- ChimeraX-users - RBVI Mailing Lists

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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Automating Map segment
by Sam W Marchant 29 Jul '21

29 Jul '21

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<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-October/013980.html> 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.

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Re: [chimerax-users] command line way for inverting selection
by Rangarajan, Amith 29 Jul '21

29 Jul '21

Hi, I am looking for a way to invert selection without reaching for the tool bar. I would like to know if there is a way to invert selection via the select command ( or some other command) thanks a lot, Amith

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ATOM has no alt loc B
by James Loy 28 Jul '21

28 Jul '21

Hi folks- I'm trying to add hydrogens to an mmCIF file (5byl) using the addh command. However, every time I try, I encounter the following error: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 712, in init run(sess, cmd) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 63, in cmd_addh add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens add_hydrogens(session, atoms, type_info_for_atom, naming_schemas, hydrogen_totals, File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/hbond.py", line 214, in add_hydrogens _attach_hydrogens(atom, altloc_hpos_info, bonding_info) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/hbond.py", line 895, in _attach_hydrogens add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens, naming_schema) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 862, in add_altloc_hyds h = new_hydrogen(atom, i+1, total_hydrogens, naming_schema, File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 882, in new_hydrogen metal_pos = metal.get_alt_loc_coord(alt_loc) File "atomic_cpp/cymol.pyx", line 587, in chimerax.atomic.cymol.CyAtom.get_alt_loc_coord ValueError: Atom /A MG 702 MG has no alt loc B I'm using ucsf-chimerax_1.2.5-1_amd64.deb installed on Ubuntu 20.04. I've done some digging, and I cannot figure out what is going on. Any help would be appreciated. Thanks in advance! -James -- James Loy, Ph. D. 614.915.9792 LinkedIn <https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/>

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The PDB code for the demo picture on the website
by BAOCHENG LIU 28 Jul '21

28 Jul '21

Hi chimerax group, I am a postdoc in UCLA using chimerax. Thanks for providing all scientists this powerful software that makes life easier. I have a question here when I was learning the cartoon/ribbon style command line. So, I saw the 4 demo pictures on the website https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style and just realized the structure just looks similar to one of my structures. Could you please tell me the PDB code for that structure so I can compare it with mine in detail? Hope it is released. Thank you. Best regards, Baocheng

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