- ChimeraX-users - RBVI Mailing Lists

Trying to open .py files on Windows gives cPickle error
by Carnes, Jason 10 Aug '21

10 Aug '21

Hello, I am collaborating with someone using ChimeraX on a Mac. Their only option to save modified files results in a .py file extension. When I try to open .py files on my Windows install of ChimeraX I get an error: "ModuleNotFoundError: No module named 'cPickle'" Is there a way to manually install cPickle on my Windows computer that will allow me to open the .py files, or are Mac & PC not compatible? Thanks, Jason Jason Carnes, PhD Research Scientist IV | Center for Global Infectious Disease Research Seattle Children's Research Institute 206-884-3137 OFFICE CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Difficulties Visualizing Isosurfaces from Cube File - Nathan Wood
by Nathan Wood 09 Aug '21

09 Aug '21

Dear ChimeraX I was having difficulty attempting to visualize computationally generated electrostatic potential isosurfaces originating from a Gaussian *.cube file. I tried to open the cube file from the shell only for it to incompletely visualize. I can provide an image if necessary. I found the following correspondence concerning cube files and isosurfaces, but unfortunately I am unable to resolve the issues of the cube file visualizing. https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html> I was curious if anyone has had experience with cubefiles. Any assistance would be greatly appreciated, Very Respectfully, Nathan Wood

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Superimpose
by Wisoot Chanit 09 Aug '21

09 Aug '21

Dear ChimeraX team, I am having a quesition. I am going to superimpose 2 monomers of P domain of norovirus GII.3 into a template PDB 6if5, but the template showed that information of its chains are missing. What should I do to make a dimer into 6if5. This is different from PDB 3mfg, which was a templete I used for my previous paper. Thank you. Jay

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Re: [chimerax-users] Saving 300dpi high resolution images with ChimeraX
by Elaine Meng 04 Aug '21

04 Aug '21

Hi Nada, ChimeraX questions should be sent to chimerax-users(a)cgl.ucsf.edu (CC'd here so you don't need to do anything this time). ChimeraX does not set the dpi. You just figure out the number of pixels you need and then save in pixels. I.e. if you want 3 inches wide at 600 dpi then you know you need 1800 pixel width, e.g. save myfile.png width 1800 If you open the resulting image file in just about any general image application like Photoshop, Gimp, or Mac Preview (etc.) then you can set the "resolution" or "dpi", but it's really the number of pixels you save in the first place that matters. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 4, 2021, at 10:04 AM, Bejar, Nada <nbejar(a)houstonmethodist.org> wrote: > > Hello, > I am Nada, a postdoctoral fellow at Houston Methodist. > > I saw your name in this thread. https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000816.html > I tried your suggestion, but any number I put on width would still give me a 96dpi. > > I switched to the old Chimera and I can change the unit to print unit and that resolves the issues, but I have all my work done on ChimeraX. > > I do need to make figures today and help would be much much appreciated. > > Nada Bejar, Ph. D. > Postdoctoral Fellow > Kiss RNA Lab > Houston Methodist Research Institute > 6670 Bertner Avenue > Houston, TX 77030 USA

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Re: [chimerax-users] Error in ChimeraX application installation linux ubuntu
by Elaine Meng 04 Aug '21

04 Aug '21

Hi Vanessa, Please send ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here, so no need to do anything this time). Since I don't know the answer, I kept waiting for somebody else to answer your question... and didn't notice until now that you had sent it to only me. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 1, 2021, at 1:51 AM, Vanessa Roy <vanessaroy(a)mail.tau.ac.il> wrote: > > Dear ChimeraX development team, > > We encountered issues while installing ChimeraX on our server and wanted to ask whether you could help us understand what the problem is? We haven't yet found a solution to our problem. > Here is the output after installation: > > # /home/apps/chimerax-1.2.5-rc-2021.05.24/bin/ChimeraX > X11 connection rejected because of wrong authentication. > qt.qpa.xcb: could not connect to display localhost:10.0 > qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. > This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. > > Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. > > Fatal Python error: Aborted > > Current thread 0x00007f479c05d740 (most recent call first): > File "/home/apps/chimerax-1.1/lib/python3.7/site-packages/chimerax/ui/gui.py", line 119 in __init__ > File "/home/apps/chimerax-1.1/lib/python3.7/site-packages/ChimeraX_main.py", line 500 in init > File "/home/apps/chimerax-1.1/lib/python3.7/site-packages/ChimeraX_main.py", line 919 in <module> > File "/home/apps/chimerax-1.1/lib/python3.7/runpy.py", line 85 in _run_code > File "/home/apps/chimerax-1.1/lib/python3.7/runpy.py", line 193 in _run_module_as_main > Aborted (core dumped) > > We would greatly appreciate your advice on how to solve this issue. > > Many thanks for your help! > > Best, > Vanessa > -- > Vanessa Roy > Gil Ast Lab > Department of Human Molecular Genetics and Biochemistry > Sackler Faculty of Medicine | Tel Aviv University

