- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] Colab Modelled, but no PDB
by Tom Goddard 25 Jul '22

25 Jul '22

Hi Anthony, Predicting a dimer where the monomer is 1182 residues, so a total of 2364 residues is guaranteed to run out of memory on Colab or Colab Pro -- the GPUs they offer don't have enough memory (at most 16 GB). The web page on AlphaFold performance test cases shows that only an Nvidia A40 with 48 Gbytes of memory handles over 2100 residues. That web page gives results for running AlphaFold via ChimeraX on Colab, but also running AlphaFold installed on our machines at UCSF with either an A40 GPU or an RTX 3090 GPU (24 GB memory). The "no templates" means structure templates were not used when running on our UCSF machines. Tom > On Jul 24, 2022, at 1:35 AM, Anthony Morgan <anthony.morgan(a)pharm.ox.ac.uk> wrote: > > Dear Tom, > > Thanks so very much, this is low-hanging fruit for you, but invaluable for me as I am a newbie. Really appreciate it. The Test link is really illuminating too thank you. > > I had wanted to try a dimer of 1182 residues each, but I am doubting that this is going to work, even with the paid service. Agreed? > On the test page, one of the runs is annotated as “no templates”. I cannot see how you can add templates to the Alphafold panel. I only see Energy Minimization under Options. Am I missing something? > > I’ve now got the pdb of the one model, thank you. It’s obvious once it’s pointed out, but I couldn’t see the wood for the trees. > > Really appreciate your time. > > Kind regards, > > Anthony > > >> On 24 Jul 2022, at 00:37, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Anthony, >> >> AlphaFold predictions on Google Colab of 1200 amino acids often fail as you can see from test cases on this web page >> >> https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html <https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html> >> >> With free Google Colab you often get a very old Nvidia K80 GPU with 12 Gbytes of memory. With Colab Pro ($10/month) I usually get an Nvidia P100 GPU with 16 Gbytes of memory which can handle slightly bigger proteins. You can check what GPU you got by pressing the "+ Code" button on the Google Colab window, then entering the command "!nvidia-smi" and pressing the play button, which gives output like this >> >> Sat Jul >> 23 23:28:55 2022 +-----------------------------------------------------------------------------+ | NVIDIA-SMI 460.32.03 Driver Version: 460.32.03 CUDA Version: 11.2 | |-------------------------------+----------------------+----------------------+ | GPU Name >> Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |===============================+======================+======================| | 0 Tesla P100-PCIE... Off | 00000000:00:04.0 >> Off | 0 | | N/A 38C P0 34W / 250W | 16259MiB / 16280MiB | 0% Default | | | | N/A | +-------------------------------+----------------------+----------------------+ >> >> >> To download a completed model after an AlphaFold error (typically out of memory), click on Files in the Google Colab window, then click on the predicted structure, "af1182_unrelaxed_model_1.pdb" in your image, and click the "..." to the right of the file and choose Download from the menu that appears. The file will then appear on your local computer in >> >> ~/Downloads/ChimeraX/AlphaFold/prediction_1 >> >> I'll see if I can add to the ChimeraX ColabFold output the GPU and also make it automatically download partial results in case an error occurs. >> >> Tom >> >> >>> On Jul 23, 2022, at 4:41 AM, Anthony Morgan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Dear All, >>> >>> I’m new to Chimera X and to Colab Alphafold (AF), hope you can help please. >>> >>> I’m running Chimera X 1.4 on a Macbook Air. >>> I want the predicted structure of a fairly large protein (1182 residues). >>> When I first ran Colabfold_predict, it terminated after 90 min (RAM issue). >>> I re-ran the same sequence *without * Energy Minimization. >>> After 20 mins, it successfully returned the first model (see attached), but ran into RAM issues again. >>> >>> Two questions: >>> >>> There is no ‘Prediction’ folder in my Downloads, so how can I download the *.pdb file of model #1 that it clearly has generated? >>> If I cannot do this, will an upgrade to Colab Pro solve this issue for this size of protein? >>> >>> Thanks for advice. >>> >>> Kind regards, >>> >>> Anthony >>> >>> <Screen Shot 2022-07-23 at 12.17.14.png> >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >> >

3 2

Movie recording
by Dmitry Semchonok 25 Jul '22

25 Jul '22

Dear colleagues, I have several maps and models that I would like to spin around independently at once and record as a movie. How to do that? Thank you in advance. Kind regards, Dmitry

3 2

Question about commands similar to openModel in Chimera
by Thu Nguyen 25 Jul '22

25 Jul '22

Good morning, I am editing a python script that previously used the command chimera.openModels.list(modelTypes=[chimera.Molecule])to return a list of open molecules. Do we have a similar command in ChimeraX or is there any other way to get a list of protein chains in ChimeraX? Thank you very much. Best regards, Thu

2 1

Colab Modelled, but no PDB
by Anthony Morgan 23 Jul '22

23 Jul '22

Dear All, I’m new to Chimera X and to Colab Alphafold (AF), hope you can help please. * I’m running Chimera X 1.4 on a Macbook Air. * I want the predicted structure of a fairly large protein (1182 residues). * When I first ran Colabfold_predict, it terminated after 90 min (RAM issue). * I re-ran the same sequence *without * Energy Minimization. * After 20 mins, it successfully returned the first model (see attached), but ran into RAM issues again. Two questions: * There is no ‘Prediction’ folder in my Downloads, so how can I download the *.pdb file of model #1 that it clearly has generated? * If I cannot do this, will an upgrade to Colab Pro solve this issue for this size of protein? Thanks for advice. Kind regards, Anthony [cid:8B6C8DAE-A4C3-4F95-8B26-037B6B318679]

2 1

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

2 2

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

2 1

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

2 3

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

2 2

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

2 1

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=…>

2 4

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

3 6

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

18 Jul '22

2 4

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

3 4

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.

2 1

a question about CMM files
by Pranav Shah 15 Jul '22

15 Jul '22

Hi Team, How are XYZ coords represented in ChimeraX? I have a volume of 794x794x272 sampled @15Å/px. When I place markers in the volume and save the resultant marker file, the coords for the points are as follows- <marker_set name="markers"> <marker id="1" x="6950.3" y="6659.4" z="2010" r="1" g="1" b="0" radius="15"/> <marker id="2" x="6977.7" y="6381.5" z="2010" r="1" g="1" b="0" radius="15"/> <marker id="3" x="9747.8" y="3926.7" z="2010" r="1" g="1" b="0" radius="15"/> </marker_set> Such large numbers seem to imply that the dimensions are measured in physical units (Å in this case). Is this correct? 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

2 1

How to view swiss docking results in ChimeraX
by Fernando Luis Cônsoli 15 Jul '22

15 Jul '22

Hi! I am a very excited biologist that has been eagerly trying to use ChimeraX to generate hypotheses for the work I collaborate in insect resistance to pesticides by analyzing the predicted structure of proteins and their interactions with ligands. I have been able to generate a 3D model of my protein of interest using the *alphafold* tool as available in *ChimeraX*. I then proceeded using the *Swiss Docking* tool to predict the interactions of selected ligands with the 3D protein model. I can see the results in swiss page, but was not able to use the link available to *uscf chimera*, and neither identify why my browser would not launch web chimera when requested. I downloaded all the data produced by Swiss Docking, but I can not open the *clusters.dock4* file generated in my installed version of *ChimeraX* to display the results as it is shown in the video available when selecting the link of the *uscf chimera* in the swiss web page. How can I do that to select for the best ligand-protein interaction predicted? Alternatively, I have uploaded my protein and ligand pdb files in my ChimeraX and calculated clashes and contacts under Structure Analysis in the Tools tab, as explained in some of the videos I have been watching with the Chimera old version. But I am not confident that what I see reflects the prediction data I was able to obtain with the Swiss Docking tool. How can I be sure that the ligand-protein interaction predicted this way is the best choice? Sorry for the long message! Hope someone will bring me some light as I struggle with python command lines! My best! Fernando Consoli

2 6

downloading and saving maps from EMDB
by Nebojsa Bogdanovic 14 Jul '22

14 Jul '22

Hello, I have a text file list of 30-40 maps from emdb that I would like to download and save using chimeraX. Each map should be named for example 5995.mrc, where 5995 is the actual EMDB id. Is there a way to do this using CLI to make it faster than downloading 1 by 1? I am not sure how to instruct chimeraX to take the file name from the open models. open 5995 from emdb #opens the file and assigns #1 save ???.mrc models #1 #save the model 1 but how to instruct chimerax to take the model's name Ideally would be something like this: Input: emdb-ID.txt Output: 40 single .mrc maps named according to their EMDBIDs. open emdb-ID.txt from emdb save all, models #1-40 name=???? Please let me know if I can implement this. Thank you and best regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

3 2

Stereo view does not work with chimerax 1.4
by Gong, Zhen 14 Jul '22

14 Jul '22

Hi, Good morning. I would like to generate a stereo view in ChimeraX 1.4 but it did not work. Here is the error message: camera stereoCould not switch graphics mode. Graphics driver did not create OpenGL context. And there is the graphics driver information: graphics driverOpenGL version: 4.1 INTEL-18.7.4 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc Any helpful suggestion is greatly appreciated. Best regards, Zhen

2 3

Issue with loading large trajectory topology and coordinate file
by Shubham Devesh Ramgoolam 12 Jul '22

12 Jul '22

Hi all, I hope you are doing well. I have a PSF file of size 62 MB and a DCD coordinate file of size 423 MB that I am trying to load in chimeraX. However, chimeraX remains unresponsive during the loading process. As such, I tried loading a subset of the coordinate file using start stop step option. However, this did not fix the issue. This is an example of the command I used: open myfile.psf coords file.dcd start 1 stop 10 step 2 Is there an alternative approach I could use? (I don’t know if this is relevant or not but whenever I closed and re-opened chimeraX after it became unresponsive, it did not ask me to send a bug report.) UCSF ChimeraX version: 1.5.dev202206290845 (2022-06-29) OS: Windows 10 Regards, Shubham Ramgoolam Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

2 1

Copy/pasting
by Dmitry Semchonok 12 Jul '22

12 Jul '22

Dear colleagues, In case I would like to copy/paste the piece of a model - what is the correct way to do that? Thank you Kind regards, Dmitry

2 1

How to complete docking with ChimeraX
by 刘金鑫 11 Jul '22

11 Jul '22

Dears, I want to use ChimeraX to dock. The old version can combine with Vina. But I cann't to find the menu in the ChimeraX. Would it be possible? Best regards Jinxin

2 4

Measuring distance between two atoms in a single protein
by McClean, Phillip 11 Jul '22

11 Jul '22

Hi Chimerax Group, I am trying to measure the distance between two atoms in a protein in Chimerax v1.4. The .pdb file I am working with was generated using Alphafold2 in the ColabFold application. I select the two atoms by using CTRL+SHIFT, go to the TOOL -> Structure Analysis -> Distances. The Structure Measurements panel appears in the lower right of the screen. When I click on the Create button, a Chimerax box appears on screen with the following message: Exactly two atoms must be selected! I was surprised to see this message since I thought I had properly selected two atoms. Any advice on how to calculate the distance would be greatly appreciated. Thanks in advance for any help you can provide. Phil McClean Professor North Dakota State University

2 2

Unable to run the option region all
by Edoardo D Imprima 11 Jul '22

11 Jul '22

Dear all, I saved two sessions with different data to make a movie using the same command lines. However, I am not able to obtain the same result when I use the command volume region. In one instance Chimerax renders the whole 3D volumes I selected with “volume #x-y region all". In a second session, with different data but virtually the same commands, the rendering halts at the step before (~disp #1). I am puzzled because in both instances the logs show the command “volume #x-y region all” as executed. And, in the “faulty session" if I manually input the same command that I passed through the script it eventually shows the complete regions of the volumes. Could you please help me to understand what am I doing wrong? I am using ChimeraX 1.4 on Linux. I am pasting here the piece of the scripts that work and do not respectively, Many thanks in advance, Edoardo Working fly p2 p1 100; wait; volume #2 show style surface level 0.8 color #5555ff; volume #3 show style surface level 0.8 color #aa557f; volume #4 show style surface level 0.8 color #f514fd; volume #5 show style surface level 0.8 color #11ffcc; volume #6 show style surface level 0.8 color #ff9429; volume #2-6 transparency 0.8; wait 20; volume all planes z,1344,60; wait 1284; ~disp #1; volume #2-6 region all; Faulty fly p1 p2 100; wait; volume #2 show style surface level 0.8 color #5555ff; volume #3 show style surface level 0.8 color #aa557f; volume #4 show style surface level 0.8 color #f514fd; volume #5 show style surface level 0.8 color #11ffcc; volume #2-5 transparency 0.5; wait 20; volume all planes z,1604,1594; wait 10; ~disp #1; volume #2-5 region all; ------------------------------------------------------ Dr. Edoardo D'Imprima Postdoctoral fellow Structural and Computational Biology Unit EMBL Heidelberg - Mahamid Group Meyerhofstraße 1 69117 Heidelberg Germany Phone: +49 6221 387-8531

2 1

color zone with markers
by HUI WANG 08 Jul '22

08 Jul '22

Dear Developers, I have a need to color a huge ring-like structure with markers, I used to know that we could color the density by the markers as well as the links between them, so It's not necessary to have too many markers. However, I cannot figure out how to color the density covered by the links now. I am using ChimeraX 1.3. Any comments or suggestions will be appreciated! Thanks! Best regards, Hui

2 2

Re: [chimerax-users] [Chimera-users] Coloring model by b-factor
by Elaine Meng 08 Jul '22

08 Jul '22

Dear Yang, I guess you are using ChimeraX (not Chimera) -- the commands are somewhat different between the two programs. There is also different address for asking ChimeraX questions that you might want to use in the future: chimerax-users(a)cgl.ucsf.edu (CC'd here). As far as I can tell, your ChimeraX command is correct. I'm not sure why you said it was not working. Maybe it is because the Log will still tell you the whole range in the structure. However, the coloring range (different than the value range) will be what you specified in the command. For example, if I open 2gbp and use color by bfactor #4/A palette red:green:blue range 35,45 It works correctly. Although the Log says: 2575 atoms, 525 residues, atom bfactor range 2 to 63.9 ... that is just telling you the values in the structure are 2 to 63.9. The red-blue-green coloring, however, is spread from 35-45 and everything below 35 is red and everything above 45 is blue. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 7, 2022, at 1:48 PM, 师扬 via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear developer, > > I am trying to color a model by b-facor and used the command like : color by bfactor #4/A palette red:green:blue range 35,45. However, the range setting was not working. So my question is how to color with a user-defined palette and a user-defined range. > > Best wishes, > Yang

2 2

Morphing animation
by Daniel VillanuevaAvalos 06 Jul '22

06 Jul '22

Hello, I am trying to export a sequence of objs for a morphing animation that I want to use in Houdini FX. The objs do export but they are apparently empty. This is what I am typing on the command line: perframe "save F:/Caltech/CALTECH/04_Growth/4_04_Enzyme_Filaments/objs/from_chimera/AdhE_dimers_morph_01/model$1.obj model #3.$1" ; coordset #3 1,51; wait 51; ~perframe Am I missing something? Thank you, Daniel.

2 1

Obtaining the list of contacting residues for the command interface select
by svle＠tiscali.it 06 Jul '22

06 Jul '22

Hi, I have three chains in a pdb. With the command interfaces select /A contacting /B bothSides true in the Log I receive the following: 19 contacting residues. It is possible to obtain the list of these residues? Thanks. Saverio Voucher MISE per P.IVA e PMI: fino a 2500€ per la Banda Ultralarga. https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busi…..

2 1

sphereFactor interpolation
by James Hodgkinson-Bean 05 Jul '22

05 Jul '22

Hi I have been playing around with developing some scripts that can measure sphericity directly from input icosahedron virus models. The scripts are working well, however my sphericity measurement is currently not represented as a relative scale between an icosahdron (sphericity = 0) and a sphere (sphericity = 1) as appears the case in chimeraX. I wondered if you could possibly tell me the equation used in ChimeraX to interpolate this scale when generating icosahedral shapes with variable sphericalFactor? Apologies if this question is to complex for a simple quick answer; I'm a first year PhD student and am new to making such calculations. If it's too complicated I'm sure I can figure it out myself. Cheers, James.

2 1

ChimeraX Version 1.4 on CentOS/RHEL 7
by Long Gui 01 Jul '22

01 Jul '22

Dear Chimera community, We are interested in the new version of the ChimeraX/1.4 but we could not find the installation file of ChimeraX/1.4 on our CentOS/RHEL 7 system. Only ChimeraX/1.3 supports CentOS/RHEL 7. So we would like to ask if there is a way to install ChimeraX/1.4 on our CentOS/RHEL 7 system? In addition, our computational source would prefer to install the program using docker. Currently I only find this docker file supports ChimeraX/1.3 https://github.com/maduprey/chimerax-docker/ ? Have anyone tried it for ChimeraX/1.4 yet? Thanks! Long 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.

