July 2022 - ChimeraX-users - RBVI Mailing Lists

Chimera X Runs But does Not Install
by Anthony Morgan 23 Jul '22

23 Jul '22

Dear All, I’m new to Chimera X, so I am probably doing something wrong. Hope you can help please. I have ‘installed' either v1.3 and, more recently, 1.4 on my Macbook Air (under OSX 10.15.5; 1.1GHz processor, Intel Iris Plus Graphics 1536 MB). * Whilst I can run Chimera X fine (the first time after ‘installing'), it doesn’t appear to be installed locally on my laptop (that I can find). * If I close the App and try and reopen in, it’s not local, and I have to run the Install .dmg every time I want to ‘run’ it, which takes an age. * Under Security > Privacy, Chimera has Full Disk Access. Is this normal behaviour? Thanks for any advice. Regards, Anthony

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Model panel for multi-state objects of dimeric protein
by Enrico Martinez 22 Jul '22

22 Jul '22

Dear ChimeraX users! I am working on the visualization of protein-ligand interactions obtained from docking. In the ChimeraX session I have a loaded session with 88 docking poses (consisting of each frame receptor and ligand) corresponded to the separate objects (1.1 .. to 1.88) >From this ensemble I need to keep only the X object from these multiple states. I have tried to use the following command: close #1 & ~ #1.x which works perfectly for the monomeric protein. But when I am dealing with the analysis of the dimer (with A and B chains) it does not work. Only close #1 still can be used to close ALL objects. Which command could be used to keep the selected state from the ensemble for both monomer and dimer in the same way? Many thanks in advance Cheers Enrico

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Match/Matchmaker multiple segments of two protein sequences
by Gong, Zhen 21 Jul '22

21 Jul '22

Dear Chimerax developers and users, I am wondering if chimerax is able to do match/matchmaker multiple segments of two protein sequences, something like: match #1:3-13, 23-70, 72-81, 86-101 to #2:7-17, 18-66, 67-76, 77-92 cutoffDistance 3 showAlignment true Maybe it can but I did not put the command in correct format. Please help. A related question would be that the default alignment algorithm in chimerax (Needleman-Wunsch or Smith-Waterman) did not do a good job when the two proteins share high structural similarities with low sequence identity. I would like to do the manual sequence alignment, save the alignment as .aln file and use that for matchmaker, iterate with cutoff and get final rmsd of aligned atoms. Is it possible to execute such procedures in chimerax? Many thanks in advance for any helpful suggestion and discussion! Best regards, Zhen

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Difficulties running ChimeraX
by Douglas Marr 21 Jul '22

21 Jul '22

Hey everyone, I've recently updated my laboratory's computer to run linux and ubuntu 22.04. Afterwards, I installed chimeraX for that distribution of ubuntu, but whenever I try to run it, the chimeraX will open, but will be completely frozen. Nothing can be clicked on, nor can the protein structure be rotated. After a few seconds, the computer reports that ChimeraX has stopped and gives me the choice to either wait or force quit. I've tried waiting a very long time, but it always remains frozen, so I think there must be something wrong with my install. Do you guys have any advice on how to fix it? Best, Douglas Marr

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Combining 2 cryo-em maps in one
by Dmitry Semchonok 20 Jul '22

20 Jul '22

Dear colleagues, What are the ways to combine 2(or more) 3D Cryo-em maps in one? Thank you Sincerely, Dmitry

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measure volume using radii
by Noriega, Heather 19 Jul '22

19 Jul '22

Hello Elaine, I hope this email finds you well. I have a couple of questions for you. I have been working on the measurement of enclosed volumes, these are the commands I have been using: molmap #1 12 volume level 0.07 "blob" surface splitbycolor #2.1 view position #3 sameAs #2 measure volume #3.2 I am curious if there is a command to change the map radius to: outer radium: 145 ave radium: 141 inner radium:84 Or if you are aware of a map that already has these coordinates? Lastly, for the volume level is there a default level that maybe is recommended once these radii are in place? The 0.07 level seems to render lower inner volumes (i.e. 2.348 x 10^6) compared to the one below for example. I am going to attach one of my PDB files if you need it. The inner volume calculation through the review is 2.48 x 10^6 cubic angstroms, just as a reference for this file. Thanks so much, and hope to hear soon. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883 AAV_3B_VP3_only.pdb <https://drive.google.com/file/d/12YVgV54awWkEqZe3UWIgUFMhCuWoYl4N/view?usp=…>

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Align command; designating the positions to align
by McClean, Phillip 18 Jul '22

