- ChimeraX-users - RBVI Mailing Lists

Python Function that implements the "center" method from the GUI
by tong.you＠icm.uu.se 01 Dec '23

01 Dec '23

Hello, For an automatic pipeline workflow, I want to have a way to center several mrc files using the Python module. However, I can't seem to find the corresponding Python function that I can use in a script to "center" an opened map. Is there a Python function to "center" a map similarily as in the GUI? Kind regards, Tong

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Independent movement of chains in movie
by Caroline Stone (JIC) 30 Nov '23

30 Nov '23

Dear ChimeraX team and list subscribers, I am making a little movie to show a complex of two proteins, but am stuck on individual movements of chain /A and /B. If I use the move command, chain /A and /B both move independently, away from each other: move x -10 atoms /A; move x 10 atoms /B However, if I attempt to do the same movement by going -1 or +1 over a series of 10 frames, I no longer get any movement of /A and /B. move x -1 10 atoms /A; move x 1 10 atoms /B I can achieve movement over a number of frames, but both chains move although I tried to specify only /A. I did this based on "move axis [ distance [ frames ]]". move x -1 10 atoms /A I feel I might be on the right track because when I use turn, I am able to trigger simultaneous independent rotation of /A and /B around their own axes (thank you for this feature by the way, last time I wondered about this it wasn't possible). cofr /A; turn y -1 90 atoms /A; cofr /B; turn y 1 90 atoms /B My ultimate goal is to open the binding interface up a bit like opening a book. I suppose I could achieve a similar effect by setting the centre of rotation for each chain behind, rather than within - if independent movement over a series of frames isn't possible, I might experiment with that. I updated to version 1.6 and searched the list, but I still see this behaviour with the move command. Perhaps I am missing something basic? Thank you for any pointers you might be able to share! Caroline

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"view" in command line vs. menu
by C. Klein 30 Nov '23

30 Nov '23

Dear Eric, Oliver, et al. you may remember my comment on the missing "focus" function. Anyhow, what I noticed now is interesting: The function of the "view" command is different in the menus vs. the command line. in the command line, "view" will zoom out and show everything in the menu, "view" will focus on the selected ligand or whatever (which is what I want a bit more, mostly) Perhaps this could be resolved with modified or rather re-surrected terminology: Focus on selection: "focus" in command line "focus on selection" in menu Zoom to fit all: "zoomall" in command line "zoom to fit all" in menu just some suggestions. But what I think is clear is that the function of commandos should be identical in menu and command line. Again, thank you very much for your important and good work on the Chimera software. Best wishes Christian OpenGL version: 3.3.0 NVIDIA 452.56 OpenGL renderer: Quadro P620/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_US.cp1252 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: windows Manufacturer: LENOVO Model: 30C5004VGE OS: Microsoft Windows 11 Pro (Build 22621) Memory: 17,010,716,672 MaxProcessMemory: 137,438,953,344 CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 comtypes: 1.1.14 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pywin32: 305 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 WMI: 1.5.1 zipp: 3.15.0 -- Prof. Dr. C. Klein; c.klein(at)uni-heidelberg.de Medicinal Chemistry Institute of Pharmacy and Molecular Biotechnology IPMB Heidelberg University, INF 364 D-69120 Heidelberg Germany Phone: ++49-6221-54-4875 FAX : ++49-6221-54-6430

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How to save a sequence in an mmCIF file?
by Guillaume Gaullier 29 Nov '23

29 Nov '23

Hello, Starting from an AlphaFold prediction, I refined a model against a map with ISOLDE. I trimmed the segments not supported by any density. The resulting mmCIF file that I saved now opens with this warning: Unknown polymer entity '1' near line 187 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Displaying the sequence of this chain shows the correct numbering (with jumps in numbering according to missing segments in the structure), but the sequence of the missing structure segments is not displayed. When I open the fasta file containing the full-length sequence, the sequence gets automatically associated to the structure, and the sequence viewer annotates the segments with missing structure correctly. I would like to save this full-length sequence in my mmCIF file so the full-length sequence with annotated missing structure segments shows up next time I open this file. But when I try to save at this point, I get the following notice: Not saving entity_poly_seq for non-authoritative sequences The documentation for "save" and "sequence" didn't help. How can I make this sequence "authoritative" and save it into my mmCIF file? Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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transition dipole moments
by gennaro.pescitelli＠unipi.it 28 Nov '23