2 1

User/expert community of chimera/chimeraX
by Shivam Gupta 01 Jul '22

01 Jul '22

Hello chimera team, Greetings of the day! I was wondering if we have any official support, user or expert community of chimera and chimeraX where I can get my queries,problems and bugs solved. Looking forward to your reply. Thanks -- 株式会社ファーマフーズ Biomedical Department グプタシヴァム Gupta Shivam 〒615-8245 京都市西京区御陵大原1-49 TEL:075-748-9811 FAX:075-948-9818 E-mail: *shivam-gupta(a)pharmafoods.co.jp <a-higashiyama(a)pharmafoods.co.jp>* URL: http://www.pharmafoods.co.jp/

4 5

Aligning a trajectory to its first frame
by Shubham Devesh Ramgoolam 30 Jun '22

30 Jun '22

Hi all, I hope you are doing well. Is there a way to align all the frames of a trajectory to its first frame for the purpose of visualization? I’m trying to visualize a residue pair in a trajectory and I have done the following: select both residues; view sel; play the movie. The issue here is that the position of the pair changes (the pair rotates across the screen) with the frame. Regards, Shubham Ramgoolam Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

4 5

ChimeraX via Remote Desktop
by Dmitry Semchonok 30 Jun '22

30 Jun '22

Dear colleagues, Could you please share the experience on remote desktop work with ChimeraX? The ChimeraX is installed on Centos 7. Probably a certain issue holding ChimeraX from starting (OpenGL)? Kind regards, Dmitry

3 2

Error when joining two pdbs
by Praveen Ranganath Prabhakar 29 Jun '22

29 Jun '22

Hi all, I am Praveen, a graduate student at UC Irvine. Hope you are doing well. I am using Chimera X. In my project, I have to join a protein to a peptide sequence via a peptide bond. I have loaded the PDB files of both the protein and the peptide sequence & I have identified where (between which atoms) the peptide bond has to be. After loading the PDBs, I use the following in the command line "*select #1:12.A@C#2:1.A@N*" (basically identifying the residue/atoms where the peptide bond has to be formed) to join but I get the error "*Expected an objects specifier or a keyword*" . I am sorry if this is a common error and I have missed something, I am new to Chimera. Also it would be great if someone could tell me if there is a way to save the final pdb after joining them? Thank you so much for your time, Best, Praveen

2 1

Marking movies in ChimeraX
by Eric Pettersen 27 Jun '22

27 Jun '22

> Begin forwarded message: > > > Hi, Eric, > > Since you are here answering my question, I would like to make use of this > opportunity to ask you a question about making movie, I want to make a > movie with five different density maps from cryo-EM with different ligands > binding in two different conformation, there is no animation interface in > ChimeraX as the same in Chimera, right? It is easier for me to use > animation in Chimera to make the movie, but I have all my sessions with > colored density map in Chimera, I know I could use commands to make such > kind of movie in ChimeraX, but I found it difficult for me. Can you give > me some suggestions what should I do? I am sorry that if this bothers you. > > Have a nice day! > > Best, > Lu

4 5

Trajectory computation slowing down overtime
by Shubham Devesh Ramgoolam 27 Jun '22

27 Jun '22

Hi all, I hope you are doing well. I have a Python script for analyzing specific residue pairs for every frame in a trajectory. It does so, by using 2 for loops: For frame in list_frames: Set current frame to frame For pair in specific_residue_pairs: Do computation The computation involves defining geometric objects(centroids, axes, planes) and performing calculations with them(distance, angles). The issue here is that as we move further in list_frames, the computation takes longer and longer. There is a somewhat linear increase in computation time, as illustrated below: [cid:image003.png@01D87E37.C872FDF0] Is there a way to maintain the same computation time for every frame in the trajectory? Regards, Shubham Ramgoolam Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

3 11

using variables in command files
by Pranav Shah 26 Jun '22

26 Jun '22

Hi Team, Is it possible for one to declare a variable in a command file that can then be passed to via the chimeraX command line interface. A minimal example of something I would like to do is - command.cxc open $file color radial palette rainbow save $outfile.png height 512 width 512 transparentBackground True In the chimeraX command line window I would then like to run open command.cxc infile.mrc outfile.png 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

3 11

Pymol view
by Rechiche, Othman 24 Jun '22

24 Jun '22

Hi everyone, Is there a way to import/open “views” set with PyMol and open them in Chimera or ChimeraX? Best Regards, Othman

3 7

How to gradually crop a volume with perframe command
by Edoardo D Imprima 24 Jun '22

24 Jun '22

Hi all, I would like to make a movie showing a volume gradually cropped along one axis .e.g. volume #1 region 0,0,0,410,375,336 (start) volume #3 region 0,0,0,410,375,31 (end). Could you please tell me how to provide the range in “perframe” command to perform this operation? Ie as trying something like this perframe "volume #1 region $1" 0,0,0,410,375,200 0,0,0,410,375,336 frames 10 without success though. Many thanks in advance, Edoardo ------------------------------------------------------ Dr. Edoardo D'Imprima Postdoctoral fellow Structural and Computational Biology Unit EMBL Heidelberg - Mahamid Group Meyerhofstraße 1 69117 Heidelberg Germany Phone: +49 6221 387-8531

2 1

user inputs for python scripts
by Pranav Shah 24 Jun '22

24 Jun '22

Hi Team, Is there a way to provide user input to python script files? I tried using sys.argv but I keep getting an out of list error message when I call the script from the ipython shell (accessed from within the chimeraX window) 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

3 2

Version 1.4 for CentOS 7?
by Ricardo Righetto 24 Jun '22

24 Jun '22

Hi, First, apologies if this has already been announced elsewhere. I see on the download webpage that there is no production release for CentOS 7 and the latest daily release for this platform was built on 2022-05-06. Any chance we could get a production release of 1.4 and/or a newer daily build for CentOS 7? Thank you very much! Best wishes, -- Ricardo Diogo Righetto

5 8

How to show fib-sem tomography data as solid volume
by Edoardo D Imprima 23 Jun '22

23 Jun '22

Hello, Could you please tell me how to display fib-sem tomography data as a compact volume that can be navigated by sliding planes? The data consists of a series of frames that I can convert as .mrc volume or .mrcs stack. I attach a snapshot taken from a review that illustrates (middle panel) the visualisation I would like to obtain. The medical-image panel in ChimeraX is very handy however, the “full” option shows the volume while I need to display the planes of each side to slice through them. Looking forward to your feedback, Best wishes, Edoardo ------------------------------------------------------ Dr. Edoardo D'Imprima Postdoctoral fellow Structural and Computational Biology Unit EMBL Heidelberg - Mahamid Group Meyerhofstraße 1 69117 Heidelberg Germany Phone: +49 6221 387-8531

4 7

where can I find the mesh option in chimeraX?
by 王超 23 Jun '22

23 Jun '22

Dear All,I want to setting the mesh option in ChimeraX like "Chimera way".Like "open Volume Viewer of a map, and click features-data display option".but I cannot find toolbar of Volume Viewer, I am puzzle where to find it?

2 4

Chimera question
by Daniel VillanuevaAvalos 23 Jun '22

23 Jun '22

Hello, I am trying to create a spirosome, and I am entering *sym #1 h,56.5,164.4,12* but the radius of the helix is wrong. How can I change it? What I am trying to do is move my obj closer to origin but I cannot find a way to do that. I can only move the pivot to center with *cofr 0,0,0*. Thank you, Daniel.

2 4

quality of life imporovement suggestion for view matrix output
by Pranav Shah 22 Jun '22

22 Jun '22

Hi Team, I use the view matrix command regularly to save orientation of the maps/models in a command file. As it currently stands, the output needs to be formatted appropriately so that the command can be run. As a one off, it is trivial to format the output from the log window into an appropriate format but, when it has to be done repeatedly as is my case it becomes quite annoying. Therefore, I was wondering if you would agree to format the output so that it can be directly copy pasted in a ready to use format? 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

2 3

alphafold in Google colab
by Roberto Marabini 20 Jun '22

20 Jun '22

Hi, Starting today, when I try to execute AlphaFold calculations using Google Colab, I get the message: ====== ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. kapre 0.3.7 requires tensorflow>=2.0.0, which is not installed. xarray-einstats 0.2.2 requires numpy>=1.21, but you have numpy 1.19.5 which is incompatible. datascience 0.10.6 requires folium==0.2.1, but you have folium 0.8.3 which is incompatible. albumentations 0.1.12 requires imgaug<0.2.7,>=0.2.5, but you have imgaug 0.2.9 which is incompatible. Successfully installed absl-py-0.13.0 biopython-1.79 chex-0.0.7 dm-haiku-0.0.4 dm-tree-0.1.6 docker-5.0.0 flatbuffers-1.12 gast-0.4.0 grpcio-1.34.1 immutabledict-2.0.0 jax-0.2.14 keras-nightly-2.5.0.dev2021032900 ml-collections-0.1.0 numpy-1.19.5 pandas-1.3.4 scipy-1.7.0 tensorflow-cpu-2.5.0 tensorflow-estimator-2.5.0 typing-extensions-3.7.4.3 websocket-client-1.3.3 wrapt-1.12.1 + pip3 install --upgrade jaxlib==0.3.2+cuda11.cudnn82 -f https://storage.googleapis.com/jax-releases/jax_releases.html Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/ Looking in links: https://storage.googleapis.com/jax-releases/jax_releases.html ERROR: Could not find a version that satisfies the requirement jaxlib==0.3.2+cuda11.cudnn82 (from versions: 0.1.23, 0.1.29, 0.1.32, 0.1.40, 0.1.41, 0.1.42, 0.1.43, 0.1.44, 0.1.46, 0.1.50, 0.1.51, 0.1.52, 0.1.55, 0.1.56, 0.1.57, 0.1.58, 0.1.59, 0.1.60, 0.1.61, 0.1.62, 0.1.63, 0.1.64, 0.1.65, 0.1.66, 0.1.67, 0.1.68, 0.1.69, 0.1.70, 0.1.71, 0.1.72, 0.1.73, 0.1.74, 0.1.75, 0.1.76, 0.3.0, 0.3.2, 0.3.5, 0.3.7, 0.3.8, 0.3.10) ERROR: No matching distribution found for jaxlib==0.3.2+cuda11.cudnn82 ======= The error seems to be obvious but, can someone point me towards a solution? Thanks Roberto

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Research associate / Group leader position at the University of Luebeck (Northern Germany)
by Guido Hansen 20 Jun '22

20 Jun '22

The Institute of Biochemistry (Director: Univ.-Prof. Dr. Thomas Krey) at the University of Luebeck has an opening for a position as a *Research associate / Group leader (m/w/d)* in full-time (currently 38.7 hours per week) for an initial period of 4 years. Within the position, the opportunity for further qualification (habilitation) is given. *Main areas of activity:* * Own research (incl. acquisition of third-party funding) on topics in structural infectiology * Supervision of technical assistants, bachelor, master and doctoral theses * Co-responsibility for the cryo-electron microscope planned at the site * Organisation and implementation of teaching (in English) in biochemistry for the Molecular Life Sciences programme (lectures, practicals, seminars, performance review and booking, preparation of certificates) * Participation in teaching (in German) in biochemistry for medical students (lectures, practicals, seminars and their performance review and booking) *Requirements:* * Completed university degree in a natural science or medical programme, e.g. biochemistry, molecular life sciences, chemistry or biology. * Completed or nearly completed PhD thesis in natural sciences (defense in 2022), preferably in the field of structural infectiology * Proven research focus in the field of structural infectiology * Experience in the field of cryo-electron microscopy * Experience in teaching natural sciences and/or human medicine (in German and English) More information can be found here https://www.biochem.uni-luebeck.de/fileadmin/files/pdf/Ausschreibung1043-22… Please contact Prof. Dr. Thomas Krey (krey(a)biochemie.uni-luebeck.de) for any further questions, and send your written application with the usual documents (cover letter with research interests, curriculum vitae, references) summarised in a single PDF document by July 4^th , 2022 (*date of receipt*) at the latest to*bewerbung(a)uni-luebeck.de*, quoting the reference number*1043/22*. Best wishes Thomas *Prof. Dr. Thomas Krey* University of Luebeck *University of Lübeck Institute of Biochemistry* phone: +49-451-3101-3100 fax: +49-451-3101-3104 e-mail: krey(a)biochem.uni-luebeck.de <mailto:krey@biochem.uni-luebeck.de> www.biochem.uni-luebeck.de <http://www.biochem.uni-luebeck.de> Ratzeburger Allee 160 23562 Lübeck Germany -- Re: email signature

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The ChimeraX Toolshed is temporarily down
by Greg Couch 17 Jun '22

17 Jun '22

Due to database corruption. Hope to have it back up soon. -- Greg

1 1

ChimeraX: chashes in no-gui execution
by Enrico Martinez 17 Jun '22

17 Jun '22

Dear ChimeraX users! I noticed that sometimes ChimeraX crashes while being executed in batch mode using bash script. Here is an example of my script that calculates hbonds and contacts between protein and ligand open mypdb.pdb #calculate h-bonds and contacts in each frame hbonds #1.1-24&protein restrict #1.1-24&ligand coordsets false interModel false makePseudobonds false log true distSlop 0.5 angleSlop 20 intraRes false saveFile hbondsALL_rep1.log clashes #1.1-24&protein& :41,49 restrict #1.1-24&ligand overlapCutoff 0.3 interModel false makePseudobonds false log true intraRes false saveFile contactsALL_rep1.log wait wait exit as you may see I added two times wait in the end of the script that could reduce the frequency of crashes. May you specify what is the default value for each wait (in seconds??) and how I could use just one wait command to set up the pause in the proper way? Many thanks in advance! Cheers Enrico

3 5

Centos7 version of ChimeraX version 1.4 possible?
by Martin Moche 16 Jun '22

16 Jun '22

Dear ChimeraX developers, Thanks for an outstanding piece of software! Is it possible to have a CentOS7 variant of version 1.4 of ChimeraX? Best regards, Martin Head of Macromolecular X-ray Crystallography<https://ki.se/en/mbb/psf-mx> | Protein Science Facility<https://ki.se/en/mbb/protein-science-facility> Medical Biochemistry and Biophysics<https://ki.se/en/mbb/department-of-medical-biochemistry-and-biophysics> 171 65 Solna | Solnavägen 9 +46 8 524 868 43 | +46 73 322 93 27 martin.moche(a)ki.se<mailto:martin.moche@ki.se> | ki.se<https://ki.se/> ______________________________________ Karolinska Institutet - a medical university När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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ChimeraX 1.4
by Eric Pettersen 10 Jun '22

10 Jun '22

UCSF ChimeraX version 1.4 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/ This will be the last release to support macOS 10.14 (Mojave). Also, ChimeraX 1.4 is not available for CentOS 7, Ubuntu 16.04 and 18.04 because the Qt 6 window toolkit does not support those older Linux distributions. Updates since version 1.3 (Dec 2021) include: - search/retrieve from EBI AlphaFold DB 3rd release, ~1 million structures - display AlphaFold predicted aligned error (PAE) plots - can BLAST UniRef100,90,50 (+ previous choices AlphaFold, PDB, NR) - AlphaFold prediction of multimers (of limited size) on Google Colab - independent centers of rotation available as mouse mode - join models with Build Structure tool or command - define axes for display and/or use in measurements - increase/decrease VDW radii relative to their current values - switch PDB residue numbering scheme (author/canonical/uniprot) - align sequences with Clustal Omega or MUSCLE - calculate % identity in sequence alignments - window toolkit updated to Qt 6.2.3 from 5.15.2 For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog

1 0

Saving PDB file as a string
by Sophie Liu 08 Jun '22

08 Jun '22

Hi, My organization has some extra information at the end of a PDB file that I would like to be printed onto the Log Console of ChimeraX. I am currently writing a bundle to do so by adding a command (however if this is best implemented by overriding the open command for PDB files then I would switch to that). I am wondering how I can have the bundle work like so: 1. the user types a command call it, "showdata" 2. the bundle would read all Models (that are pdb files) that are being displayed 3. for each model it would read the PDB text file, and say go to indices 200-251 of the string and display that in the Log console I hope this makes sense. I am mainly struggling on how to access the original PDB text of the model. Best, Sophie

2 4

Licensed software source
by Jeya Priya Senthilkumaran 07 Jun '22

07 Jun '22

Hi Community, To use ChimeraX licensed software. I have few queries Do we have a separate source {tar file} to be downloaded or the same source from https://www.cgl.ucsf.edu/chimerax/download.html should be used? While purchasing the license, will we be provided with separate source to download the software? We have bought license, now we need to upgrade to newer version of ChimeraX ,do we have instructions to upgrade to the newer version? In case, we have installed open source of the software, how should we upload the license to the ChimeraX? Kind Regards, Jeya Priya Scientific Cloud Computing [cid:image001.png@01D874F0.89D1F100]<https://www.zifornd.com/> [cid:image002.png@01D874F0.89D1F100] M +91 8098223555 [cid:image003.png@01D874F0.89D1F100] www.zifornd.com<http://www.zifornd.com/> [cid:image004.png@01D874F0.89D1F100] IST (Time Zone) [cid:image005.png@01D874F0.89D1F100] Follow us on [cid:image006.png@01D874F0.89D1F100]<https://www.linkedin.com/company/zifo-technologies/> ******************* CAUTION ******************* This e-mail is intended exclusively for the individual(s) to whom it is addressed and may contain information that is PRIVILEGED and CONFIDENTIAL. If you are not the intended recipient, please notify the sender and delete the original message. Further, you are not to copy, disclose or disseminate this e-mail or the information contained to any other person and any such actions are unlawful. Zifo Technologies has taken every reasonable precaution to ensure that this e-mail and attachment(s) has been swept for viruses, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment(s). Zifo Technologies is neither liable for the proper and complete transmission of the information contained in this e-mail nor for any delay in its receipt. *************************************************

2 3

Save the map after surface dust
by Dai, Xin 07 Jun '22

07 Jun '22

Dear ChimeraX developers, I'm trying to save a density map following the command "surface dust". However, the map saved remains to be the original one. Is there any command to save the cleaned map? I found this old post http://www.cgl.ucsf.edu/pipermail/chimera-dev/2015/001263.html asking the same question using Chimera. But unfortunately, it's not working for me. Thank you, Xin

2 2

Analog of Chimera "addcharges" command in ChimeraX
by Rafi Brent 06 Jun '22

06 Jun '22

To whom it may concern, I have about 20,000 pdb files to which I'd like to add Hydrogens, add partial charges, and convert to the mol2 format using either Chimera or ChimeraX. I have not had much success with Chimera, as the process slows down quite drastically over time when run through the GUI, and when I run Chimera from the terminal (using chimera --nogui python_script.py), I run into errors with ANTECHAMBER that do not occur when my script is run through the GUI. I'll write to the Chimera support email with more details, and I'd appreciate any advice if you have any, but based on these errors I'm thinking that there is likely a better way to perform this task using ChimeraX. I noticed that the "addcharges" command no longer exists in ChimeraX, and the "write" command which I was using to convert to mol2 files in Chimera appears to have been replaced as well. Because of this, any recommendations about how to run my operation using the closest analogs to the original Chimera methods would be greatly appreciated. Thanks so much for any advice you may have. Sincerely, Rafi Brent

2 1

Docking window for html viewer automacially
by Shubham Devesh Ramgoolam 03 Jun '22

03 Jun '22

Hi all, I hope you are doing well. I am using the following code to open chimeraX along with an HTML file when a condition is met: subprocess.call([path_chimeraX, path_html]) Now, in this scenario, is it possible include some codes(perhaps as arguments for subprocess?) that will dock the window for the HTML viewer automatically while also hiding the log and command line interface upon startup of chimeraX? Or should I use a different approach? Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

3 5

Rescaling IMOD segmentation models in ChimeraX
by Martinez, Matthew 02 Jun '22

02 Jun '22

Hi everyone, I have a question regarding the rescaling of data in ChimeraX. I'm depicting a subtomogram average at their aligned positions in a tomogram, which doesn't contain scaled pixel information, and I want to also load in IMOD segmentation data to depict with the subtomogram average. I'm able to readjust the pixel size of the tomogram easily with the Map Coordinates dialog box, but is there a way to rescale IMOD segmentation models once in ChimeraX? I can do this within IMOD, but it would be more convenient to do it in ChimeraX with the volume. Thanks in advance for any help! Best regards, Matt

2 2

Isolde | ARG Sidechain Bond Angle Outliers
by Anderson, Jacob 31 May '22

31 May '22

I have been using Isolde inside Chimerax 1.3 - it works fantastic! However, when I go to validate on OneDep, invariably all the ARG have outliers, specifically the NE-CZ-NH1 bond angle. Has anyone else observed this and overcome it? Perhaps something wrong with my build?

