chimera lacks, but that is not exported in scene files. Tom > On Jan 4, 2017, at 11:14 AM, Giorgio Luciano wrote: > > Hello thanks for the reply. So the idea is this. Genrally I need to import molecules in other software (maya+renderman, cinema4d+arnold). One of the problem I had was to "save" in some way the information of the materials of the models. Let's say I have calculated a properties of my molecule and I wanted to code it in the color (hydrophobicity for example, a particular charge density and so on). So since it was not easy to mantain it I generally did the following > 1) save as dae > 2) import in meshlab > 3) create a blank texture and then color the texture from the info in the vertex texture. > In this way I can then export the info in all the software I want (including zbrush for example and so use subsequently KEYSHOT for a fast cool render). > If needed I can create a small video about that :) > Now the problem is that I cannot do it anymore in the new chimera :) So every format that can save the model+colors would be perfect. DAE seems the one to work better for now (can be imported withouth loss in meshlab and blender) > Thanks for creating such a great software :) > Giorgio > > Il giorno mar 3 gen 2017 alle ore 20:46 Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> ha scritto: > Hi G, > > ChimeraX will eventually export OBJ and Collada 3d formats but we don’t have a schedule for that. It currently exports STL for use with 3d printers (single color). We also can save X3D, again added for 3d printers (multi-color). Some ChimeraX code (cellPACK tool) reads Collada, but does not write it, but the PyCollada library is in ChimeraX so that is a start towards writing it. We have a hundred different features we want to get into ChimeraX eventually and their priority depends on how compelling the use is. It would help if you told us why you want OBJ and Collada export, and why it is an advantage to get it into ChimeraX versus using the current capability in Chimera 1. > > Tom > > > > > On Dec 29, 2016, at 11:01 AM, Giorgio Luciano <giorgio.luciano(a)gmail.com <mailto:giorgio.luciano@gmail.com>> wrote: > > > > Dear all, just a message to ask if in CHIMERA X is on the roadmap an obj, dae export. > > G. > > _______________________________________________ > > 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

obj export ? other 3d format ?
by Giorgio Luciano 29 Dec '16

29 Dec '16

Dear all, just a message to ask if in CHIMERA X is on the roadmap an obj, dae export. G.

1 0

Testing 2
by Conrad Huang 16 Dec '16

16 Dec '16

Please ignore

1 0

Testing
by Conrad Huang 16 Dec '16

16 Dec '16

Please ignore

1 0