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Maps comparison
by Dmitry Semchonok 04 Aug '21

04 Aug '21

Dear colleagues, I have 2 cryo-em maps of different resolutions. What will be the correct strategy to compare them and what are the tools and steps? Thank you Sincerely, Dmitry

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C-alphas rendered as dots
by Pranav Shah 03 Aug '21

03 Aug '21

Hi Team, I am working with a huge model (and a correspondingly huge map), which makes the handling on my GPU accelerated desktop an agonisingly frustrating experience. In order to speed up simple (rigid-body) fitting of the map and model, I decided to use the -C-alpha trace of the pdb. However, the pdb gets rendered as a bunch of disconnected dots whereas the same pdb in Chimera is rendered correctly with all things. Is this a normal behaviour for ChimeraX? I could use Chimera, but I prefer the way ChiemraX handles large maps as compared to Chimera. In the absence of a quick fix, would there be a way to increase the size of the atoms? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Showing C-alphas
by Casey 30 Jul '21

30 Jul '21

I am trying to show a single sphere at c-alpha carbons for some point mutants that i designed. When I use the command: show /a:473,476,477 atoms I can see all the atoms in chain A for residues 473, 476, 477. Using: show /a:473,476,477@cb atoms I can show "two spheres" for the c-alpha and c-beta carbon. When I use: show /a:473,476,477@ca atoms nothing happens and i don't see any spheres. If I show the full atom and then do: hide /a:473,476,477@ca* atoms Just the c-alpha sphere gets hidden. Why is it that i can't just show the c-alpha spheres? Unfortunately for my figure i make silhouettes of my model and so i can't just hide the other atoms by making them fully transparent

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Re: [chimerax-users] Automating Map segment
by Tom Goddard 30 Jul '21

30 Jul '21

To group by connectivity looks like you need to add d._group_con.value = True To figure out this stuff you would need to look at the Segger user interface code, it is in the ChimeraX distribution (under site-packages/chimerax/segger/segment_dialog.py) or on GitHub https://github.com/tomgoddard/segger/blob/master/Segger/src/segment_dialog.… <https://github.com/tomgoddard/segger/blob/master/Segger/src/segment_dialog.…> Tom > On Jul 30, 2021, at 10:42 AM, Sam W Marchant <smarchant(a)UCSD.EDU> wrote: > > Thanks so much im trying to group by connectivity and I am having trouble finding the right line of code to add that ability. Any thoughts? > >> On Jul 29, 2021, at 3:56 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Sam, >> >> I did an initial port of Segger from Chimera to ChimeraX (also called Segment Map) but that code was written by Greg Pintilie and he has not worked the ChimeraX version so there is no new command to run it in a script. It would probably not be too hard to write some Python to run it. The Chimera script mentioned in the mailing list is attached to my message about it. >> >> https://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-October/013979.html <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_pip…> >> >> That won't work in ChimeraX, but here I attach the equivalent for ChimeraX. >> >> Segger was developed to segment molecules in EM maps, so I have doubts that it will do much good for your light microscopy. But you can decide that by running it by hand on some time steps and see if you like the result. >> >> Here is a different approach we used to quantify protrusions of crawling neutrophils in light sheet microscopy by placing markers that might be of interest. >> >> https://www.cgl.ucsf.edu/chimera/data/protrusion-sep2015/protrusions.html <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chime…> >> >> Tom >> >> >> >>> On Jul 29, 2021, at 3:24 PM, Sam W Marchant via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hi, >>> I am looking to apply the Map Segmenting to multiple time series of light sheet imaging and so I was wondering if there is either a command or a python function to automate the process. It looks here <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_pipe…> that you said it was going to be added to ChimeraX but I cannot find any info on how to do it. If not you mentioned a script in this answer, could you potentially send that to me? >>> Thanks, >>> Sam Marchant. >>> _______________________________________________ >>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mai…> >> >> <segscript.py> >

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How to Align Chromosome Models with Different Number of Atoms?
by Cardiff Jiang 30 Jul '21

30 Jul '21

Dear ChimeraX User List, How can I compare two chromosome 3D models (PDB files) that have different numbers of "atoms"? Matchmaker tool reports, "Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'align' command to superimpose small molecules/ligands." align #1 toAtoms #2 reports, "Unequal number of atoms to pair, 49 and 63." align #1 toAtoms #2 matchNumbering true reports, "Pairing dropped 49 atoms and 63 reference atoms. No atoms paired for alignment." align #1:1-40 to #2:1-40 reports, "No atoms paired for alignment." How should I compare two chromosome 3D models below? Thank you. [image: image.png] Best regards, Zichen "Cardiff" Jiang

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