2 2

ChimeraX - XMAS pluggin modification questions
by Moya Clark, I.O. de (Isabel) 31 May '22

31 May '22

Good morning, I am a student intern at the Richard Scheltema Laboratory, and I am going to be continuing with the modification of the XMAS bundle submitted to ChimeraX recently. Right now, we are trying to extend the bundle to be able to extract specific distances between specific amino acids for two different proteins but for a molecular dynamics simulation. Either by loading a trajectory coordinates + topology files or by using the “morph” command and then “coordset slider”. So, the idea would be to extract the distances between the alpha carbons, of a set of pre-selected amino acids, in each frame of the simulation. Do you have any suggestions about any modules or methods that I should look into to extract this information in each frame? I saw there is a CooordSets class but I do not know if this would be the right way to go about it. Kind regards, Isabel de Moya Clark

2 5

no text in log gui after ubuntu 22.04 upgrade
by Sean Connell 30 May '22

30 May '22

Hi, I was wondering if you have some suggestions for me to solve a problem I have after upgrading to ubuntu 22.04. I am running UCSF ChimeraX version: 1.3 (2021-12-08) and after upgrading ubuntu the log window in the GUI has no text. If I use the command "log save chimerx.html" and open chimerax.html in a browser I can see everything I expect in the log. It is just not being displayed. I installed using the Ubuntu 20.04 (Linux) 64-bit deb on the download page. many thanks for your help in advance sean -- --------------------------------- Sean Connell, PhD Ikerbasque Associate Structural Biology Unit, BioCruces Bizkaia Health Research Institute, Plaza Cruces s/n, 48903, Barakaldo, Spain Phone: +34 634 623 493 sean.connell(a)gmail.com https://www.biocrucesbizkaia.org <https://www.biocrucesbizkaia.org/areas-investigacion/bc3.19> frozenribosomes.com ---------------------------------

2 3

Filled helix tube when clipped
by Zheng Ruan 27 May '22

27 May '22

Dear ChimeraX users, I'm curious to know if there is a way to have the helix tube filled when after using the clip command? I know that the clip plane of surface representation can achieve this as found in this example (https://www.rbvi.ucsf.edu/chimerax/feature_highlights/pmc.png) However, I'm not able to make it when I display my structure in cartoon cylinder representation. I attached an example image that I made. Thank you for your input. Best, Zheng

2 1

Nonstandard residues
by Abhilash Padvannil 27 May '22

27 May '22

Hi, I am trying to open PDB (multi subunit complex) from phenix refinement in ChimeraX. One of the chains is A7. While the PDB’s open normally in coot, ChimeraX recognizes a couple of chains as nonstandard residues and is showing XXXX for the entire length of the amino acid sequence (ALA as ALAA 7 , MET as META 7) and so on. The residues correspond to subunit with chain ID A4. Attached is the sequence view Please suggest how to fix this. Thanks Abhilash. [cid:10AB2EAB-7B93-4DBA-8BFF-7329E82724B0@mcb.ucdavis.edu]

2 1

lighting Flat + ambiant Occlusion ?
by Thibault TUBIANA 27 May '22

27 May '22

Dear Chimera X community and developpers :) I would like to create a flat representation for a protein but with ambiant occlusion, a little bit like on the example joined (made with [ https://3dproteinimaging.com/ | https://3dproteinimaging.com ] ). Is it something that it is possible with ChimeraX ? I've been playing with the shaddows but the "flat effect" is disappearing then :/ Thank you :) Thibault. -- Thibault Tubiana, PhD Postdoctoral Fellow @ [ https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanism… | IMAPP ] Institute for integrative biology of the cell ( [ https://www.i2bc.paris-saclay.fr/ | I2BC ] ) - CNRS UMR 9198

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chimerax-1.4-rc2022.05.25 generic Linux 64-bit doesn't work
by Xiaoguang Xue 26 May '22

26 May '22

Dear developers, It seems the most recent chimerax-1.4-rc2022.05.25 generic Linux 64-bit doesn't work correctly for me. I got the following errors: NOTE: Traceback (most recent call last): File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/ChimeraX_main.py", line 1021, in <module> exit_code = init(sys.argv) File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/ChimeraX_main.py", line 573, in init from chimerax.ui import initialize_qt File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/chimerax/ui/__init__.py", line 21, in <module> from .gui import MainToolWindow, initialize_qt, menu_capitalize File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/chimerax/ui/gui.py", line 130, in <module> from Qt.QtWidgets import QApplication ModuleNotFoundError: No module named 'Qt' BUG: ModuleNotFoundError: No module named 'Qt' File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/chimerax/ui/gui.py", line 130, in from Qt.QtWidgets import QApplication _See log for complete Python traceback._ Best, XG

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Coordset command not working in nogui mode
by Shubham Devesh Ramgoolam 26 May '22

26 May '22

Hi all, I hope you are doing well. I have a python script for measuring the distance between aromatic rings of specific residues for different frames of a trajectory. To measure the distance, I am first defining centroids at the center of aromatic rings and then use the command distance. This process is repeated for each frame to be analyzed. To navigate between frames, I am using the command ‘coordset #1 {desired frame}’. When executing the script in no gui mode, the centroids are always defined with respect to the residue’s location in frame 1 even though the command coordset has changed the frame. In gui mode, the script only works if a delay is created between changing the frame and defining the new centroids. I introduced that delay by asking for a dummy user input (I ran the script from python Shell): run(session, 'coordset #1 ' + {new_frame}) y = input('dummy') run (session, 'define centroid /A:8 & aromatic-ring radius 0.3 color yellow mass false name d1’) My chimeraX version: 1.4rc202205060510 (2022-05-06) Should I be using a different command for changing frames of trajectories when in nogui mode? Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

4 5

Display the boundary of a density map
by C.J. 25 May '22

25 May '22

Hi, If a similar function to chimera to show the boundary of a density map in ChimeraX? In Chimera, it is in "Volume viewer" > "Features" > "Data display options" > "Show outline box using color" option. Thanks! Jianhao

2 1

relative position of a marker
by C.J. 25 May '22

25 May '22

Hi, I place a marker in a cryoEM map with "Volume Tracer" tool. How can I know the relative position of the marker to the origin or center of the map? Thank you! Best, Jianhao

3 4

Surface Coloring of EM density maps by radius
by Das, Sayan 25 May '22

25 May '22

Hi, I'm trying to figure out if there is any way to color the electron density map by radius(something similar to the surface color feature on Chimera) in ChimeraX. I'm trying to color the map of a virus from the center to the outside of the capsid proteins using a series of color range based on its radius from the center. Is this feature available in ChimeraX? Any leads will be helpful. Thanks, Sayan.

2 1

Executing a script in chimerax python shell for an interactive session
by Shubham Devesh Ramgoolam 25 May '22

25 May '22

Hi all, I hope you are doing well. I have a python script that allows the user to visualize specific residue pairs. Here is an overview of how the script functions: * Ask the user to input the path of a .cxs file (created previously) and a text file containing the pairs to be visualized * Print the names of the pairs along a uniquely assigned number * Ask the user to input a number in order to visualize the pair assigned to it To run the script currently, I have to do the following: i)Open chimerax ii)Show the shell iii) Call the script from the shell Now, is it possible to include some codes in the script that would allow me to just open chimerax, click on File -> Open -> this script, and then the shell would show up and the execution would continue there? Right now, if I ran the script using File -> Open -> this script, I would get this error: Traceback (most recent call last): File "C:/Users/Shubham/Desktop/this_script.py", line 8, in session_path = input('Enter file (.cxs) to be visualized with path: \n') RuntimeError: input(): lost sys.stdin Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

3 3

How to get all values from Fit List table
by Ioannis Skalidis 25 May '22

25 May '22

Hello all, I am doing some fit searches in Chimera X and I would like to use the values reported not only for "Correlations and times found" (which is reported in the log and can be copied) but also the "Ave" and "Inside" values reported for each fit in the Fit list. But unfortunately, I cannot copy any of the values in the Fit List. Is there any workaround available so I can get all these values? Thanks a lot, Yiannis. -- Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/

2 3

Multi color information export for 3D printing in ChimeraX
by M. Elizabeth Stroupe 24 May '22

24 May '22

Hi- Is there a way to export the multi-color information in ChimeraX for 3D printing? I have figured out how to combine the .mtl and .x3d information in Chimera, but would like to use rendering in ChimeraX that is not available in Chimera. Thank you (and sorry if you have answered this a million times - I couldn't find it in the archive despite my best efforts!). Beth --- Dr. M. Elizabeth (Beth) Stroupe Professor, Department of Biological Science Director, Graduate Program in Molecular Biophysics Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306

2 1

Assembling 2 proteins
by SANTOSH RAMA BHADRA RAO TATA 24 May '22

24 May '22

Hi, I would like to create a pentamer, how can I assemble 5 different proteins subunits into a pentamer. I was trying to use matchmaker but I couldn't. can you please help me with some video how to get in use it or if there is any other way to use the software and create pentamer please let me know. Thanking you, With best wishes, Tata Santosh Rama Bhadra Rao, PhD Scholar, C/O Prof Helen Irving, La Trobe university, Bendigo, Vic-3550, Australia. Email: 19807877(a)students.latrobe.edu.au; S.Tata(a)latrobe.edu.au Phone: 0499263974

2 1

(no subject)
by Andrea Dallapè 24 May '22

24 May '22

Dear ChimeraX Team, I would like to ask you if there's a simple and easy method (without using external software) to label the steric clashes, as in the attached image (the red line between the ball densities). Thank you for your help and attention! Andrea

3 3

Colouring submodels using a palette
by Lorena Zuzic 24 May '22

24 May '22

Hi all, I have a model that contains 256 submodels of a ligand across trajectory frames. I would like to colour the individual models using a palette (e.g., blue:orange) so that the time progression across frames is depicted in colour. Is there a way to assign palette range to submodels? Best wishes, Lorena

2 2

Asking copyright for one of your picture
by Catherine Duverger 23 May '22

23 May '22

Hello, I'm a French artist and I want to ask you for using one of your picture in a project. How it's possible to use it for a double exposure photography in order to prepare an exhibition in Rennes France. I probably made a book in 200 ex. Thanks a lot to answer if it's possible. Catherine

2 2

Selecting atoms outside (or inside) a density map's contour
by Mateusz Dobrychłop 23 May '22

23 May '22

Dear ChimeraX Team, I'm a structural bioinformatician working on my PhD thesis. I've been a long time user of Chimera, and I'm now using ChimeraX to create figures for my dissertation. I genuinely love both programs. Thank you for creating them. I found myself stuck trying to perform one operation in ChimeraX that is very easy to perform in Chimera. What I'm trying to do is select (and color) all atoms of an atomic model, that are located outside of a density map's contour. In Chimera, I was able to just select the model and use the shortcut "ac oa" and that was it. Unfortunately I am not able to find a way to do that in ChimeraX. I even tried to select the atoms in Chimera, then save the selected atoms as a PDB file, and then the inverted selection as a separate PDB file, and then open the two files in ChimeraX and color them separately. This could even work for a full atom representation, but does not work well for ribbon representation. That said, if the solution to my problem could be to somehow transfer the list of atoms that are outside the map from Chimera to ChimeraX, that would work for me as well. I will appreciate any tips and suggestions! Kind regards, Mateusz

2 2

OpenGL woes on Windows
by Pranav Shah 21 May '22

21 May '22

Hi Team, I have installed the latest RC of chimerax on a windows box running v10 Pro. The box has an Nvidia RTX6000 GPU card as well. I have updated the Nvidia drivers to the latest version yet when I start ChimeraX, i see the following error message - ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 3.0 Try updating your graphics driver. Nvidia driver version - Version: R510 U6 (512.78) WHQL; Release Date: 2022.5.16; Operating System: Windows 10 64-bit, Windows 11 Do you guys have any suggestions for trouble shooting? 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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Problems with the first installation
by mykalxxxxx 20 May '22

20 May '22

Deer developer, This is my first time install ChimeraX. What should I do if I get this prompt after installation .Thanks. (QT 5.12.12 was already installed,windows 11,ChimeraX 1.4rc202205060510). | | mykalxxxxx | | 邮箱：mykalxxxxx(a)163.com |

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Map "Blobs" tool - Generate objects?
by Ricardo Righetto 20 May '22

20 May '22

Hi again, Pardon for resurrecting another old thread: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001139.html I have needed to extract selected blobs as separate surfaces (and also separate volumes) recently and found a way to do it within ChimeraX version 1.3 (2021-12-08), here's how: 1. Right mouse → Blob → right click desired blob to color it (any color different from the rest of the volume) 2. Split the surface based on colors: sop splitbycolor #1.2 3. Use the desired split surface to mask the original volume data: vol mask #1 surf #2.2 fullMap true 4. Save as a new volume: save my_segmented_piece.mrc #3 Hope this helps :-) Best wishes, -- Ricardo Diogo Righetto

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feature request : yellow/ochre clipping planes
by Pranav Shah 18 May '22

18 May '22

Hi Guys, Would it be possible to reinstate the same color scheme used to delineate the clipping planes in Chimera into ChimeraX. The current lines are too thin and have the same color as the default map color value. This makes the manipulation of the planes harder especially when working on a smaller screen. 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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Re: [chimerax-users] [Chimera-users] interface plot
by Elaine Meng 18 May '22

18 May '22

Oops, I meant to send this to chimerax-users(a)cgl.ucsf.edu , not chimera-users(a)cgl.ucsf.edu (apologies to the latter folks)! Elaine > On May 12, 2022, at 12:27 PM, Elaine Meng via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Pranav, > If you mean that you wanted a list of the interface residues, you can use the "interfaces" network diagram edge context menu to select the residues, then list them in the Log with "info residues sel" ... and either cut-n-paste from the Log to text file or use "log save" to save it as an HTML file. The "info" command should really allow saving a text file directly, but it doesn't do that yet. I believe we have an open ticket to fix that omission. > > In the chain-chain network diagram, e.g. when the mouse cursor is over the edge representing the chain B-C interface, context-menu choices include > > Select Contact Residues of B and C > Select Contact Residues of B with C > Select Contact Residues of C with B > > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#diagram> > > Or if you get a new daily build, another way to select the residues is to use menu: Select... Contacts, the Chains section of the resulting dialog: > <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> > > Then use "info residues sel" and possibly "log save" as mentioned above. > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save> > > Alternatively, you could use "measure buriedarea" specifying the two chains and "list true", which also reports each residue's buried area. (thus avoiding having to select and use "info") > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> > > Example: > measure buriedarea (/A&protein) with (/B&protein) list true > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On May 12, 2022, at 9:06 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: >> >> Indeed! Although, as a suggestion, would it be possible to highlight >> in the description that in order for the plot to inherit residue >> colors, one needs to invoke the plot _after_ the residues have been >> identified and colored? Also, could I save the output of the analysis >> to a text file? >> 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 >> >> On Thu, May 12, 2022 at 4:53 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>> haha, glad you like it!! >>> >>> Best, >>> Elaine >>> >>>> On May 12, 2022, at 8:27 AM, Pranav Shah via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>> >>>> <3 >>>> <3 >>>> <3 >>>> <3 >>>> <3 >>>> >>>> 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 >>>> <image.png>_______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users(a)cgl.ucsf.edu >>>> Manage subscription: >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Re: [chimerax-users] exporting crosslinks histogram
by Tom Goddard 17 May '22

17 May '22

Hi Pim, I added a Save Plot As... menu entry to the crosslinks histogram, can save as svg or pdf or png. I also added bins, maxLength, minLength and height options to the command to control how many bins, the x scale and height of y scale (in counts per bin). These changes will be in tomorrow's ChimeraX daily build which will become ChimeraX 1.5 eventually. Too late to make it into ChimeraX 1.4. Tom > Dear ChimeraX team, > > I am analysing multiple datasets generated using crosslinking-ms, loaded as separate pseudobond files on my model. The crosslinks histogram plots works just fine and I’d now like to put some plots neatly side-by-side. My questions: > > - can the histogram be saved or exported? Ideally as an svg or pdf file. But png or jpg would also already be useful. > I could export the .pb files and plot them elsewhere, but that seems like a workaround. > > - is it possible to specify the x and the y axis of the generated histograms, as well as the bin size? This would be helpful to show them side-by-side. > > Many thanks in advance, > > Pim > -running v1.2.5 on mac os catalina 10.15-

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Re: [chimerax-users] [Chimera-users] Set scale factors from displayed contours?
by Tom Goddard 17 May '22

17 May '22

Hi Oliver, In tomorrow's daily ChimeraX builds you can use volume maximum #1,2 scale fromlevels and it will scale each map by 1/level where level is the displayed surface level before taking the maximum. This allows merging maps that have different intensity levels. Thanks for the suggestion. This will be in ChimeraX 1.5 but not in 1.4 and is not in Chimera. Tom > On May 6, 2022, at 2:38 PM, Elaine Meng via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Oli, > Oh, I see, you already figured out the scale factors (essentially) by adjusting thresholds interactively. So the automation would simply be doing the math of taking the ratio of the thresholds and scaling the map(s) according to that, which sounds more feasible. > > I can make a feature request ticket (probably ChimeraX), but can't make promises as I would not be the one to triage it. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On May 6, 2022, at 1:42 PM, Oliver Clarke via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >> >> Hi Elaine, >> >> I don't think I explained very well - I mean to say, calculate the scale factors from the displayed thresholds. >> >> E.g. if the user has set map1 to a threshold of 1.0, and map2 to a threshold of 2.0, in order to make them visually equivalent in a combined map, map1 needs to be scaled by a factor of 2. >> >> It would be great if this could be done automatically as a flag for the volume or vop command (as there is already a flag to provide per map scale factors). >> >> Cheers >> Oli >> >>> On May 6, 2022, at 4:39 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>> Hi Oli, >>> Our volume expert Tom is on vacation until mid-month and might not be reviewing questions for a while... so I will give my not-so-expert thoughts: >>> >>> To me, the initial identification of "overlapping bits" sounds quite subjective and thus difficult to encode. If the user could designate the boundaries of this area (by drawing a box?), perhaps automatic scaling of one map to make its values as similar as possible to the values of another map inside that box could be done. However, drawing the box would probably be just as time-consuming as the process that you are already using. >>> >>> Also, new developments/agorithms would be going only into ChimeraX, not Chimera. ChimeraX has mostly the same "vop" options as Chimera, except included in the "volume" command instead of "vop": >>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#vop> >>> >>> Best, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>>> On May 6, 2022, at 1:23 PM, Oliver Clarke via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>>> >>>> Hi, >>>> >>>> When combining maps using vop maximum (or volume maximum in chimerax), we often want to adjust the scale factors of the maps such that the overlapping bits of two aligned maps are visually on the same scale. It is possible to calculate the appropriate scale factors from the displayed thresholds, but this becomes a little time consuming when combining many maps. >>>> >>>> Would it be possible to add a flag, something like "get scalefactor from display thresholds" that would take care of this automatically? >>>> >>>> Cheers >>>> Oli >>> >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

1 0

Removing text labels generated with command distance
by Shubham Devesh Ramgoolam 16 May '22