18 Jul '22

Hi, I have been trying to properly code the align command. I would like to use the command to determine the RMSD value between corresponding sections of two highly homologous proteins. Here are the details: Model 1 is to be aligned to Model 2; each model only has one chain Model 1 positions (residues=amino acids) 11-323 Model 2 positions ( residues=amino acids) 24-336 When I pair each of the amino acids that are being aligned, everyone of the pairs has the same number of atoms. Here is what I thought would work: align #1:11-323 to_atoms #2:24-336 Here is the error message: Unequal number of atoms to pair, 2483 to 2371 I am still trying to understand the nomenclature for understanding residues and atoms. Thanks for any help you can provide. Phil McClean

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showing detergent around the protein
by Dmitry A. Semchonok 18 Jul '22

18 Jul '22

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ChimeraX 1.4 frozen on RHEL 8.6 and 9.0
by Steven Chou 17 Jul '22

17 Jul '22

Dear ChimeraX developers, I installed ChimeraX 1.4 (both stable release and daily built) on RHEL 8.6 and 9.0. I installed all the ChimeraX 1.4 dependencies using "yum install" from RHEL installation USB. After the installation, I was able to start the GUI, but unable to click any button on the GUI, therefore, I was unable to report the bug from the GUI either. I also tried ChimeraX 1.3 stable release on RHEL 8.6, and everything was normal. Steven -- Steven Chou

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ChimeraX/1.3 could not start in CentOS 7
by Long Gui 15 Jul '22

