June 2018 - ChimeraX-users - RBVI Mailing Lists

pdb and map colors
by Andrey Feklistov 25 Jun '18

25 Jun '18

My question is about ChimeraX 0.6: is it possible to highlight different parts of a pdb (based on the protein sequence) with different colors and then color a corresponding map accordingly. I can't find an option 'Sequence' like in the old Chimera, is it possible to do this from a command line? Thanks!

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Re: [chimerax-users] [Chimera-users] ChimeraX won't start on Ubuntu 16.04
by Greg Couch 22 Jun '18

22 Jun '18

(This is really a question for the chimerax-users mailing list, not the chimera-users one.) If you can wait a week or so, I'll have a ChimeraX .deb package for Ubuntu 16.04 (and another for 18.04). But to answer your question, you do not need a system-wide replacement of Qt5. libQt5core.so.5 is in CHIMERAX/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5Core.so.5, where CHIMERAX is where ChimeraX was installed. So add that directory to the LD_LIBRARY_PATH environment variable and rerun ldd on libqxcb.so. And please let me know what you find out so I can make sure the .deb package avoids that problem. Regards, Greg On 06/21/2018 10:34 AM, Petr Leiman wrote: > Dear ChimeraX users and Developers, > > ChimeraX v. 0.5 or 0.6 would not start on our stock Ubuntu 16.04 > machines. The error message is as follows: > > This application failed to start because it could not find or load the > Qt platform plugin "xcb" > in "". > > Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, > offscreen, vnc, xcb. > > Reinstalling the application may fix this problem. > Fatal Python error: Aborted > > Current thread 0x000014f406ce7740 (most recent call first): > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/chimerax/ui/gui.py", > line 93 in __init__ > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", > line 485 in init > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", > line 788 in <module> > File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line > 85 in _run_code > File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line > 193 in _run_module_as_main > Aborted (core dumped) > > A few more errors while checking for missing libraries (ldd) of > ChimeraX-supplied libqxcb.so, libqxcb-glx-integration.so > or libqxcb-egl-integration.so > /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5.9' not found > /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5' not found > /usr/lib/x86_64-linux-gnu/libQt5XcbQpa.so.5: version > `Qt_5_PRIVATE_API' not found > /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5: version `Qt_5' not found > /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5 > > Do I need to do a system-wide replacement of Qt5 for a different > flavor (OpenGLES)? > > Thanks, > > Petr > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Questions about ChimeraX and problems re-downloading Chimera
by Steven Douglas Aird 21 Jun '18

21 Jun '18

Dear Elaine, Is there a way in ChimeraX to specify colors for individual species of amino acids? I would like to color cysteine residues to illustrate disulfide bonds. There appears to be no ‘byresidue' or ‘byaminoacid’ command. Since I had formerly done this in Chimera, I sought to re-download that from: https://www.cgl.ucsf.edu/chimera/download.html This page has been unresponsive for hours and the download cannot be completed. Thanks for your help, as always. Sincerely yours, Steve Aird Steven D. Aird Technical Editor Faculty Affairs Office Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp<mailto:steven.aird@oist.jp>

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Color clip plane
by Reza Khayat 15 Jun '18

15 Jun '18

Hi, I'm coloring a cryo-EM image reconstruction based on its local resolution. Thus, the image reconstruction will contain multiple colors. Is it possible to color the clipping plane the same as the underlying image reconstruction? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070

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Deactivate model
by Reza Khayat 12 Jun '18

12 Jun '18

?Hi, Is it possible to deactivate a model like in Chimera? I wan to manually align a cryo-EM image reconstruction to another before using the fit command. The orientations are too different for fit to work. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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naming chain ids
by Andrew Macrae 06 Jun '18

06 Jun '18

To whom it concerns I am wondering if it is possible to change the names of the models in chimera X in a similar manner that was possible in chimera. When I split a large complex such as the ribosome it is nice to rename them so I don't need to memorize or reference the PDB what all the numbers and or letters mean. Thanks Cheers, Andrew MacRae

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