16 May '22

Hi, I hope you are doing well. I have a python script, to be executed in nogui mode, which does the following: -open a pdb file -define centroids for specific residues -draw pseudobonds between specific residues -> I am using the command distance for this purpose The issue arises when I have to save the session (.cxs) when in nogui mode, I am getting this error: QGuiApplication::font(): no QGuiApplication instance and no application font set. I believe it is because of the text labels created by the command distance. So, I included the following in my code: run(session, ‘hide #2.*’) and I can now save the session. I noticed in the model panel that the pdb file is assigned to #1 and the pseudobond to #2. The text labels are created as a submodel of the pseudobond (so #2.1, 2.2,..), hence why the ‘hide #2.*’ Will this fix always work? Is the model assignment also dependent on the pdb file being opened? Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Where is the renumber sequence tool in ChimeraX?
by Phan, Isabelle 16 May '22

16 May '22

The sequence of my structure includes a tag and I want to renumber from -7 so that the first residue is the start Met. I tried the old chimera command resrenumber = FAIL. I googled and searched the docs, read the list of commands one by one, and still could not figure it out. The API has a renumber_sequence() function but I don't understand the description (what’s "the given residues”? The chain?) and was unable to find an example on how to call this from the interface. I opened the python shell and typed: from chimerax.core.commands import run run(renumber_residues('#1/A:*', -7)) # FAIL Sorry if this is trivial, I am still completely baffled by ChimeraX despite using it for years. Thanks, Isabelle 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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align 400 copies of the same density map into a circle
by SHIQING LIAO 16 May '22

16 May '22

Hi there, I am a new user and would really appreciate any input on the task I want to do using Chimerax. Currently I have a mrc map, and it is a part of a cylindrical tube-shaped structure (like the area I drew in the picture). The map looks like a curved plane from the side of the cylinder, if it helps. If I piece 400 identical copies of map with some rotation and transition, I would ideally get a cynlider shaped strutcure, without top and bottom (like the picture below). The reason why I want to piece the mrc together is that I don't have the full look of the tube, but I know the rough radius (that's how 400 was derived), and I want to make a model for the full tube, using the model of the composing protein. I managed to manually fit the models of individual protein into one map. For the other mrc copies, I tried to do the same again but it took a lot of time and not very accurate, so I'm looking for any coding solutions that might help. I'm currently thinking if it is possible for me to place a marker at the center of one mrc map. Then make 400 copies of the map with the marker. Then write a code to tell each 1/400 mrc map to rotate 0.9 degrees around the marked center and move to a coordinate. Then I can repeat the same for the protein models I mapped to one mrc map. But I have no idea how to achieve it, and any suggestions would be greatly appreciated! Thank you so much for helping me!!! Best, Shiqing [image: cf23fde5-632f-4568-9700-9307f24e0f6c.png]

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crossfade issue
by Omid Haji-Ghassemi 16 May '22

16 May '22

Dear ChimeraX community, I am having some issues with the crossfade command while making a movie. For some reason the command stretches out the image while running the transition. I am just doing a simple transition for a movie as part of a more complicated movie. To illustrate the problem I made a simple script that reproduces the issue. movie record supersample 3 size 640,480 wait 60 crossfade; cartoon hide #1/D-F; wait 60 movie encode framerate 60 output test.mov Be great if someone can let me know what I am doing wrong. Best, Omid --------------------------------------------------- --------------------------------------------------- Dr. Omid Haji-Ghassemi Assistant Professor, Biological Sciences Department University of Calgary https://hajighassemilab.org

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Re: [chimerax-users] [Chimera-users] Making a movie from map series while keeping map's colors
by Elaine Meng 16 May '22

16 May '22

Hi Michal, Since this is a ChimeraX question I'm putting it on chimerax-users(a)cgl.ucsf.edu -- otherwise the Chimera users will be confused! In the future you may want to use that address for ChimeraX questions. If I remember correctly, "vseries" re-renders the surfaces at the time of playback, unless you specify storing more of them with the "cacheFrames" option -- so try using "vseries" with "cacheFrames 20": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html> See previous answer to a similar question: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003271.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 16, 2022, at 12:45 AM, Michal Arie Shmuelov via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi everyone, > I have 20 maps (from 3D variability analysis) that I open as series in chimeraX. > I’m coloring the map series using the command “color zone #X near #X distance X” (coloring the map according to pdb model). > Next I’m trying to make a movie of this map series while retaining the map colors. > For some reason when the morph/ vseries starts to run the colors disappear. > Can someone help me to solve this problem? > What are the commands that I should write? > Thanks, > Michal >

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Python code for obtaining chain information
by Shubham Devesh Ramgoolam 16 May '22

16 May '22

Hi, I hope you are doing well. I have a python script in which I need generate a list of all the chains present in a structure: e.g [A,B] However, I do not know which module to import in order to write a code for this. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Showing Bond/PBond to Cartoon/Ribbons
by Anderson, Jacob 13 May '22

13 May '22

There has been a prior post on this problem, but I wanted to ask about some asymmetry I see in ChimeraX when displaying residues emanating from ribbons/cartoons. https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002850.html For example, sometimes when I select a residue on a ribbon/cartoon and write "show sel atoms,bonds", I get a floating residue. However, other times I get a nice connection between the beta carbon and the ribbon (the desired behavior). How can users get a consistent behavior where there is a connection from the beta carbon to the ribbon? Good Example - connected to ribbon [cid:6ddcc2ee-f9b2-4060-8e3f-fde8ccc74881] Two floating examples: [cid:46516984-036d-4a39-9713-9056a161548a]

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no gui mode and redirecting output of some commands
by Shubham Devesh Ramgoolam 12 May '22

12 May '22

Hi, I hope you are doing well. I have a python script (myscript.py) as follows: from chimerax.core.commands import run import os os.chdir("C:\\Users\\Shubham\\Desktop") run(session, "open C:\\Users\\Shubham\\Desktop\\PDB_Script\\1ebt.pdb") # location of my pdb file run(session, "sel aromatic & protein") run(session, "log clear") run (session, "info residue sel") run(session, "log save aromatic_list.html") I am using the following prompt for calling chimerax from command prompt: Gui enabled: chimerax --script C:\\Users\\Shubham\\Desktop\\myscript.py Gui disabled: chimerax --nogui --script C:\\Users\\Shubham\\Desktop\\myscript.py With gui mode enabled, the html file, aromatic_list.html, is created. However, when disabling gui, nothing is created. I suspect this is because I am relying on the log which may not be functional when gui is disabled? Is there a way of redirecting the output of certain commands (e.g info, distance, angle) to a desired text file when disabling gui? I tried with sys.stdout but it did not work (empty text files were created.). Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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interface plot
by Pranav Shah 12 May '22

12 May '22

<3 <3 <3 <3 <3 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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Cartoon “Highlight color” and “Suppress false” Feature
by Gupta, Arun 12 May '22

12 May '22

Hello ChimeraX team, I am just wondering whether the “Pymol Cartoon highlight color” feature of helix and strand has been brought in the newer or the daily build versions of the ChimeraX. Someone has been just recently verbally referring to me that this feature has been updated in the newer versions of ChimeraX, but I couldn’t locate the mention in the ChimeraX mailing list. Also, I have noticed that “cartoon suppress false” command doesn’t work for the NMR ensemble PDBs I think it's more to do with specifying the “cartoon suppress false” command for the individual PDB model within ensemble PDBs. I did try to play around with selection notation for individual model with “cartoon suppress false” command but couldn’t get it right. Can you please specify the exact command notation to work around with NMR ensemble PDBs Thanks! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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Model number of geometric objects(axes, planes)
by Shubham Devesh Ramgoolam 11 May '22

11 May '22

Hi, I hope you are doing well. I am writing a python script to do the following: 1. Define planes and axes 2. Measure the angle between specific planes and between specific plane and axis The issue I am facing is that I need the model number of these geometric objects when using the command angle. Is there a command that will give the model number of the geometric objects? (In chimera, I would assign a number to the geometric objects when defining them and I would refer to it in the command angle. In chimeraX, I could assign a name to the geometric object but the command angle accept only model number for axes and planes.) Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Re: [chimerax-users] [Chimera-users] Get rotation between two views?
by Elaine Meng 11 May '22

11 May '22

Hi Oliver, Not exactly -- the closest thing I can think of is ChimeraX command "view matrix" but then you'd have to figure it out by comparing the camera matrices given for the two views, if that's even possible. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix> When I make figures that differ by N-degree rotation I have to just save one view, then use a command to make that exact rotation, and then save another view before saving the session. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2022, at 8:50 AM, Oliver Clarke via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > In either Chimera or X, is there a way to obtain the orientational relationship between two views? > > E.g. if I have two views saved, I would like to be able to say "view 1 is related to view 2 by a 45deg rotation about X and a 25deg rotation about Y" - this would be very useful for figure making/writing purposes. Does this exist? > > Cheers > Oli

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select atoms nearest to chain
by Pranav Shah 10 May '22

10 May '22

Hi Elaine, How does one select atoms on one chain that are close to another chain based on a distance cut off? for eg: chain A and B form an interface. I now want to know which residues on chain A fall within a distance of 4Å from chain B and vice versa. 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

2 2

AlphaFold colouring of models predicted outside of ChimeraX
by James Hodgkinson-Bean 10 May '22

10 May '22

Hi Recently I’ve been performing batch AlphaFold predictions on colab. I was wondering if it’s possible to apply the confidence colour pallete to these structures in chimera if they have not been predicted in ChimeraX directly? Thanks, James.

2 2

exporting crosslinks histogram
by Pim Huis in 't Veld 10 May '22

10 May '22

Dear ChimeraX team, I am analysing multiple datasets generated using crosslinking-ms, loaded as separate pseudobond files on my model. The crosslinks histogram plots works just fine and I’d now like to put some plots neatly side-by-side. My questions: - can the histogram be saved or exported? Ideally as an svg or pdf file. But png or jpg would also already be useful. I could export the .pb files and plot them elsewhere, but that seems like a workaround. - is it possible to specify the x and the y axis of the generated histograms, as well as the bin size? This would be helpful to show them side-by-side. Many thanks in advance, Pim -running v1.2.5 on mac os catalina 10.15- --- Pim J. Huis in ’t Veld, PhD Postdoctoral researcher in the lab of Andrea Musacchio Dept. of Mechanistic Cell Biology Max Planck Institute for Molecular Physiology ---

2 1

Align Structures at Specific Residues
by Cameron Larson 10 May '22

10 May '22

Hello, I would like to know how to align structures at specific residues. For example, how do I align an ion channel at the selectivity filter instead of aligning the entire structure? Does this ability exist with chimeraX? -Thanks CL

3 2

exporting crosslinks histogram
by Pim J. Huis in t Veld 10 May '22

10 May '22

Dear ChimeraX team, I am analysing multiple datasets generated using crosslinking-ms, loaded as separate pseudobond files on my model. The crosslinks histogram plots works just fine and I’d now like to put some plots neatly side-by-side. My questions: - can the histogram be saved or exported? Ideally as an svg or pdf file. But png or jpg would also already be useful. I could export the .pb files and plot them elsewhere, but that seems like a workaround. - is it possible to specify the x and the y axis of the generated histograms, as well as the bin size? This would be helpful to show them side-by-side. Many thanks in advance, Pim -running v1.2.5 on mac os catalina 10.15-

1 0

Crossfade just one element
by Rabuck-Gibbons, Jessica 09 May '22

09 May '22

Hello, Would there be a way to apply crossfade ust one part of the model while making a movie? For example, I’m trying to make a movie of several different ligands in one protein. In Chimera, I can show or hide the ligands over a certain number of frames, but this functionality doesn’t seem to exist in ChimeraX. Crossfade is the closest command, but it crossfades the rocking motion as well as the show and hide motion. Is there a way to get around this? Thanks, Jessica [cid2741084884*image001.png(a)01D84823.06CD9060]<https://www.takeda.com/> [cid2741084884*image002.jpg(a)01D84823.06CD9060]<https://www.takeda.com/> Jessica Rabuck-Gibbons Scientist I, Structural Biology Drug Discovery Sciences Takeda Development Center Americas, Inc. (TDCA) 9625 Towne Centre Drive San Diego, CA 92121 USA jessica.rabuck-gibbons(a)takeda.com<mailto:jessica.rabuck-gibbons@takeda.com> The content of this email and of any files transmitted may contain confidential, proprietary or legally privileged information and is intended solely for the use of the person/s or entity/ies to whom it is addressed. If you have received this email in error you have no permission whatsoever to use, copy, disclose or forward all or any of its contents. Please immediately notify the sender and thereafter delete this email and any attachments.

2 1

Side by side view in ChimeraX (like pymol grid_mode)
by Thibault TUBIANA 06 May '22

06 May '22

Hello all :-) In ChimeraX, is there a way to display multiple models into the same windows like the "grid_mode" mode in Pymol ? Thank you! Best regards, Thibault Tubiana.

2 2

Chimerax scripting error and passing user supplied arguments
by Ryan Woltz 06 May '22

06 May '22

Dear community, I'm sorry if this is a repeated question, I've seen a few posts about taking in a file for the command line and doing some things then exiting. I got most of this down and I'm sure at this point it is just a matter or correcting a few lines of code. I'm trying to automate a protein modeling protocol and I have 1000 decoys at this point. Now I need to insert the 5 metals into 5 different pockets into all my decoys for a final relax before selecting my top model. I have a template pdb with all the metals in place. For 4 of these metals I have used rosetta align mover to align a decoy onto the template around a single metal binding site, save the pdb, then add on the metal coordinates then repeat for the next binding site. So this method works because the chain is continuous around these metal binding sites. However the final metal binding site is in the center and coordinated by 4 chains coming together and the positioning needs to be very precise. Chimera or chimerax solves this very well but I don't know how to put this into a script. I have a few solutions if someone can help me edit this to work. My script (chimera-data-processing.cxc) looks like this right now. cd results/ open S_0001_X-4-all-chain-A.pdb ###X = 1-1000 open hsk2-cam-homology-from-map-refined-6cno-alignment-template-1-all-chain-A.pdb info align #1:240-244,765-769,1290-1294,1815-1819@o to_atoms #2:240-244,765-769,1290-1294,1815-1819@o matchAtomNames true; wait 300 save S_0001_X-4-all-chain-A-sf-aligned.pdb #1 format pdb relModel #2; wait 30 cd ../ close quit This script is perfect if run for have a single model with the exact name written into the script after typing: chimerax-daily --nogui chimera-data-processing.cxc I have two main solutions A) run a while loop that counts down and passes a filename to chimerax: while ( X < 1000 ) chimerax-daily --nogui chimera-data-processing.cxc S_0001_X-4-all-chain-A.pdb hsk2-cam-homology-from-map-refined-6cno-alignment-template-1-all-chain-A.pdb Where in the chimerax script I take the arg1 (S_0001*.pdb) and arg2 (hsk2*.pdb)(assuming chimera-data-processing.cxc is arg0) and modify to look like this: open $arg1 open $arg2 ... save $arg1-sf-aligned.pdb #1 format pdb relModel #2; wait 30 Option B is to use the foreach command described in the open command documentation ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html) However, a copy and past of that command: *open myscript.cxc foreach ~/data/*.cif * *or* *open chimera-data-processing.cxc foreach results/S_0001_*-4-* all-chain-A.pdb results in this error: Missing filename suffix foreach I also tried this: chimerax-daily --nogui chimera-data-processing.cxc foreach results/S_0001_*-4-all-chain-A.pdb But it just runs the command. this seems to ignore everything after the first filename. I also read that if I used foreach inside the script I could use $file to replace the filename it is currently working on, would there be a way to fave $file1 and $file2? to automate this I'd also like the change the name of the template file I'm aligning to. I also attempted the python method using sys.arg = arg[1] then running things but I couldn't get it to work because I have no experience in python. What is the suggested way to complete this task? Again this is in a much larger script with user inputs so ideally it would look like this in a script (very shorthanded just for the concepts). I can also run a python command script in my bash sctipt pdb transformations if (y = 5) ###alignment metal number) while ( x < 1000) ###arg0 = command script arg1 = pdb to align arg2 = template pdb with metals chimerax-daily --nogui chimera-command-script.cxc $filenamebase$x-$alignmentnumber-*.pdb $template.pdb ###strings for variables are provided when script is initialized. ###code to extract metal coords for S_0001_$x-4-*.pdb done fi chimera-command-script.cxc: open arg1 open arg2 align model #1 to model #2 on specific atoms save arg1-new-filename.pdb close exit if someone would like a follow-up email with my attempt at chimera python sctipt using runcommand I'm very happy to supply that as a foundation to help fix, I just thought this one is easier to fix since it is really close, the script works but only for 1 pdb at a time. Apologies for bad scripting terminology and confusion with python, I've had to teach coding to myself so I might have misused terms. Thanks for any help that can be given, Ryan

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volume threshold-level
by Dmitry Semchonok 05 May '22

05 May '22

Dear colleagues, Is there a tool in chimeraX that can set the correct volume threshold level when the Molecular weight of the molecule is known? Thank you! Kind regards, Dmitry

3 2

transparency vs. opacity
by Pranav Shah 04 May '22

04 May '22

Hi Elaine, I am trying to control the opacity/transparency of maps..however it seems to me that these two different concepts within the framework although they are used to achieve the same effect... My understanding is that transparency controls the surface being displayed whereas opacity controls the opacity of the color assigned to the surface. Is there room to unify these two concepts in ChimeraX? On an operational level, how do I control the opacity of a color in chimeraX commandline? Currently I am assigning colors based on hexcodes for specific shades... but there isnt a way to take into account the opacity of that shade with hexcodes only... 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

2 1

fitmap
by Dmitry A. Semchonok 04 May '22

04 May '22

2 1

Color by RMSD for nucleic acid
by Rundlet, Emily 03 May '22

03 May '22

Hi ChimeraX developers, Is there a way to color nucleic acids by seq_rmsd? When I use the following, no atoms are colored. mm #1 to #2 matrix Nucleic showAlignment true color byattribute seq_rmsd #2 Thank you in advance for your help! -Emily ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer

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security bug in ChimeraX 1.1 and earlier on WIndows
by Greg Couch 03 May '22

03 May '22

FYI, ChimeraX uses the Qt user interface toolkit, and recently a security bug was found in it on Windows. It affects ChimeraX 1.1 and earlier. See https://kb.cert.org/vuls/id/411271 for details. Our recommended fix is to update to the current version of ChimeraX. -- Greg

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Help pages tool hyperlink from Tool index
by William Hofsøy 02 May '22

02 May '22

Hi, I am currently writing some help pages for my tools and noticed that on the Tool index page in the chimerax help pages my tools get listed but not hyperlinked to the pages I write. Is there a way I can fix this? I also noticed that my commands are not listed here. --William

2 1

Dali server alignment
by HONG ZHAN 02 May '22

02 May '22

Dear all, I am trying to align molecules based on Dali server output. However, I can’t download the superposition results from the Dali server webpage (or anyone know?), but I can generate an alignment file with 2D structural alignment from the Dali server. Is there a way to use matchmaker to superpose molecules based on output alignment from Dali server? How to run structure conservation calculation to color the molecule? If I just give Dali’s alignment file, it still calculate conservation based on sequence not structure. Best, Hong