15 Jul '22

Dear ChimeraX developers, I am installing the ChimeraX/1.3 in one of our GPU workstation (CentOS Linux 7). The installation processed well but after I tried to start the chimerax program, it showed: QFactoryLoader::QFactoryLoader() checking directory path "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms" ... QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqeglfs.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqeglfs.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "eglfs" ] }, "archreq": 0, "className": "QEglFSIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("eglfs") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqlinuxfb.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqlinuxfb.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "linuxfb" ] }, "archreq": 0, "className": "QLinuxFbIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("linuxfb") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqminimal.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqminimal.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "minimal" ] }, "archreq": 0, "className": "QMinimalIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("minimal") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqminimalegl.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqminimalegl.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "minimalegl" ] }, "archreq": 0, "className": "QMinimalEglIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("minimalegl") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqoffscreen.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqoffscreen.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "offscreen" ] }, "archreq": 0, "className": "QOffscreenIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("offscreen") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqvnc.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqvnc.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "vnc" ] }, "archreq": 0, "className": "QVncIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("vnc") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-egl.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-egl.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "wayland-egl" ] }, "archreq": 0, "className": "QWaylandEglPlatformIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("wayland-egl") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-generic.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-generic.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "wayland" ] }, "archreq": 0, "className": "QWaylandIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("wayland") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-xcomposite-egl.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-xcomposite-egl.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "wayland-xcomposite-egl" ] }, "archreq": 0, "className": "QWaylandXCompositeEglPlatformIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("wayland-xcomposite-egl") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-xcomposite-glx.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-xcomposite-glx.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "wayland-xcomposite-glx" ] }, "archreq": 0, "className": "QWaylandXCompositeGlxPlatformIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("wayland-xcomposite-glx") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "xcb" ] }, "archreq": 0, "className": "QXcbIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("xcb") QFactoryLoader::QFactoryLoader() checking directory path "/usr/libexec/UCSF-ChimeraX/bin/platforms" ... Cannot load library /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so: (libxcb-icccm.so.4: cannot open shared object file: No such file or directory) QLibraryPrivate::loadPlugin failed on "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so" : "Cannot load library /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so: (libxcb-icccm.so.4: cannot open shared object file: No such file or directory)" 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 0x00007f107e0f8740 (most recent call first): File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 159 in __init__ File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 577 in init File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in <module> File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main Aborted (core dumped) I have also typed: ldd /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so linux-vdso.so.1 => (0x00007ffc9f19e000) libQt5XcbQpa.so.5 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libQt5XcbQpa.so.5 (0x00007f760e4a4000) libfontconfig.so.1 => /lib64/libfontconfig.so.1 (0x00007f760e245000) libfreetype.so.6 => /lib64/libfreetype.so.6 (0x00007f760df86000) libz.so.1 => /lib64/libz.so.1 (0x00007f760dd70000) libQt5Gui.so.5 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libQt5Gui.so.5 (0x00007f760d43e000) libQt5DBus.so.5 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libQt5DBus.so.5 (0x00007f760d1b2000) libQt5Core.so.5 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libQt5Core.so.5 (0x00007f760c9bc000) libGL.so.1 => /lib64/libGL.so.1 (0x00007f760c712000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f760c4f6000) libX11-xcb.so.1 => /lib64/libX11-xcb.so.1 (0x00007f760c2f4000) libxcb-icccm.so.4 => not found libxcb-image.so.0 => not found libxcb-shm.so.0 => /lib64/libxcb-shm.so.0 (0x00007f760c0ef000) libxcb-util.so.1 => /lib64/libxcb-util.so.1 (0x00007f760bee8000) libxcb-keysyms.so.1 => /lib64/libxcb-keysyms.so.1 (0x00007f760bce5000) libxcb-randr.so.0 => /lib64/libxcb-randr.so.0 (0x00007f760bad5000) libxcb-render-util.so.0 => not found libxcb-render.so.0 => /lib64/libxcb-render.so.0 (0x00007f760b8c6000) libxcb-shape.so.0 => /lib64/libxcb-shape.so.0 (0x00007f760b6c2000) libxcb-sync.so.1 => /lib64/libxcb-sync.so.1 (0x00007f760b4ba000) libxcb-xfixes.so.0 => /lib64/libxcb-xfixes.so.0 (0x00007f760b2b2000) libxcb-xinerama.so.0 => /lib64/libxcb-xinerama.so.0 (0x00007f760b0af000) libxcb-xkb.so.1 => /lib64/libxcb-xkb.so.1 (0x00007f760ae92000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f760ac6a000) libXext.so.6 => /lib64/libXext.so.6 (0x00007f760aa58000) libX11.so.6 => /lib64/libX11.so.6 (0x00007f760a719000) libxkbcommon-x11.so.0 => /lib64/libxkbcommon-x11.so.0 (0x00007f760a511000) libxkbcommon.so.0 => /lib64/libxkbcommon.so.0 (0x00007f760a2d1000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f760a0cc000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f7609dc4000) libm.so.6 => /lib64/libm.so.6 (0x00007f7609ac2000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f76098ab000) libc.so.6 => /lib64/libc.so.6 (0x00007f76094dd000) libxcb-icccm.so.4 => not found libxcb-image.so.0 => not found libxcb-render-util.so.0 => not found libgthread-2.0.so.0 => /lib64/libgthread-2.0.so.0 (0x00007f76092da000) libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00007f7608fc3000) libexpat.so.1 => /lib64/libexpat.so.1 (0x00007f7608d99000) libuuid.so.1 => /lib64/libuuid.so.1 (0x00007f7608b93000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f7608983000) libpng15.so.15 => /lib64/libpng15.so.15 (0x00007f7608758000) libdbus-1.so.3 => /lib64/libdbus-1.so.3 (0x00007f7608507000) libicui18n.so.56 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libicui18n.so.56 (0x00007f760806e000) libicuuc.so.56 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libicuuc.so.56 (0x00007f7607cb5000) libicudata.so.56 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libicudata.so.56 (0x00007f76062d2000) /lib64/ld-linux-x86-64.so.2 (0x00007f760ea02000) libGLX.so.0 => /lib64/libGLX.so.0 (0x00007f76060a2000) libGLdispatch.so.0 => /lib64/libGLdispatch.so.0 (0x00007f7605dce000) libXau.so.6 => /lib64/libXau.so.6 (0x00007f7605bca000) libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f7605967000) libsystemd.so.0 => /lib64/libsystemd.so.0 (0x00007f7605736000) libcap.so.2 => /lib64/libcap.so.2 (0x00007f7605530000) librt.so.1 => /lib64/librt.so.1 (0x00007f7605328000) libselinux.so.1 => /lib64/libselinux.so.1 (0x00007f7605101000) liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f7604eda000) liblz4.so.1 => /lib64/liblz4.so.1 (0x00007f7604ccb000) libgcrypt.so.11 => /lib64/libgcrypt.so.11 (0x00007f7604a4a000) libgpg-error.so.0 => /lib64/libgpg-error.so.0 (0x00007f7604844000) libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f760462a000) libdw.so.1 => /lib64/libdw.so.1 (0x00007f76043d9000) libattr.so.1 => /lib64/libattr.so.1 (0x00007f76041d3000) libelf.so.1 => /lib64/libelf.so.1 (0x00007f7603fbb000) I have searched the ChimeraX mail list and found several previous email talking about this issue but I have tried all of them For instance, I have re-install the libxcb library: sudo yum reinstall libxcb but none of it could work. Would you like to check this and let me know how to solve this problem? Thanks a lot! Long Gui, Ph.D. Postdoc Researcher, Nicastro Lab University of Texas Southwestern Medical Center Long.Gui(a)utsouthwestern.edu Tel: (214)-645-1561 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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ChimeraX-users July 2022