28 Nov '23

Dear developers, first of all, thnak you for your great software, I just started using it. My question: is there a way to plot transition moments (electric and magnetic), as calculated e.g. by TD-DFT calculations in ORCA or Gaussian? If not directly from a log/out file, is tehre a way to manually add a vector arrow? Thanks Rino Pescitelli

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Inquiry Regarding Feasibility of Implementing Protein Operations in Python
by g0423019 g0423019 28 Nov '23

28 Nov '23

Sorry. The earlier email by ms04000106(a)gmail.com was not sent using a university email address. It has been resent using the university email address. Dear UCSF ChimeraX, I hope this email finds you well. My name is Mayu Shibuya, and I am a student at Iwate University, currently affiliated with the wet biology laboratory. I am reaching out to seek guidance on the feasibility of utilizing the software for a specific task. Specifically, I am interested in performing addh and addcharge operations and automating these processes using a Python script. However, I do not know whether the addh and addcharge operations can be executed in Python. Could you kindly provide guidance on the possibility of achieving this with the software? If it is indeed feasible, I would greatly appreciate any instructions or methods you recommend for implementing these operations in a Python script. Thank you for taking the time to consider my inquiry. I greatly appreciate your assistance and look forward to hearing from you soon. Best regards, Mayu Shibuya Iwate University g0423019(a)iwate-u.ac.jp

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Inquiry Regarding Feasibility of Implementing Protein Operations in Python
by 澁谷まゆ 28 Nov '23

28 Nov '23

Dear UCSF ChimeraX, I hope this email finds you well. My name is Mayu Shibuya, and I am a student at Iwate University, currently affiliated with the wet biology laboratory. I am reaching out to seek guidance on the feasibility of utilizing the software for a specific task. Specifically, I am interested in performing addh and addcharge operations and automating these processes using a Python script. However, I do not know whether the addh and addcharge operations can be executed in Python. Could you kindly provide guidance on the possibility of achieving this with the software? If it is indeed feasible, I would greatly appreciate any instructions or methods you recommend for implementing these operations in a Python script. Thank you for taking the time to consider my inquiry. I greatly appreciate your assistance and look forward to hearing from you soon. Best regards, Mayu Shibuya Iwate University ms04000106(a)gmail.com

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hide dust
by Andrea Smith 28 Nov '23

28 Nov '23

Hi, I have cartoon and map visible for a part of my molecule (one protomer from a tetramer). When I click on hide dust, the dust is hidden but at the same time the map appears for the rest of the tetramer. Is there a way to hide dust around the visible part of the map while keeping a part of the map hidden? Thanks, Andrea

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(no subject)
by Murphy, Kenneth 26 Nov '23

26 Nov '23

Hi, Would there be a way to save convservation scores from a large multiple sequence alignment into a file that could be re-loaded later instead of having to reload the actual alignment file? In looking at WDFY4, the alignment of the 3124 residue protein from 523 different species, the alignment fasta file takes around 10 minutes to load. After calculating the scores, the program shows the alignment and then the showing the convervations of residues in the protein is my goal of analysis. But it takes the same 10 minutes every time I open the session. I haven't found a way to save the scores themselves and load that in directly. Is there a way to do that? thanks it's a great program. ken murphy ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Reading .xyz vs. Orca .out file
by Michael Patzschke 23 Nov '23

23 Nov '23

Dear colleagues, Recently the following problem has appeared: When I open an orca output file and chose the ball and stick option for displaying molecules, the radii of the balls are all wrong. This problem does not show up when I open the corresponding .xyz file. I try to attach an example to illustrate the problem. I would appreciate any help in this matter. Kind regards, Michael Patzschke __________________ Dr. Michael Patzschke Institute of Resource Ecology Chemistry of the f-elements Theoretical Chemistry Helmholtz-Zentrum Dresden - Rossendorf e. V. Telefon: +49 (0351) 260 2989 E-Mail: m.patzschke(a)hzdr.de <mailto:p.kaden@hzdr.de> Web: http://www.hzdr.de <http://www.hzdr.de/> Addresse: Bautzner Landstrasse 400 | 01328 Dresden Vorstand: Prof.Dr. Dr. Sebastian M. Schmidt, Dr. Diana Stiller Vereinsregister: VR 1693 beim Amtsgericht Dresden

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