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Re: [chimerax-users] ChimeraX question
by Tom Goddard 29 Apr '22

29 Apr '22

Hi Ryan, ChimeraX has a "morph" command. Here's an example using it open 2vaa open 2vab matchmaker #2 to #1 morph #1,2 save morph.pdb model #3 allCoordsets true Morphing of course only contains the atoms that are in both structures. So if you have an unbound and a bound state, and the bound tapasin is only in one structure then it will not be included in the morph since there is nothing to morph it to in the unbound state. You can delete chains that the two structures do not have in common before morphing, or you can use the same true option to the morph command "morph #1,2 same true" which will ignore chains which do not appear in both structures. Tom > On Apr 29, 2022, at 9:28 AM, Kissinger, Ryan (NIH/NIAID) [C] <ryan.kissinger(a)nih.gov> wrote: > > Hi Tom, > > I’m trying to create a morph animation in ChimeraX and I am having a lot of trouble finding decent tutorials online. I have pdb entries for unbound MHC1 and Tapasin and bound MHC1 and Tapasin. If possible I would like to morph between the bound and unbound forms. I would like to do this with ribbon and the atomic models. Any advice? > > Best Regards, > > Ryan

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Re: [chimerax-users] ChimeraX crossfade
by Elaine Meng 28 Apr '22

28 Apr '22

> On Apr 27, 2022, at 9:43 AM, Daisy Sassoon <DES867(a)student.bham.ac.uk> wrote: > > Hi Elaine, > I hope you are well. > I am currently making an animation using chimeraX and am having some issues using the crossfade command. Crossfade will successfully fade colour changes until I try and record the animation. When using movie record/encode, the crossfade function blacks out the entire screen. I have tried extending the wait times after but this does not change anything. > Do you have any advice? > > My code is shown below: > [... edited out by Elaine ...] > > Many thanks, > Daisy > > Sent from Mail for Windows Hi Daisy, I don't know why it doesn't work for you. I tried your script and for me, the recorded movie looks the same as what is shown interactively. Unless you are including data that needs to remain private, it is best to send questions to chimerax-users(a)cgl.ucsf.edu so that any other experts can respond, or if it is a bug, use Help... Report a Bug instead of sending e-mail. (Report a Bug will still send notifications to the team, including any information you type into the dialog plus other information like what ChimeraX version you are using and on what type of computer. It may be an issue with the graphics on your specific system.) I'm CC-ing chimerax-users(a)cgl.ucsf.edu on this reply but omitting your script in case it needs to remain private. However, here are some specific notes on the script: (1) the "view 3" command causes an error so I had to comment it out of your script to try it (2) there is no reason to "select all" unless you really want a green outline around everything, including the 2D label text (3) although your "crossfade 100" command works fine for me both with and without recording, you could also try using "movie crossfade frames 100" ... however, the results are slightly different. The crossfade command shows movement at the same time as the fade, whereas the movie crossfade command does not show any movement during the color fade. They are both valid commands, just different ones. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#crossfade> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Apple silicon (M1 chip) native version?
by Jeffrey D. Hartgerink 28 Apr '22

28 Apr '22

Are there any plans for an Apple Silicon (M1 chip) native version of ChimeraX? While things work ok via the Rosetta emulator, it would be great to have the performance from a native app. -------------------------------------- Jeffrey D. Hartgerink, Ph.D. Prof. of Chemistry and Bioengineering Rice University, MS 602 6100 Main Street Houston, TX 77005 jdh(a)rice.edu / 713-348-4142 hartgerink.rice.edu

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Can not save image as tiff format
by 张宁 27 Apr '22

27 Apr '22

Hello ChimeraX group, I want to save the image as tiff format, but it gives me the error "No map chosen to save", could you please help me address this issue? here are two screenshots. Thanks, Ning

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Re: [chimerax-users] [Chimera-users] Questions in ChimeraX comparing with Chimera
by Elaine Meng 27 Apr '22

27 Apr '22

Dear Long Gui, (1) There is no way to open more than one session file in the same instance of ChimeraX, sorry. You can open multiple data files, of course, and have multiple maps, structures, etc. all at the same time, just not from multiple session files. (2) I'm told that the current way to show solid style (also called image style in ChimeraX) planes with zero transparency is to use command volume #2 colormode l8 (the last thing is the letter L except lowercase l and the number 8). See image display options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid> Theoretically the following command should also work but currently does not: volume #2 transparency 0 ...although a low almost-zero number should work: volume #2 transparency 0.01 See general display options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 27, 2022, at 11:25 AM, Long Gui via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera users, > > I have been recently transferring to ChimeraX from the conventional Chimera and I am currently struggling with two features existing in Chimera but not in ChimeraX. > > • How could I combine two or several different ChimeraX files? I have been doing in Chimera as I was opening new chimera files by "Files...Open...", this is a window pop-up as the following and if I click "No", the new Chimera will be added to the cold Chimera as the old one was not closed. However, when I performed the similar operation in ChimeraX, there is no such window and the new ChimeraX would REPLACE the old one. I wonder if there is a way (probably using command to open? but I did not find the correct open options.) to open the new ChimeraX without closing the old one? > <save.png> > • I am also working with tomogram slices and cellular segmentation. Previously, in Chimera I can set this Transparency value to 0 and the Plane of the tomogram will be totally opaque. Now in ChimeraX I have used the command "transparency #2 0" (#2 is the tomogram files) but it still look quite different from my previous images in Chimera. Is there a way to set it up in ChimeraX so it could look similar as before? > <Transparency.png> > > Thanks again and I am very grateful if any advice or help could be provided. > > Long Gui, Ph.D. > Postdoc Researcher, Nicastro Lab > University of Texas Southwestern Medical Center

1 0

Identifying residues based on PAE plot?
by mailman-bounces＠cgl.ucsf.edu 27 Apr '22

27 Apr '22

From: "Jan Gebauer" <jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de>> Subject: Identifying residues based on PAE plot? Date: April 27, 2022 at 3:04:30 AM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Reply-To: "Jan Gebauer" <jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de>> Hi everyone, love the "new" work in the dailys for ChimeraX and visualising the PAE and pLDTT scores. As I calculate my AF structures on my own, this helps a lot to analyses the structures. I have one question/suggestion however: If I select a region in the PAE plot, it gets coloured in the the "3D-view", however, I found no way to actually get the residues number or a proper selection for the coloured residues. Is there a way? I'd like to colour multiple selections differently... Another nice feature would be a pLDTT plot, as this enables easier detection of unordered stretches... As always: Many thanks for all the good work! Best Jan -- Dr. Jan Gebauer | 💎 Head of C2f |🔬 Member of AG Prof. Baumann Institut für Biochemie | University of Cologne Zuelpicher Str. 47 | 50674 Cologne | Germany 📞 +49 (221) 470 3212 📠Fax: +49 (221 470 5066) 📧 jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de> 🌐http://px.uni-koeln.de/ <http://px.uni-koeln.de/> 💎Visit the Cologne Crystallisation facility (C2f) !🌐http://c2f.uni-koeln.de/ <http://c2f.uni-koeln.de/>

2 1

Trouble running ChimeraX 1.3 on Windows 7
by Yu Zhou 27 Apr '22

27 Apr '22

Hi there, I got this error message "api-ms-win-core-path-l1-1-0.dll is missing" when i tried to run ChimeraX 1.3 after installation. My OS is Window 7 and I have no trouble running ChimeraX 1.2.5. I greatly appreciate your help. Yu Zhou

2 1

Unable to restore session: need to update bundle
by Rafael Molina 27 Apr '22

27 Apr '22

Dear ChimeraX staff, I cannot restore a ChimeraX session and ChimeraX suggests to update atomic bundle to version 1.31 or newer (have 1.13.2). When I go to all bundles (https://cxtoolshed.rbvi.ucsf.edu/apps/all <https://cxtoolshed.rbvi.ucsf.edu/apps/all>) I cannot find the way to update it properly. Could you help me to fix the error? Thx ---------------------------------------------------------- Rafael Molina, PhD Dept. Crystallography & Structural Biology. Institute of Physical Chemistry Rocasolano Spanish National Research Council (CSIC) Serrano 119. 28006-Madrid. Spain Phone: +34 91 561 94 00 ext. 961121 E-mail: rmolina(a)iqfr.csic.es <mailto:rmolina@iqfr.csic.es> My Research Gate Profile <https://www.researchgate.net/profile/Rafael-Molina-11> ----------------------------------------------------------

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Re: [chimerax-users] [Chimera-users] Tomogram display
by Elaine Meng 26 Apr '22

26 Apr '22

Hi Shen, If you are asking whether ChimeraX has similar features to Chimera: (1) yes, ChimeraX has a volume viewer tool and "volume" command for density maps, with many of the same options as Chimera <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> (2) ChimeraX has the same fitting into maps as Chimera <https://rbvi.ucsf.edu/chimerax/docs/user/tools/fitmap.html> (3) ChimeraX also includes segmentation <https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.html> (4) similar to Chimera's Volume Tracer, ChimeraX has markers and links and tools for placing them into maps <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html> Details between the two programs are not exactly the same, however. There may be some specific thing you need that still requires Chimera, but you can certainly use both programs. To ask questions about ChimeraX specifically, you may wish to use the other mailing list chimerax-users(a)cgl.ucsf.edu CC'd here. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 26, 2022, at 5:13 AM, Han, Shen via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > I want to ask some questions regarding displaying tomogram in ChimeraX. is it possible to reveal the density in the tomogram and trace the objects throughout the tomogram (also docking model in the density) in ChimeraX? > Best wishes, > Shen > _________ > Dr. Shen Han > Postdoctoral Researcher > Max Planck Institute for Multidisciplinary Sciences > Department of Molecular Biology / Cramer Lab > Am Faßberg 11, Göttingen > 37077, Germany

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Re: [chimerax-users] [Chimera-users] Creating Bonds between Models
by Elaine Meng 25 Apr '22

25 Apr '22

Hello Draven, You could continue to use Chimera for this, since there is a Join Models section in the Build Structure tool (in menu under Tools... Structure Editing). <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.…> We are at this very moment working on adding this functionality to ChimeraX, so if you get today's daily build, you can form peptide bonds between different models with the command "build join peptide" -- it is not yet available as a graphical interface, however, and the kinks are still being worked out. There is a still a bug if you specify "phi" when the model that is being moved contains more than one chain. If you want to specify "phi" but one of the models has more than one chain, use the "move" option to make the other model move instead. Here is the help for this brand-new command in my personal preview since it is not yet up on the website, although it should appear there tomorrow: <https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/commands/build.html#…> The ability to add other types of bonds (nonpeptide) between models is not available yet. You can combine multiple models into one and then form a bond, but that does not take care of positioning between the models like the joining capability above. Instead you would have to manually move the models into the proper positions first. Both Chimera and ChimeraX have a "combine" command to merge multiple models into one without repositioning. By the way, if you want to ask questions about ChimeraX specifically, there is a separate mailing list chimerax-users(a)cgl.ucsf.edu CC'd here. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 25, 2022, at 12:37 PM, Draven Houser via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, > I am trying to build a structure in chimeraX that is a combination of several other known structures. To do this I need to be able to create bonds between different models in the software, but this doesn't seem to be possible for the moment. Can anyone suggest a workaround for this? Thanks! > Best regards, > Draven Houser

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Re: [chimerax-users] [Chimera-users] Open Castp file in Chimera X
by Tom Goddard 21 Apr '22

21 Apr '22

Hi Bixia, You will need to download the read_castp.py file from that web page. Then if it is your downloads directory you would use open ~/Downloads/read_castp.py In other words you have to tell it exactly where the file is unless it is in the directory where you downloaded the file. Also you can use the ChimeraX "cd" command to change to a new current directory in ChimeraX. Best to email this question to the ChimeraX mailing list instead of the Chimera mailing list. Tom > On Apr 21, 2022, at 4:42 PM, Zhang, Bixia via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Good afternoon, > I am trying to open .poc file from CASTP server in Chimera X. And I found this chimeraX recipehttps://rbvi.github.io/chimerax-recipes/castp/castp.html <https://rbvi.github.io/chimerax-recipes/castp/castp.html>. However, when I used the command open <help:user/commands/open.html> read_castp.py, it saidNo such file/path: read_castp.py. I am working on a Linux unbuntu box and I don't know if this is making any difference. Could you please help with this issue? > Thank you so much! > Best, > Bixia > > Read CASTP pockets file - ChimeraX Recipes <https://rbvi.github.io/chimerax-recipes/castp/castp.html> > We for the ChimeraX atom specifier from chain identifier, residue number and atom name. For example, the above lines are for atoms /A:45@NH2, /B:27@O, /B:27@CG1 in ChimeraX syntax belonging to pockets 2, 1 and 1. > rbvi.github.io <http://rbvi.github.io/> > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

2 1

Re: [chimerax-users] palettes and color keys
by Martti Tolvanen 21 Apr '22

21 Apr '22

A followup question regarding palettes and color keys: Is there any way to create two color keys for two different properties or for two different models? My motivation to ask this stems from a dimer model I got from AlphaFold multimer. When I use the default alphafold palette, the individual monomers are hard to see, most of the interface being in the dark blue, marking highest confidence. I can apply a different palette to one of the chains, but it would be also nice to show the color keys for both palettes. Martti Tolvanen Lecturer in Bioinformatics U of Turku, Finland -----Original Message----- From: chimerax-users-request(a)cgl.ucsf.edu [mailto:chimerax-users-request@cgl.ucsf.edu] Sent: 12. huhtikuutata 2022 22:00 To: chimerax-users(a)cgl.ucsf.edu Subject: ChimeraX-users Digest, Vol 64, Issue 15 Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users or, via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..."

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ChimeraX command for rmsd color range in angstrom
by Dario Passos 20 Apr '22

20 Apr '22

Dear Chimera community, does anyone know how to add a range of values for the rmsd colors in Chimera X? Something like this (below) in angstrom: => *color byattribute seq_rmsd #1 palette blue:white:red threshold 0:3;6* Thanks, Dario

2 2

Toolshed backend update
by Greg Couch 19 Apr '22

19 Apr '22

FYI, the ChimeraX toolshed will be down this evening (10 p.m PDT, 5 a.m. GMT) to upgrade the back-end. If all goes well, it will be back up within an hour. There should be no user visible changes after the update. However, the back-end change will allow Bundle developers to submit bundles that have commas in the dependencies. -- Greg

1 0

Re: [chimerax-users] Render psuedobonds for RMF models?
by Tom Goddard 19 Apr '22

19 Apr '22

Hi Matthew, Yes. The coarse grain models made from reading RMF files create spheres that are actually atoms, and any atoms can be connected by pseudobonds. I don't know much about RMF in Chimera and ChimeraX. Ben Webb and Conrad Huang worked on that and Conrad retired 2 years ago. It may be that reading RMF creates pseudobonds that are specified in the RMF file. Another way to create pseudobonds is to open a pseudobond file https://www.cgl.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles <https://www.cgl.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles> For that you need to figure out the names of the "atoms" (which may represent coarse grain beads) you want to connect. You can open the RMF and hover the mouse over a sphere and a popup will show its name. Also the ChimeraX distance command can create pseudobonds https://www.cgl.ucsf.edu/chimerax/docs/user/commands/distance.html Tom > On Apr 19, 2022, at 8:41 AM, Hancock, Matthew wrote: > > This Message Is From an External Sender > This message came from outside your organization. > > Hi Tom, > > I am a UCSF graduate student in Andrej Sali's group and have a question about Chimera/ChimeraX functionality. I am curious if it is possible to render psuedobonds for multi-scale structures that are read from RMF files. Similar to how it can be done for pdb structures. > > Best > Matthew

1 0

Chimera(X) in Centos stream 9
by Antonio Díaz Quintana 19 Apr '22

19 Apr '22

Dear all, I am unable to install Chimerax and Chimera—yes I still use the old one because its great tools—using the rpm package in Centos Stream 9, because lack of LibOSMesa package in this distribution. I tried using dnf, but a mesa-libGL library (21.3.4...) is already installed Similarly, it seems my OS distribution does not contain python Tk, nor I can get suitable python with Tk-devel from repository, so I get the following message. Could I get any help? Meanwhile I got it on my old Win10, 11 years-old laptop. Both programs work well there. Best, Antonio -- Dr. Antonio J. Díaz Quintana Instituto de Investigaciones Químicas Universidad de Sevilla - CSIC Avda. Americo Vespucio 49 41092 Sevilla Spain Phone: +34 954 48 9631

1 0

matchmaker question: restrict moving parts to selection?
by Vorländer,Matthias Kopano 18 Apr '22

18 Apr '22

Hi everyone, Is it possible to align parts of a model to another while only moving the specified residues but not the rest of the molecule? A use case would be having an alphafold model from one species where the individual domains are correctly predicted, but don't agree with the relative orientation of the domains observed in a reference structure from another species. I envision this similar to the "fitmap" option "moveWholeMolecule false". Example: Mm #1:100-200 to #2/100-200 MoveWholeMolecule false This should leave the residues 1-99 in model #1 unchanged. I hope my question is clear. Thanks a lot in advance, Matthias Get Outlook for Android<https://aka.ms/AAb9ysg>

3 4

Saving multiple MRC with derivative names
by Nebojsa Bogdanovic 18 Apr '22

18 Apr '22

Hi, I was looking into the possibility of saving 5 mrc maps after batch z-flipping them. The commands would looks something like this: 1. cd /folder/with/maps 2. open *.mrc 3. volume flip #1-5 4. save [name]*-zflip*.mrc models #6-10 Ideally, the script would save each new (flipped) map as a new .mrc with the suffix "-zflip" or whichever suffix user specifies in the script line 4. Is there such an option if it's implemented? Thank you for the awesome ChimeraX Best regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

2 1

0417_1
by 泡沫 17 Apr '22

17 Apr '22

How do you make similar pictures 发自我的iPhone

2 1

Hello
by Brandon Palmer 13 Apr '22

13 Apr '22

My name is brandon palmer I work with Biocryst and came across your software. So far been reading through and I enjoy it's features, and I had a question. Would you happen to have apk version for the use of a Vive 3 Headset? CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 1

Re: [chimerax-users] [Chimera-users] Chimera X color by attribute middle range value
by Elaine Meng 12 Apr '22

12 Apr '22

Hi Marcell! In ChimeraX, you can control which colors go with which values in the "palette" option of the "color byattribute" command. This option can take color/value pairs, and the "range" option is not needed in your situation (if I understand correctly). As you found, if you only give the range, it will spread out the colors evenly. Here's an example of value,color pairs if you want to color by attribute named "blah" using dodger blue for 0.2, red for 1.0, and gold for 4.0: color byattr blah palette 0.2,dodgerblue:1.0,red:4.0,gold <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> There are lots of named colors, although you could use hex codes instead if the named ones aren't quite what you want. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html> ChimeraX does not yet have a color-by-attribute GUI although that is something we would like to have eventually. The Color Key tool is just for drawing a color key to explain the coloring, but does not itself affect the structure coloring. By the way, you may be interested in the chimerax-users(a)cgl.ucsf.edu mailing list (CC'd on this reply) for questions/discussion specifically about ChimeraX. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 11, 2022, at 5:07 PM, Zimanyi, Marcell via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Chimera Community, > > I have a .defattr file where I have assigned a value to a few residues on my protein. I'd like to set the range to be 0.2, 1, and 4 so that values with 1.0 will be the middle color. I currently don't see a way to set the middle value for the range. In Chimera, I could set the middle range value in the define attribute GUI. In Chimera X, I'm using color byattribute range 0.2,4 because the range argument will only accept two values. I see that I can bring up the color key gui, but when I change the color key I don't see a way to update the coloring on the residues themselves. > > Could you please help me figure out how to set attribute range with 3 values as in Chimera? > > Thanks, > Marcell

2 1

Command line disappared
by mhc128＠student.bham.ac.uk 12 Apr '22

12 Apr '22

Hello, I am currently completing a project requiring use of ChimeraX. I'm new to the program, and somehow the command line itself has disappeared for me. I have looked throughout the help section but could not find anything specific on re-enabling the use of the command line. Is there anything I am missing? Thanks for your time.

4 4

Setting the same sdLevel threshold for several volumes
by Moisés Maestro López 11 Apr '22

11 Apr '22

Good morning, I would like to set the threshold of multiple CryoEM Volumes (10-20) at the same time, and I would like to put all of them at the same sdlevel. I use the command: volume #1 sdLevel 2 But this only work for one volume, if I use volume all sdLevel 2, or volume #1 #2 #3 sdLevel 2 It does not work and the threshold are random. In chimera I had a script that I use for doing that but I have not found the way to do it in ChimeraX. In Chimera, I normally called the script with an alias. alias ^allsd runscript ~/chimeraScriptSD.py allsd 3 And the script (chimeraScriptSD.py) was: import sys import chimera from VolumeViewer import Volume mlist = chimera.openModels.list(modelTypes=[Volume]) sdlevel = 2 if len(sys.argv)>1: sdlevel = sys.argv[1] for m in mlist: chimera.runCommand('volume '+str(m)+' sdlevel '+ str(sdlevel)) But I do not know how to do this in ChimeraX. The key point I do not know how to do is to do a loop that say “for any volume in all the opened volumes”. Thanks for your help Moisés

2 4

Dependency trouble
by William Hofsøy 08 Apr '22

08 Apr '22

Hi, I was attempting to install my chimerax bundle on a different computer and encountered the error: No module named 'PyQt5' So I added this line to the bundle_info.xml under the Dependencies tag: <Dependency name="PyQt5"/> But I still get the same error?

4 6

Re: [chimerax-users] [Chimera-users] Openning XYZ files with ChimeraX
by Elaine Meng 07 Apr '22

07 Apr '22

> On Apr 7, 2022, at 5:29 PM, Henrique Castro via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, everyone, > I'm trying to adapt to ChimeraX and when trying to open an XYZ file I'm receiving the message "Opener for format 'XYZ file' is not installed; see log for more info". Is it possible to work with his format as in the Classic Chimera? > -- > Henrique C. S. Junior Hi Henrique, The message said to look at the Log, where it says: Install the SEQCROW bundle to open "XYZ file" format files. ... and "Install the SEQCROW bundle" is even a link that you can click to go directly to the SEQCROW installation page. So try installing that (which is easy, just click "Install") and then try opening your XYZ file. By the way, for asking questions about ChimeraX specifically, we recommend using the address chimerax-users(a)cgl.ucsf.edu (CC'd on this message). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

wynton --nogui : how to use cd command ?
by Rangarajan, Amith 06 Apr '22

06 Apr '22

Hello everyone, i am new to using chimerax in --no gui mode $ chimerax --nogui UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. cmd> pwd Executing: pwd Current working directory is: /wynton/home/jacobson/avranga1008 cmd> cd /wynton/scratch/avranga1008/0-binana/0-docked-poses cd /wynton/scratch/avranga1008/0-binana/0-docked-poses ...^ Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword please share your thoughts on how to change dir in the no gui mode. thanks, amith

3 2

measure neighboring distance of histidine side chain
by HONG ZHAN 05 Apr '22

05 Apr '22

Dear all, I am interested to get a list of distances between histidine residues in my built model. Because I would like to see which crosslinker can potentially help to maintain the structure better during purification. I have noticed that I can measure one residue in chain A to all other atoms in chain B using contact function, however, I want to get a list of distances between any histidine imidazole (neighboring distance), is there a way to do that in ChimeraX? Super thanks in advance. Best, Hong

2 2

display options for model with 2 chains
by Mauricio Losilla 05 Apr '22

05 Apr '22

Hi, I am new to ChimeraX, thank you for making this great software available. I loaded a pdb file that has 2 amino acid chains aligned (chimerax.png). These chains are a model (gray) and template (purple). As you can see, the two chains look weaved or blended. I would much prefer to display the uninterrupted template around to model, to visually represent their fit. Is there a way to do this? I am attaching a second image (ideal_display.png, generated elsewhere) with the visual outcome I am after (the purple chain is the template, the rainbow-colored chain is the model). Thank you *Mauricio Losilla, PhD* Integrative Biology; and Ecology, Evolution, & Behavior Michigan State University he, him, his

4 16

Trouble with imports in ChimeraX bundle
by William Hofsøy 05 Apr '22

05 Apr '22

Hi, I have been doing some restructuring and refactoring of my project and started having trouble with my imports and modules not being found. previously all my imports were relative for instance: "from . import tool" However this is a bit impractical now that I have a folder structure, so I have been trying to use absolute imports like from "src.toolname.pythonfile import class" but it seems my folder structure differs from how it is after installing it into ChimeraX. I am using pycharm as my editor and the automatic import paths they set up also fails, meanwhile i looked at the sys.path and there the structure is chimerax/packagename where packagename contains the files contained in my src. So I was wondering if there is a way to set this up properly?

2 1

Selection of the specific state from multi-model PDB
by Enrico Martinez 05 Apr '22

05 Apr '22

Dear ChimeraX users! Working in ChimeraX with multi-model PDBs I may use the following command to close all states but not the first (1.1): close #1.2-end How could I keep only the desired state (e.g I would like to display only the state #1.5 and close others)? Many thanks in advance Cheers Enrico

2 1

Feature Request From Chimera
by Anderson, Jacob 05 Apr '22

05 Apr '22

Love ChimeraX - the UI is really enjoyable! I was curious if I could put in a plug for biomtSet true option to be ported to ChimeraX's sym command! I expect a lower priority, but would love to use this tool in ChimeraX in some future version.

3 2

Re: [chimerax-users] [Chimera-users] Question regarding chimerax module
by Tom Goddard 04 Apr '22

04 Apr '22

Hi Prathvi, There is no ChimeraX Python library yet, it is only distributed as a standalone application including its own Python. But we have funding to make a library for PyPi and/or Anaconda so that should happen in the next year. You can use the ChimeraX Python Jupyter shell to try out Python code, menu entry Tools / General / Shell. Tom > On Apr 2, 2022, at 10:30 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello again Elaine, > > Is it possible to install the chimerax module in anaconda for usage in jupyter notebook? > > -- > Prathvi Singh, > Research Fellow, > Department of Biological Sciences & Bioengineering, > Indian Institute of Technology, Kanpur-208016 > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

2 1

Re: [chimerax-users] ChimeraX-users Digest, Vol 64, Issue 4
by Martti Tolvanen 04 Apr '22

04 Apr '22

As a pragmatic solution to the task of seeing both chains even when one is sometimes behind the other (as is inevitable with any superimposed models), you could make one ribbon semi-transparent. -Martti -----Original Message----- From: chimerax-users-request(a)cgl.ucsf.edu [mailto:chimerax-users-request@cgl.ucsf.edu] Sent: 2. huhtikuutata 2022 22:00 To: chimerax-users(a)cgl.ucsf.edu Subject: ChimeraX-users Digest, Vol 64, Issue 4 Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users or, via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..."

1 0

Saving ChimeraX log, saving protein sequence to file
by Elaine Meng 03 Apr '22

03 Apr '22

Hi Prathvi, These answers are both for ChimeraX so I CC'd the chimerax-users list. (1) ChimeraX command "log save" saves it as HTML <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html> (2) in ChimeraX, open the structure, show the sequence of the chain of interest (menu: Tools... Sequence... Show Sequence Viewer, choose chain if there is more than one chain preset). Showing the sequence can also be done with the ChimeraX "sequence chain" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#chain> Then in the sequence viewer window, the context menu has a choice to save the contents (File... Save As...). <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context> You show a context menu in ChimeraX with Ctrl-click or right-click (depending on your system) in the tool window. <https://rbvi.ucsf.edu/chimerax/docs/user/window.html#context-menu> In Chimera, #2 is similar, use main tools menu to show sequence, use sequence-viewer tool's menu to save it to file. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 2, 2022, at 9:51 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks a lot Elaine. It helped enormously. I just have 2 more questions: > > 1. After running the dssp command in chimeraX, is there a command to save the reply log to file using a command? I searched for it & landed up at: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003739.html but chimeraX throws the "Unknown command" error. > > 2. Is there a way to extract polypeptide sequence from a PDB file & save as a FASTA file or even a simple text file which simply contains a string representing the amino acids as single letters alphabets? >

1 0

How to draw the surface of cavity
by 令怡 01 Apr '22

01 Apr '22

Dear ChimeraX Staff, Hello! I would like to know if there's a way to display the cavity like this? I've been studying for a long time without a clue. Thank you for your attention! Best Regards, Lingyi | | Xu, Lingyi Ph.D. | | Zhejiang University School of Medicine | 签名由网易邮箱大师定制

2 7

Analysis of Hydrogen bonds in multi-model pdb
by Enrico Martinez 01 Apr '22

01 Apr '22

Dear ChimeraX users! Another question related to the analysis of the multi-model pdb obtained from protein-ligand docking calculations. I am using ChimeraX to visualise protein-ligand interactions between each pose predicted by docking and protein in my script: # calculate H-bond in first 10 frames of the multi-model pdb hbonds #1.1-10&protein restrict #1.1-${hb_poses}&ligand coordsets false interModel false makePseudobonds false log true intraRes false saveFile output.log Is it possible to print (or save somewhere?) the number of the state that has 1) the maximal number of the hydrogen bonds? 2) has a particular hydrogen bond of my interest? Cheers, Enrico

2 2

A question about model position matrix
by Zheng Ruan 31 Mar '22

31 Mar '22

Dear ChimeraX users, I'm trying to understand the model position matrix. According to the documentation, "Each matrix is reported as 12 comma-separated numbers, corresponding to a 3x3 rotation matrix and a translation vector in the fourth column. Ordering is row-by-row, such that the translation vector is given as the fourth, eighth, and twelfth numbers." When I load a model into ChimeraX and use "view matrix" command to check the model position, I got "#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0". The rotation matrix for #1 is an identity matrix with translation vector to be 0 for all directions. However, if I rotate the model using the command "turn z 90 models #1" and then check the model position using "view matrix", I got something like "#1,1.1102e-16,-1,0,689.33,1,1.1102e-16,0,-1.9358,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0". The translation vector for #1 becomes (689.33, -1.9358, 0). Since I only applied a simple rotation of the model along z-axis, why the translation vector becomes non-zero in this case? I hope to have a better understanding of how ChimeraX handles the model position matrix to describe model positions. Thank you so much! Best, Zheng

3 5

Bundle Module Import
by Zeng, Katie 31 Mar '22

31 Mar '22

Hi all, I am currently working on a membrane builder bundle called AmberLipidBundle. I have folder './src/ui' (containing several .py files, e.g. lipid_form.py) and I import it inside .py files with the line 'from AmberLipidBundle.ui.lipid_form import xxx'. I have been testing the bundle using the command 'devel build [path]' and everything works fine. But when I switch to the command 'devel install [path]', I get an error: chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Membrane Builder in bundle AmberLipidBundle: No module named 'AmberLipidBundle.ui' Do you have any idea how to fix this? Thank you so much for your help! Best Regards, Katie

2 2

get current clipping plane positions
by Pranav Shah 31 Mar '22

31 Mar '22

Hi Elaine and Co., Is there a way to read the current clipping plane positions in chimerax? 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

2 2

get current clipping positions
by Pranav Shah 30 Mar '22

30 Mar '22

Hi Elaine and Co., Is there a way to read the current clipping plane positions in chimerax? 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

1 0

Selection of the organic ligand
by Enrico Martinez 30 Mar '22

30 Mar '22

Dear ChimeraX users! Normally I use the selection name "ligand" to select all atoms of the organic ligand. For example: define centroid ligand name lig_com sometimes depending on the pdb file, this command also selects one residue (located in the pdb file just near the ligand), considering it also as a part of the ligand.. May I use another selection to explicitly exclude all 20 natural amino-acids from the ligand selection? Many thanks in advance! Enrico

2 2

Re: [chimerax-users] [Chimera-users] using old cmd files in chimerax
by Elaine Meng 29 Mar '22

29 Mar '22

Hi Bryan, If I understand correctly, by "old" you mean works in Chimera... and would like to know how to get to the same end results except in ChimeraX, so I also CC'd chimerax-users(a)cgl.ucsf.edu. Since ChimeraX and Chimera commands do have differences, you cannot simply open Chimera command files in ChimeraX. Possible routes to getting what you want: (1) text-edit the cmd file to change Chimera commands to ChimeraX commands, change the filename suffix of that plain-text file to .cxc and then open it in ChimeraX. ChimeraX does have the capability to read ResMap maps and then use the values to color a surface, so this is a viable route. The downside is that it requires knowing or looking up the differences in the commands. Many commands are highly similar so it wouldn't necessarily be as bad as it sounds, however. You can open both the original map and the ResMap map files with ChimeraX command "open", control which is shown as a surface with the ChimeraX Volume Viewer tool or "volume" command, and color the surface by the values of the other map using "color sample". See ChimeraX User Guide: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map> (2) or simply dispense with trying to use a command script and instead use ChimeraX tools and/or commands interactively. You can use ChimeraX menu: File... Open to open the maps (aka volume data), and there is a Surface Color tool (same function as "color sample" command): <https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html> (3) in the more general case of Chimera command scripts involving atomic data, you can open/run the script in Chimera, export a session from Chimera as a ChimeraX python file (Chimera menu: File... Export Scene or Chimera command "export") and then open that file in ChimeraX to regenerate the session contents. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html> However, this Chimera->ChimeraX export feature does not (yet) cover maps, map isosurfaces, and a few other things. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 28, 2022, at 12:01 PM, Hansen, Bryan (NIH/NIAID) [E] via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > How do I used/open old cmd scripts I have or outputs from things like resmap in chimerax? >

1 0

addh
by Voss Jonathan Mark 28 Mar '22

28 Mar '22

Hello, I would like to protonate ASP, GLU, and HIS side chains throughout a model. I'm a little confused about the syntax of the useAspName, useGluName, etc. option. I've looked around but haven't found any examples. Could you provide one? Furthermore, once a side chain is protonated, will ISOLDE recognize that site as being charged? Or does this need to be specified somehow? Best -Jon

3 3

Question about using ChimeraX
by 令怡 25 Mar '22

25 Mar '22

Dear developers, Hello! I recently encountered some problems when using ChimeraX. When displaying the structure with cartoon, some helix is displayed as loop (Fig A). How to force it to be displayed as helix? I checked the User Guide and used the command "setattr sel residues is_helix true" for the selected amino acids, but only some amino acids can be displayed as helix (Fig B). Is that need to change ss_ id? I have tried, but it didn't work. I will appreciate it if you could answer my question. Looking forward to your reply! Best Regards Lingyi

2 2

Analysis of the protein-ligand docking results with the X-ray data
by Enrico Martinez 25 Mar '22

25 Mar '22

Dear ChimeraX users! First, I very much appreciate the support of the Chimera team related to my questions! I have another question regarding analysis of the protein ligand interactions in the docking poses saved in multi-model format. I need to find a possibility (e.g. via some script that could be executed in the chimeraX) to compare each docking pose with the X-ray structure (loaded as the separate model) in order to select automatically the model (= docking solution) which may fit better to the X-ray structure. The problem is that the ligand used in the docking is not the same as in the X-ray structure (although they are quite similar in the functional groups). Assuming that the both pdbs ((docking poses, and X-ray structure)) have been superimposed (based on the protein atoms) how could I automatically switch to the model (in the docking ensemble) that has the closest position of the ligand as in the X-ray structure? Here is the example of the workflow: open docking_ensemble.pdb open xray.pdb # fit X-ray structure to the first docking solution based on the protein atoms match #2 to #1.1 # compare each docking pose (ligand with X-ray and determine which model has the most similarity to it # determine the model #1.X which would have closest similarity to the X-ray structure # close all the models, with the exemption of the model #1.X close ~ #1.X I would be grateful for any suggestions for possible algorithms! With kind regards, Enrico

2 2

Problem with ChimeraX
by Gawargi, Flobater I 23 Mar '22

23 Mar '22

Hi, I am a new Chimerax user and I have encountered a problem that I hope you can help me fix. I installed 1.4 version and it shows "Startup Messages notes available bundle cache has not been initialized yet Updating list of available bundles failed: Internal Server Error” all I am trying to do is use alpha fold to predict structure of 2 proteins separated by comma. And it shows this error "Missing or invalid "sequences" argument: Sequences argument "cvfpfvflgkqyssctsdgrrdgrlwcattsnfdtdkkwgfcpdqgyslflvaahefghalgldhssvpealmyplysylegfplnkddidgiqylygrgskpdprppattttepqptapptmcptipptayptvgptvgptgapspgptsspspgptgapspgptapptagsseasteslspadnpcnvdvfdaiaeiqgalhffkdgwywkflnhrgsplqgpfltartw" is not a chain specifier, alignment id, UniProt id, or sequence characters” I am using an M1 MacBook, but I have also tried it on windows running windows 10 and got the same issue. I would appreciate your input to fix this issue. Thank you, Flobater Gawargi The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

2 1

Re: [chimerax-users] [Chimera-users] tile function
by Elaine Meng 23 Mar '22

23 Mar '22

Hi Bryan, I'm happy to report that current versions of ChimeraX work the way that you describe. I.e. you need to get the daily build <https://www.rbvi.ucsf.edu/chimerax/download.html#daily> ...since according to the ChimeraX change log, this feature was added in January, after the 1.3 release. <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> By the way, there is a chimerax-users(a)cgl.ucsf.edu address for asking about ChimeraX, which I've CC'd on this message. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 23, 2022, at 11:39 AM, Hansen, Bryan (NIH/NIAID) [E] via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > > Is there an option with the tile command in ChimeraX to get the volumes to rotate in place like it did with Chimera or maybe a different command now that I haven’t found yet? Right now when I use Tile the maps rotate together round a single axis, but I liked it a lot in chimera with the tile were the maps rotated on their own axis. Thanks I’m sure it’s most likely a command option that I missed in the documentation or a new command I haven’t found yet. > > Bryan Hansen > Computational Biologist / Electron Microscopist > NIH/NIAID/RTB/RML/EMU > Rocky Mountain Laboratories > 903 S. 4th St > Hamilton, MT 59840 > 406.363.9202 > > *********************************************************** > The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > *********************************************************** > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

1 0

Query regarding plugin development
by KUSHAGRA RUSTAGI 23 Mar '22

23 Mar '22

Greetings, I am Kushagra Rustagi an undergraduate student at IIT Roorkee who is working on developing a ChimeraX plugin. I had some doubts: 1. Can we open a session in ipython? Basically while developing codes for chimerax is there a way to open chimera command line in ipython? 2. For example if we want to run an inbuilt function of any particular class in ChimeraX and we want to find all methods associated with that class. How do we go about doing it? 3. How to go about exploring surface generation functions in ChimeraX? Regards, Kushagra Rustagi

2 1

chimerax fails to start
by ZOUHIR Samira 23 Mar '22

23 Mar '22

Hello, I have an issue starting ChimeraX_1.3 for ubuntu20.04. "chimerax" command gives the following: NOTE: available bundle cache has not been initialized yet NOTE: Updating list of available bundles failed: Internal Server Error WARNING: WebEngineContext used before QtWebEngine::initialize() or OpenGL context creation failed. WARNING: QGLXContext: Failed to create dummy context ERROR: Could not create OpenGL context BUG: Failed to create OpenGL context for format QSurfaceFormat(version 2.0, options QFlags<QSurfaceFormat::FormatOption>(), depthBufferSize 24, redBufferSize -1, greenBufferSize -1, blueBufferSize -1, alphaBufferSize -1, stencilBufferSize 8, samples 0, swapBehavior QSurfaceFormat::DefaultSwapBehavior, swapInterval 1, colorSpace QSurfaceFormat::DefaultColorSpace, profile QSurfaceFormat::NoProfile) Aborted (core dumped) Any advice please? Best, Sam

2 1

how to vizualise hydrogen bonds between ligand and back-bone of protein?
by Enrico Martinez 23 Mar '22

23 Mar '22

Dear ChimeraX users! I am using the following command to calculate and save in the log information regarding hydrogen bonds based on the consideration of multi-frame pdb of the complex # calculate hydrogen bonds for the first 14 frames of pdb hbonds #1.1-14}&protein restrict #1.1-14}&ligand coordsets false interModel false makePseudobonds false log true intraRes false saveFile log.txt which gives me something like this: structure_name: 18 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): #1.1/? ASN 142 ND2 #1.1/A UNL 1 N #1.1/? ASN 142 2HD2 3.313 2.522 #1.1/? SER 144 N #1.1/A UNL 1 O #1.1/? SER 144 H 2.953 2.224 #1.1/A UNL 1 O #1.1/? LEU 141 O #1.1/A UNL 1 H 2.753 1.877 #1.2/? ASN 142 ND2 #1.2/A UNL 1 N #1.2/? ASN 142 2HD2 3.240 2.429 #1.2/A UNL 1 O #1.2/? HIS 163 NE2 #1.2/A UNL 1 H 3.317 2.389 #1.3/? SER 144 N #1.3/A UNL 1 O #1.3/? SER 144 H 3.005 2.272 #1.3/A UNL 1 O #1.3/? LEU 141 O #1.3/A UNL 1 H 2.738 2.098 #1.3/A UNL 1 O #1.3/? SER 144 OG #1.3/A UNL 1 H 3.054 2.250 #1.6/A UNL 1 O #1.6/? HIS 163 NE2 #1.6/A UNL 1 H 3.172 2.528 #1.7/? CYS 145 SG #1.7/A UNL 1 O #1.7/? CYS 145 HG 3.828 2.949 #1.7/A UNL 1 O #1.7/? LEU 141 O #1.7/A UNL 1 H 3.201 2.393 #1.8/? GLY 143 N #1.8/A UNL 1 O #1.8/? GLY 143 H 3.060 2.238 #1.8/? HIS 163 NE2 #1.8/A UNL 1 O no hydrogen 3.084 N/A #1.9/? GLN 189 NE2 #1.9/A UNL 1 O #1.9/? GLN 189 1HE2 3.148 2.139 #1.10/? GLN 189 NE2 #1.10/A UNL 1 O #1.10/? GLN 189 1HE2 2.941 2.289 #1.10/A UNL 1 O #1.10/? GLN 189 OE1 #1.10/A UNL 1 H 2.985 2.213 #1.11/? GLN 189 NE2 #1.11/A UNL 1 O #1.11/? GLN 189 1HE2 2.803 1.910 #1.14/? ASN 142 ND2 #1.14/A UNL 1 O #1.14/? ASN 142 2HD2 3.199 2.369 ----------------------------------------------------------------------------- I noticed that in the log there is always information regarding interactions between the ligand and the side chains of the protein but nothing regarding hydrogen bonds involved backbone of the protein (Which is confirmed by X-ray data for my complex). for the test I used py@ol to visualise h-bonds and may see in the 12th frame the hydrogen bond involved backbone of the protein.. How could I modify my script to consider additional hydrogen bonds involving backbone atoms ? Thank you very much in advance! Cheers Enrico

5 20

Drawing rotation axis in ChimeraX
by lvhailiyaohui 23 Mar '22

23 Mar '22

Dear Sir or Madam, This is Yaohui Li, a ChimeraX user educationally. We are trying to prepare a figure with rotation axis by chimeraX, but haven’g found a way to draw the rotation axis yet. Could you give us any suggestions on drawing the rotation axis in ChimeraX? Thanks a lot! Looking forward to hearing from you! Bests, Yaohui 网易VIP邮箱提醒：安全收发邮件，务必核实往来邮件地址、银行账号等机密信息，请通过电话或视频等多种方式确认信息真实性，提高警惕，请勿轻易透露个人重要信息。 Alert message of Netease Vipmail：Never provide your password, security questions, verification codes, or any other personal important information details to anyone else. You can identify mail message by telephone,video-chat or other ways.You should make sure that your email address, bank account and other confidential information as secure as possible. Thank you for keeping your email account secure.

3 3

ChimeraX does not work on windows server running RDS
by Fabian Glaser 22 Mar '22

22 Mar '22

Dear Elaine, When we try to run ChimeraX 1.3 on server 2016 windows on a computer farm (for teaching purposes), nothing happens, despite that the installation worked perfectly well. Any suggestion what we could do? Thanks a lot in advance, Fabian -------------------------- Fabian Glaser, PhD Structural and Computational Biology Unit The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel

4 5

find clash/contacts for protein-ligand complexes
by Enrico Martinez 21 Mar '22

21 Mar '22

Dear ChimeraX users! I would like to use the "find clash/contacts" command to find if the position of the ligand (predicted by docking) is in the proximity to the two residues located in the binding pocket. I have already tried #check contacts in first 10 docking poses contacts #1.1-10&protein& :41,49 restrict #1.1-10&ligand interModel false makePseudobonds false log true intraRes false saveFile contactsALL_rep$.log This gives me the output about 84 detected contacts: #1.14/? MET 49 CE #1.14/A UNL 1 C 0.191 3.449 #1.4/? MET 49 CG #1.4/A UNL 1 C 0.147 3.613 #1.7/? HIS 41 NE2 #1.7/A UNL 1 C 0.131 3.389 #1.10/? MET 49 CE #1.10/A UNL 1 C 0.120 3.520 #1.3/? HIS 41 CD2 #1.3/A UNL 1 C 0.095 3.425 #1.3/? MET 49 CG #1.3/A UNL 1 C 0.089 3.551 #1.8/? MET 49 CG #1.8/A UNL 1 C 0.070 3.510 #1.5/? MET 49 CG #1.5/A UNL 1 C 0.023 3.617 #1.4/? MET 49 CE #1.4/A UNL 1 C 0.006 3.754 ... #1.10/? HIS 41 CG #1.10/A UNL 1 C -0.377 3.837 #1.1/? HIS 41 O #1.1/A UNL 1 C -0.378 3.618 #1.14/? HIS 41 CD2 #1.14/A UNL 1 S -0.382 3.924 may I further limit the number of the detected contacts (e.g. via modifying geometrical criteria) in order to be able to draw a conclusion about the proximity of the ligand to the selected residues, which may be done according to the values in the Overlap column? Many thanks in advance! Enrico

2 1

Re: [chimerax-users] ChimeraX does not work on windows server running RDS
by Tom Goddard 21 Mar '22

21 Mar '22

Hi Fabian, If Chimera works and ChimeraX does not it may be that your system graphics driver does not support the more modern OpenGL graphics version (3.3) required by ChimeraX. Our UCSF servers are down -- below is a PDF of the ChimeraX troubleshooting page which talks about inadequate graphics drivers. Maybe starting in debug mode will indicate if that is a problem. Tom > On Mar 21, 2022, at 11:14 AM, Fabian Glaser <fabian.glaser(a)gmail.com> wrote: > > Dear Tom, > > Thanks a lot for your quick answer. > Yes, Chimera works, and ChimeraX does not show anything, the link you provided seems to be not available at this moment. > > Can we provide you with additional information? > > Thanks, > > Fabian > > -------------------------- > Fabian Glaser, PhD > > Structural and Computational Biology Unit > The Lorry I. Lokey Center for Life Sciences and Engineering > Technion - Israel Institute of Technology, Haifa, Israel > >> On 21 Mar 2022, at 20:08, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Fabian, >> >> Do you mean the ChimeraX window does not appear? The ChimeraX troubleshooting web page describes how to start in debug mode to get an error message which might indicate the problem >> >> https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#winstart <https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#winstart> >> >> Have other versions of ChimeraX or Chimera worked on these computers? >> >> Tom >> >> >> >>> On Mar 21, 2022, at 5:26 AM, Fabian Glaser via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Dear Elaine, >>> >>> When we try to run ChimeraX 1.3 on server 2016 windows on a computer farm (for teaching purposes), nothing happens, despite that the installation worked perfectly well. >>> >>> Any suggestion what we could do? >>> >>> Thanks a lot in advance, >>> >>> Fabian >>> >>> -------------------------- >>> Fabian Glaser, PhD >>> >>> Structural and Computational Biology Unit >>> The Lorry I. Lokey Center for Life Sciences and Engineering >>> Technion - Israel Institute of Technology, Haifa, Israel >>> >>> _______________________________________________ >>> 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://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >> >

2 1

ChimeraX does not work on windows server running RDS
by Fabian Glaser 21 Mar '22

21 Mar '22

Dear all, When we try to run ChimeraX 1.3 on server 2016 windows, nothing happens, despite that the installation worked perfectly well. Thanks a lot, Fabian -------------------------- Fabian Glaser, PhD Structural and Computational Biology Unit The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel

1 0

Superimposition with chimeraX
by 이현숙 20 Mar '22

20 Mar '22

Hello. I would like to superimpose chemical structure to protein structure. Protein structure was created by tool - structure predict - alphafold. Chemical structure was added to the protein structure( via tool - structure edit - add smile string - build structure) My question is : when chemical structure is added on the protein structure, chemical structure is located at the active site OR just located at the center of protein structure ? I want the 1st one (located at the active site) then how can I do through ChimeraX? Thank you. Hyunsook

2 1

Aligning volumes without resampling - Saving a map relative to another
by Helge Paternoga 17 Mar '22

17 Mar '22

Hi, I would like to know if it is possible to save a .mrc map relative to another one. Basically, I would like to superpose two volumes and compare them outside of ChimeraX (i. e. using Coot) without resampling in ChimeraX, as it is my understanding that resampling changes the volume in question. I noticed that "fitmap" outputs the rotation etc. in the log, but I do not know if and how I can apply this to a map. Many thanks in advance, Helge

4 8

Uninstalling ChimeraX
by Shivam Gupta 17 Mar '22

17 Mar '22

Dear Support team, I am using a ChimeraX commercial license ( RHEL-8 ) but now I am trying to uninstall it using the command 'yum remove chimerax' with and without root privileges but hard luck. I also tried to use 'ChimeraX_main.py --uninstall' from its own directory but again no success. Could you please guide me over uninstalling chimerax. Thank you Looking forward to hearing from you soon. Have a nice day ahead. Thanks -- 株式会社ファーマフーズ Biomedical Department グプタシヴァム Gupta Shivam 〒615-8245 京都市西京区御陵大原1-49 TEL:075-748-9811 FAX:075-948-9818 E-mail: *shivam-gupta(a)pharmafoods.co.jp <a-higashiyama(a)pharmafoods.co.jp>* URL: http://www.pharmafoods.co.jp/

2 1

map segmentation
by Dmitry Semchonok 17 Mar '22

17 Mar '22

Dear colleagues, Fast questions. 1. How to segment the selected segment? So I have a) segmented the map using the segment map tool b) selected 1 piece. b) I want to segment that selected piece on the smaller parts 2. how to increase the threshold of the segmented map? Thank you Kind regards, Dmitry

3 2

Fwd: Chimerax ISOLDE install Error
by Eric Pettersen 17 Mar '22

17 Mar '22

> Begin forwarded message: > > From: HONG ZHAN <hzhan3(a)wisc.edu <mailto:hzhan3@wisc.edu>> > Subject: Chimerax ISOLDE install Error > Date: March 17, 2022 at 8:02:25 AM PDT > > > Hi all, > > I am installing ISOLDE on my daily build ChimeraX (v1.4.dev202203170703 (2022-03-17) and it showed this error: > > Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-win_amd64.whl > Looking in indexes: https://pypi.org/simple <https://pypi.org/simple>, https://cxtoolshed.rbvi.ucsf.edu/pypi/ <https://cxtoolshed.rbvi.ucsf.edu/pypi/> > Processing c:\users\unchwaniwala\downloads\chimerax_isolde-1.3-cp39-cp39-win_amd64.whl > Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program files\chimerax 1.4.dev202203170703\bin\lib\site-packages (from ChimeraX-ISOLDE==1.3) (1.0) > ERROR: Could not find a version that satisfies the requirement ChimeraX-AtomicLibrary~=4.2 (from chimerax-isolde) (from versions: none) > ERROR: No matching distribution found for ChimeraX-AtomicLibrary~=4.2 > > I tried to look up online but not very useful information I found. Is a missing package I should install? Or how can I chnage the range for ChimeraX-AtomicLibrary? > > Thanks! > Hong

3 2

Placing Centroid at center of selection
by German Barcenas 16 Mar '22

16 Mar '22

Hello, I am trying to place a centroid <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/define.html#centroid> marker at the center of a selection of atoms, for example in the middle of a benzene ring that is at some arbitrary position in my system. I want to do some distance measurements here. I can do something like this: shape sphere color orange radius 0.25 center sel where the center sel places the sphere where I want, but these spheres can't be used to make measurements. Instead I think I need a marker object, such as: define centroid radius 0.25 color orange But I don't know how to recreate that `center sel` position. I have tried define centroid radius 0.25 color orange position center define centroid radius 0.25 color orange position center sel define centroid radius 0.25 color orange position sel These do not work. I am under the impression that the centroid is a marker object and should have some position argument. Can anyone help me? Thanks, -- German Barcenas Ph.D Candidate | Materials Science and Engineering Materials Modeling and Theory Group Boise State University germanbarcenas(a)u.boisestate.edu | 940-577-5094

2 2

Chimera and ChimeraX commercial license
by Jai Vekeria 15 Mar '22

15 Mar '22

Hello, My name is Jai, I am a data scientist at Tectonic Therapeutics in Watertown MA, I would like to purchase 5 commercial licenses for Chimera and ChimeraX, I am assuming based on the little technical information included on the product page, that any windows 10 64-bit machine would suffice, we have some machine with a 1 Gb of ram and a 1.2Ghz processor and no GPU that we plan to use. Thanks, Jai Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful. This email has been scanned for viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business. Providing a safer and more useful place for your human generated data. Specializing in; Security, archiving and compliance. To find out more visit the Mimecast website.

3 2

Outputting ChimeraX RMSD values after using matchmaker in a .PY script?
by Steven Truong 14 Mar '22

14 Mar '22

Dear ChimeraX admins, I am using matchmaker (mmaker) since the RMSD calculations done using the function have been very useful. However, I’m currently having some trouble outputting these values. At first, I tried to use matchmaker in a .PY script and then output these values via “log save”. Unfortunately, I haven’t been able to get this to work because whenever I try to do “log save” in a script (in terminal/command line), I get “no log tool to save”. Is there a way to “log save” if running a .PY script in a command line? Or is there a simpler way to get the values I need from matchmaker? Thank you for your help, Steven Truong sdt45(a)cam.ac.uk<mailto:sdt45@cam.ac.uk>

2 1

solvate
by Joe Greenstone 13 Mar '22

13 Mar '22

In Chimera, solvation can be done via Tools/Structure Editing/Solvate How is solvation done in ChimeraX ? Thanks in advance.

2 1

Aligning small molecules, ligands
by Noriega, Heather 12 Mar '22

12 Mar '22

Hello, I hope you are well Elaine. I am wondering if there is a way to align my combined model UNL to my model 2. In hopes this could be a reference model of my docking done in Chimera for future builds. I did figure out the bonding, thank you. :) I attached the session, and have read the align command. I am just unsure how to manipulate it to superimpose the ligand. align matchatoms (the whole model 2) toAtoms (UNL on model 1). Thanks for your help. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

2 2

2D Residue Plot
by Avinoam Aryeh Singer 11 Mar '22

11 Mar '22

Hey there, I was wondering whether there was a way to control the angle of the 2D residue plot generated from the "Interfaces" tool, such that creating plots from two aligned proteins will give me comparable plots. As you can see in the image below, the two structures are slightly rotated relative to one another, despite being aligned. Thanks! Avi Singer ?[cid:05b972a6-633f-4ee1-a7ce-ee7cf1f78284] Avinoam Singer PhD Candidate | Keating Lab Massachusetts Institute of Technology

4 7

Joining models together in ChimeraX
by Christopher Camitta 10 Mar '22

10 Mar '22

Hi all, I am trying to join together two protein structures (in my case, one protein without the N-terminal domain combined with the NTD of a related protein). I came across a tutorial on how to do this in Chimera ( https://2019.igem.org/wiki/images/f/f3/T--UNSW_Australia--Daniel_Winter_Chi…) but from what I can tell ChimeraX's Build Structure tool doesn't have the options required to do this. Is there a way to join together two models in ChimeraX? Thanks, Chris

2 1

ChimeraX
by Alejandro Amor 10 Mar '22

10 Mar '22

Hi there: I am trying to download ChimeraX for academic use and can't find a link to do it. Can you please provide some guidance? Thanks, Alex ______________________________ Alejandro Amor-Coarasa, PhD Assistant Professor of Nuclear Medicine in Radiology Director of the Radiochemistry Laboratory Albert Einstein College of Medicine 1300 Morris Park, 703-GB Bronx, NY 10461 Work: 718-430-3776 cell: 786-543-1534 e-mail: alejandro.amor(a)einsteinmed.org

2 1

Analysis of the protein-ligand interactions using ViewDock
by Enrico Martinez 09 Mar '22

09 Mar '22

Dear ChimeraX users! I would like to use ChimeraX to calculate protein-ligand contacts established in docking calculations for the ensemble of the docking solutions (88 conformations of the ligand saved in multi-model format). Basically using the GUI of the UCSF Chimera previously I could do the following routine for the analysis of docking results: 1. Open the protein PDB 2. Use the Surface/Binding Analysis > ViewDock tool to open the docking poses 3. Using the Model Panel, select all docking poses 4. Use the Surface/Binding Analysis > FindHBond tool to locate all H-bonds. Make sure to check "Only find H-bonds with at least 1 end selected". You can check "write information to file" to save the H-bonds. May I adapt this protocol with the ChimeraX to perform such computing in batch (no-gui mode)? What should be the differences in the commands between Chimera and ChimeraX ( I've already seen that ViewDock is available in the ChimeraX as well...) Many thanks in advance! Cheers Enrico

2 8

Unable to vary atomRadius by relative amounts
by Christopher Handelmann 04 Mar '22

04 Mar '22

Hi, I am trying to adjust the size of multiple individual residues in a molecule. I am attempting this with the "size [Target] atomRadius +[value]" command. When I run this, it doesn't perform a relative shift of each atom size in the residue but appears to set all atoms in the residue to an absolute size of the value. The documentation states that including the plus sign should make it a relative change. I am using ChimeraX 1.2.5. I appreciate your help figuring this out, Christopher Handelmann

2 1

How to view consurf result in chimerax
by Shin, Yeonoh 03 Mar '22

03 Mar '22

Hello, I ran MSA in Consurf website, however I can not open the color-coded pdb result in Chimera or ChimeraX. When I click the link, attached error shows up. When I tried to open the link in chimeraX command line, another error shows up (attached). Could you tell me what I need to do to see the color-coded result in Chimera or X? Thank you. Yeonoh

2 1

Commands - bond angle and minimize
by chung kelvin 02 Mar '22

02 Mar '22

Hello all and Elaine, I am new here and would greatly appreciate Elaine and the Chimera Team, ChimeraX is so wonderful and you guys are not just providing the support to scientists, but advancing drug discovery and life science for humanity. Long story short, I have 3 problems in creating an enzyme-substrate model 1. I make a bond between the substrate and the enzyme, however, I could not make a right bond angle (kindly see the attached file, the bond angle between "Ser70 OG", "UNL1 C7", and "UNL1 O2", should be 120). I tried the command "bond angle", but don't know how to use it, and could not find the description about this command. How could this command be used? Could the bond angle be changed in Chimera? 2. 3. If the bond angle can be fixed, I need to eliminate any clashes before conducting energy minimization, however, the Tool "Rotamer" could not be applied to this covalently bound ligand. Is there some way to generate "rotamer" for this case? 4. 5. In the old version Chimera, there is a Tool called "minimize structure" and "Join Model (under "Build structure")" would it be any similar Tool in ChimeraX? 6. Again, thank you very much for your help. Cheers Kelvin Chung ABCT Department The Hong Kong Polytechnic University

2 3

Permission denied writing file...
by 翼翱张 01 Mar '22

01 Mar '22

Hi Sir/Madam, When I press the button ‘save snap shot to desk’, it shows ‘Permission denied writing file C:\Users\zhang\Desktop\image1.png’. how should I open the permission? Please help me. Looking forward to your reply. Sincerely, Wing 从 Windows 版邮件<https://go.microsoft.com/fwlink/?LinkId=550986>发送

3 2

Surface rendered trajectory
by Venkatareddy Dadireddy 01 Mar '22

01 Mar '22

Hi, I am visualizing MD trajectory in ChimeraX and making movie of a trajectory. I want to incorporate "time stamp" of a trajectory into my movie. How can I do it in ChimeraX? Thank you, Venkat

3 2

Re: [chimerax-users] How to view SwissDock output in ViewDockX
by Eden Fussner - Dupas 27 Feb '22

27 Feb '22

Hi Elaine, I’m not sure if you’ve answered this elsewhere - but I am having the same issue another user was having. The output of Swissdock isn’t being recognized by the ViewDockX tool. I am trying to pick the best model stearic acid in this PLAT protein (an AlphaFold model). Any help would be most appreciated. Warmly, Eden

2 3

Stack thickness question and cine playing?
by Rubenstein, Jason 25 Feb '22

25 Feb '22

Hi! Two questions: 1. This 3D dataset is only about 30 mm thick in the Z direction. When ChimeraX is displaying it, it shows the thickness about 50x too thick. Any way to adjust this? [cid:007921ae-20a5-4928-963c-23013d90a69e] 1. this is a "4D" dataset, with 20 phases of 3D stacks. Any way to "play" the cine? Thanks! Jason Rubenstein, M.D. Codirector, Cardiac MRI Associate Professor, Medical College of Wisconsin

3 5

Surface zone and movie recording
by Lewandowski, Jozef 25 Feb '22

25 Feb '22

Hi, I would like to use "surface zone" command to visualise a substrate channel in an animation of an MD trajectory. For that I would like to regenerate the surface every frame with "perframe". However, if I do that when I record the movie the entire surface (instead of just the selected zone) will flash before the zone is displayed. Is there any way so that only the surface zone will be displayed from frame to frame without the entire surface flashing? I essentially just would like to follow the changes to the substrate channel without any distractions. Thank you, Józef ------------------------------------------------------------------------------------------------------ Józef R. Lewandowski Professor | Department of Chemistry | University of Warwick<http://www2.warwick.ac.uk/> j.r.lewandowski(a)warwick.ac.uk<mailto:j.r.lewandowski@warwick.ac.uk> | External: +44 (0) 24 76151355 | Internal: 51355 Millburn House: F07 | Coventry CV4 7AL | Find us on the interactive map<http://www2.warwick.ac.uk/about/visiting/maps/interactive/> Lewandowski group website<https://www2.warwick.ac.uk/fac/sci/chemistry/research/lewandowski/lewandows…> | Warwick solid-state NMR group website<http://www2.warwick.ac.uk/fac/sci/physics/research/condensedmatt/nmr/>

3 2

Ask for help with chimeraX
by 培慧张 25 Feb '22

25 Feb '22

Dear UCSF ChimeraX： We love the software you developed, ChimeraX. With high-performance rendering of large structures and data, the ability to quickly and microfiber slim readers and write millimeter ciliates, fast and robust solvent elimination surfaces, interactive ambient occlusion lighting, and curved cylindrical "tube" spirals with cartoon integration, our research team especially loves your software. Compared with UCSF Chimera1.16, we found that ChimeraX lacks the function of Organization, but we really need this function, how can we choose to use ChimeraX to solve the problem of missing this function? Can we use this feature as an external software plug into The SummerX? Hope to get help from your school and restore me, thank you.

3 6

Re: [chimerax-users] correct format for attribute information file (.defattr)
by Rangarajan, Amith 24 Feb '22

24 Feb '22

Hello everyone, I am trying to add mutation counts as a attribute and use it to generate a map of hotspots on the protein . I followed the format provided on chimerax documentation and i am getting this error : SyntaxError: Line 12 in KIT-mutations-count.defattr is either not of the form 'name: value' or is missing initial tab File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\defattr.py", line 107, in defattr raise SyntaxError("Line %d in %s is either not of the form 'name: value'" i am on windows 11 using chimerax 1.3. thanks amith

2 3

perspective or orthoscopic view - how to change
by Dmitry Semchonok 24 Feb '22

24 Feb '22

Dear colleagues, How to change the camera view for 3D map for from the perspective to orthoscopic or vice versa Thank you Sincerely, Dmitry

5 6

Ask for help with chimeraX
by 泡沫 24 Feb '22

24 Feb '22

     We love the software you developed, ChimeraX. With high-performance rendering of large structures and data, the ability to quickly and microfiber slim readers and write millimeter ciliates, fast and robust solvent elimination surfaces, interactive ambient occlusion lighting, and curved cylindrical "tube" spirals with cartoon integration, our research team especially loves your software. Compared with UCSF Chimera1.16, we found that ChimeraX lacks the function of Organization, but we really need this function, how can we choose to use ChimeraX to solve the problem of missing this function? Can we use this feature as an external software plug into The ChimeraX?       Hope to get help from your school and restore me, thank you.

1 0

Re: [chimerax-users] alphafold predict stops after MSA step (google colab pro)
by Rangarajan, Amith 23 Feb '22

23 Feb '22

Hi, I am new to using alphafold for prediction, i tried today with a reasonable size model ( 400 AA ) of a kinase domain. i opted to use 'high RAM " available on colab pro and after running for an few hours , the job stops without any error, the colab notebook had disconnected due to inactivity and it did not generate any models. please share with me your experience of using alphafold from within chimerax , helpful tips to get the job to finish . here is the output ( output on google colab): Sequence length 401 Have Colab GPU runtime Installing HMMER for computing sequence alignments Installing matplotlib to plot sequence alignment coverage Installing AlphaFold Installing OpenMM for structure energy minimization Finding fastest mirror for sequence databases using united states Searching sequence databases (147 Gbytes). Search will take 29 minutes or more. Searching uniref90 sequence database, 59 Gbytes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 Searching smallbfd sequence database, 17 Gbytes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Searching mgnify sequence database, 71 Gbytes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 Computing multiple sequence alignment 327620 similar sequences found (311112 uniref90, 16008 smallbfd, 500 mgnify) [cid:4e178c51-cd4c-4958-b2e8-fa714cbfcd07] Computing structures using 5 AlphaFold parameter sets: model_1 thanks a lot again for all your support, best amith

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Drawing objects in ChimeraX?
by de Miranda Seabra, Gustavo 23 Feb '22

23 Feb '22

Hi, I was wondering if it is possible to draw objects in ChimeraX. More specifically, I'd like to show the gridbox used for docking calculations, so it would be nice if I could draw a cube, and even better if it can be drawn as a surface that could have color, transparency, etc. How to do this in ChimeraX? Thanks a lot! -- Gustavo Seabra Research Associate Professor Center for Natural Products, Drug Discovery, and Development (CNPD3) Department of Medicinal Chemistry College of Pharmacy University of Florida, Gainesville, FL, USA

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Re: [chimerax-users] Regarding generating volume surface in ChimeraX for large maps
by Tom Goddard 22 Feb '22

22 Feb '22

Hi Rakesh, ChimeraX displays just a single plane when you open a map file larger than 256 Mvoxels -- often the situation for electron microscopy tomograms, for example a 2048 by 2048 by 100 map (400 Mvoxels), but also for large electron microscopy single particle reconstructions, e.g. 800 x 800 x 800 (512 Mvoxels). Maps larger than 16 Mvoxels will not be shown at full resolution (step 1), instead the step size will be chosen to only display at most 16 Mvoxels when the map is first opened, again to improve load speed for common interactive use cases. So if you are writing a script and need the full map shown always include a volume command to assure it is shown how you want, for example to show all planes, volume #1 region all style surface or to assure it is shown at full resolution volume #1 step 1 region all style surface and to make sure the threshold level is what you want you can specify it too volume #1 level 4.5 step 1 region all style surface There are volume command options that set the 256 MVoxel limit for planes (option name "voxelLimitForPlane") and 16 MVoxel full resolution limit (option name "voxelLimit") that you can use to change the default for the current session, but unfortunately ChimeraX currently does not offer a way to save new default values. These are all documented https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling Tom > On Feb 18, 2022, at 12:47 PM, Rakesh Ramachandran <rakeshramachandran10(a)gmail.com> wrote: > > Hi Tom, > > I am trying to segment volume using 'volume splitbyzone' in ChimeraX for a large number of maps. But what I observed is that some of the maps are displayed as planes instead of surfaces and this affects the volume splitbyzone command. > > I tried using 'volume style surface' but it doesn't seem to work unless I manually set it in the GUI. What option do I use to generate surfaces for map volumes automatically from the command line in such cases? > > -- > Regards > Rakesh Ramachandran > Postdoctoral Scholar > Department of Bioengineering and Therapeutic Sciences > University of California, San Francisco > Byers Hall Room 501 > 1700 4th Street > San Francisco, CA 94143, USA

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Editing preset for initial colors
by Niels Bradshaw 22 Feb '22

22 Feb '22

Hi Elaine, Is there a way in chimera X to change the initial colors preset for new models? I’m not into the default tan color, so I end up changing the color immediately every time I open a new model. In previous versions of Chimera, I had disabled color by model and set all new models to open with grey. In pymol, I defined the colors for the first 10 models I open in the startup script, which is even more convenient. Having the option to have the default to color by chain could also be nice if that is possible. I tried some workarounds like redefining the tan color, but it appears that is not allowed. Thanks, Niels

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Re: [chimerax-users] Mailman privacy alert
by Ralph Loring 22 Feb '22

22 Feb '22

Hi, I keep getting these notifications that ChimeraX on both my laptop and my office computer is not registered and I need to register them again. I think between the two computers, I've registered the program four times in the past two months. What's up with this? Ralph Loring Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu On Thu, Feb 17, 2022 at 8:32 PM <chimerax-users-bounces(a)cgl.ucsf.edu> wrote: > An attempt was made to subscribe your address to the mailing list > chimerax-users(a)cgl.ucsf.edu. You are already subscribed to this mailing > list. > > Note that the list membership is not public, so it is possible that a bad > person was trying to probe the list for its membership. This would be a > privacy violation if we let them do this, but we didn't. > > If you submitted the subscription request and forgot that you were already > subscribed to the list, then you can ignore this message. If you suspect > that > an attempt is being made to covertly discover whether you are a member of > this > list, and you are worried about your privacy, then feel free to send a > message > to the list administrator at chimerax-users-owner(a)cgl.ucsf.edu. >

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Re: [chimerax-users] Bundle dependency
by Anthony James Schaefer 21 Feb '22

21 Feb '22

Katie, I'm not sure. I tried adding pdb-objects to one of my bundle's dependencies, and it was installed. I'm testing this on a ChimeraX 1.4 daily build. My bundle_info.xml has this: <Dependencies> <Dependency name="ChimeraX-Core" version=">=1.2.dev"/> <Dependency name="pdb-objects"/> </Dependencies> and my log has this after installing (along with a bunch of other stuff): Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\normn\documents\github\chimerax_themes\dist\chimerax_themes-0.3.1-py3-none-any.whl Requirement already satisfied: ChimeraX-Core>=1.2.dev in e:\chimerax 1.4.dev202202010639\bin\lib\site-packages (from ChimeraX-themes==0.3.1) (1.4.dev202202010639) Collecting pdb-objects Using cached pdb_objects-0.1.3-py3-none-any.whl (6.6 kB) Installing collected packages: pdb-objects, ChimeraX-themes Successfully installed ChimeraX-themes-0.3.1 pdb-objects-0.1.3 --- Successfully installed ChimeraX-themes-0.3.1 pdb-objects-0.1.3 Installed ChimeraX-themes (0.3.1) Towards the bottom, it says it installed pdb-objects and my bundle. I can then go into the shell and import pdb_objects without error. Best, Tony ________________________________ From: Zeng, Katie <jingrou.zeng18(a)imperial.ac.uk> Sent: Monday, February 21, 2022 2:59 PM To: Anthony James Schaefer <tony.schaefer(a)uga.edu> Subject: Re: Bundle dependency [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi Tony, Thanks for pointing that out. I've now changed the dependency to pdb-objects, but I still get the same error when I try to use the bundle in ChimeraX. Have you got any idea why it's giving this error? Best Regards, Katie ________________________________ From: Anthony James Schaefer <tony.schaefer(a)uga.edu> Sent: 21 February 2022 17:57 To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu>; Zeng, Katie <jingrou.zeng18(a)imperial.ac.uk> Subject: Re: Bundle dependency This email from tony.schaefer(a)uga.edu originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. Katie, It looks like PDB objects on PyPI is called pdb-objects, not pdb_objects. For dependencies, ChimeraX looks for the package name and not the import name. Best, Tony ________________________________ From: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu> on behalf of Zeng, Katie via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Sent: Monday, February 21, 2022 11:50 AM To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] Bundle dependency [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi, I'm currently working on building a membrane builder bundle and it requires the use of a python library called 'pdb_objects'. Following the tutorial on the website, I'm adding the following line to my bundle_info.xml file under the dependencies tag: <Dependency name="pdb_objects"/> It still gives me an error of <No module named 'pdb_objects'> when I load my bundle in ChimeraX. How can I allow the use of this library in my bundle? Thanks for your help! Best Regards, Katie

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Bundle dependency
by Zeng, Katie 21 Feb '22

21 Feb '22

Hi, I'm currently working on building a membrane builder bundle and it requires the use of a python library called 'pdb_objects'. Following the tutorial on the website, I'm adding the following line to my bundle_info.xml file under the dependencies tag: <Dependency name="pdb_objects"/> It still gives me an error of <No module named 'pdb_objects'> when I load my bundle in ChimeraX. How can I allow the use of this library in my bundle? Thanks for your help! Best Regards, Katie

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Re: [chimerax-users] No suitable models found for viewDockX
by Rangarajan, Amith 21 Feb '22

21 Feb '22

hello chimeraX, I am trying to open a glide docking result using viewdockx and i am getting this error message ('no suitable models found"). I tried opening the file as .mae file ( protein and ligand are both in same model )and a pv.mae file ( protein and ligand are in diff models). I am still getting the same error. I am using chimerax ver 1.3 please help me see what i am missing. thanks amith

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Question about Coulombic electrostatic potential
by Sunisa Yoodee 21 Feb '22

21 Feb '22

Dear UCSF ChimeraX We used the ChimeraX program to calculate electrostatic potential. By using the coulombic command, a molecular surface was generated and colored. However, we also need the electrostatic potential value (kcal/(mol*e))of the protein. Could you please give some advices how to get this value? Best Regards, Sunisa Yoodee -- *Sunisa Yoodee*, Ph.D Medical Proteomics Unit, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, THAILAND Tel: 66-8-06691102 e-mail: yd.sunisa(a)gmail.com

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Define axis tool missing?
by James Hodgkinson-Bean 20 Feb '22

20 Feb '22

Hi I am currently doing some geometric analysis of a protein complex, and was wanting to define certain axis normal to planes I have defined; on the online chimerax documentation there seems to be an option “define axis”, however in my actual chimeraX program, this command doesn’t work, and is not listed under the “help define” command which shows how to define planes and centroids. I am running ChimeraX version 1.3 (2021-12-08), which I downloaded recently. Any assistant would be much appreciated 😊 P.S I absolutely love chimeraX!! It is one of the best pieces of software I’ve ever used. Cheers, James.

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