id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14548 Graphics glitches on external display Tristan Croll Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22631 ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description On my Windows machine I regularly notice this weird behaviour that occurs if I have a ChimeraX session open when I plug my laptop into an external display - the graphics window develops weird glitches as if some frames are being displayed out of order. Probably notably, if I use ""movie record"" to try to capture the effect it goes away, only to come back when I stop recording. If I unplug from the external display it also seems fine. The session that the attached video comes from was actually started while plugged into the external display (resolution 3840 x 2160), and was working fine. When I unplugged to show the session on my laptop display (1920 x 1080) everything was still fine - but when I plugged back into the large display (using it as the sole display) is when things went wonky. If I open my laptop so the displays are tiled then the glitch also goes away (regardless of which screen it is shown on). Log: > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7v1m structureFactors true Summary of feedback from opening 7v1m fetched from pdb --- warning | WARNING: multiple experimental reflection datasets found: F_meas_au, F_meas_sigma_au, intensity_meas, intensity_sigma Automatically choosing ""F_meas_au, F_meas_sigma_au"". notes | Fetching compressed mmCIF 7v1m from http://files.rcsb.org/download/7v1m.cif Fetching compressed 7v1m structure factors from http://files.rcsb.org/download/7v1m-sf.cif Resolution: 2.8340275528626875 Launching live xmap mgr took 1.7294037342071533 seconds. Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 40,38,30, pixel 0.899,0.899,0.934, shown at level 0.126, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 40,38,30, pixel 0.899,0.899,0.934, shown at level -0.111,0.111, step 1, values float32 Opened (LIVE) 2mFo-DFc_sharp_24 as #1.1.1.4, grid size 40,38,30, pixel 0.899,0.899,0.934, shown at level 0.411, step 1, values float32 7v1m title: Structural basis for the co-chaperone relationship of sNASP and ASF1b [more info...] Chain information for 7v1m --- Chain | Description | UniProt 1.2/A 1.2/B | Histone H3.3 | H33_HUMAN 1-135 1.2/C 1.2/E | Histone H4 | H4_HUMAN 1-102 1.2/D 1.2/F | Histone chaperone ASF1B | ASF1B_HUMAN 1-158 1.2/G 1.2/H | Isoform 2 of Nuclear autoantigenic sperm protein | NASP-2_HUMAN 30-100 160-323 7v1m mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > view protein > select /A 583 atoms, 590 bonds, 75 residues, 1 model selected > alphafold match #1/A trim false Fetching compressed AlphaFold P84243 from https://alphafold.ebi.ac.uk/files/AF-P84243-F1-model_v4.cif 1 AlphaFold model found using UniProt identifier: P84243 (chain A) AlphaFold prediction matching 7v1m --- Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id A | P84243 | H33_HUMAN | 1.21 | 136 | 75 | 100 Opened 1 AlphaFold model > select #1/C 620 atoms, 627 bonds, 80 residues, 1 model selected > select #1/E 605 atoms, 612 bonds, 78 residues, 1 model selected > alphafold match #1/E trim false 1 AlphaFold model found using UniProt identifier: P62805 (chain E) AlphaFold prediction matching 7v1m --- Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id E | P62805 | H4_HUMAN | 5.79 | 103 | 78 | 100 Opened 1 AlphaFold model > open 3av2 Summary of feedback from opening 3av2 fetched from pdb --- note | Fetching compressed mmCIF 3av2 from http://files.rcsb.org/download/3av2.cif 3av2 title: The human nucleosome structure containing the histone variant H3.3 [more info...] Chain information for 3av2 #4 --- Chain | Description | UniProt A E | Histone H3.3 | H33_HUMAN 0-135 B F | Histone H4 | H4_HUMAN 0-102 C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129 D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125 I J | 146-MER DNA | > matchmaker #3 to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7v1m, chain A (#1.2) with AlphaFold H4_HUMAN chain E, chain E (#3.1), sequence alignment score = 113.3 RMSD between 47 pruned atom pairs is 1.016 angstroms; (across all 68 pairs: 2.656) > matchmaker #3 to #1/E Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7v1m, chain E (#1.2) with AlphaFold H4_HUMAN chain E, chain E (#3.1), sequence alignment score = 450.2 RMSD between 65 pruned atom pairs is 0.764 angstroms; (across all 78 pairs: 5.789) > matchmaker #4 to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7v1m, chain A (#1.2) with 3av2, chain A (#4), sequence alignment score = 580.7 RMSD between 69 pruned atom pairs is 0.899 angstroms; (across all 75 pairs: 1.338) > cartoon #4 > select clear > nucleotides slab > style nucleic stick Changed 5980 atom styles > hide #4&protein > hide #!3 models > hide #!2 models > hide nucleic > ~cartoon nucleic > clipper isolate #1/A,E > hide #4&~protein > color #4 brown > color #4 byidentity > clipper isolate #1/D,F,G,H > close Deleting Crystallographic maps(7v1m-sf.cif) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_sharp_24 > open 7v1m 7v1m title: Structural basis for the co-chaperone relationship of sNASP and ASF1b [more info...] Chain information for 7v1m #1 --- Chain | Description | UniProt A B | Histone H3.3 | H33_HUMAN 1-135 C E | Histone H4 | H4_HUMAN 1-102 D F | Histone chaperone ASF1B | ASF1B_HUMAN 1-158 G H | Isoform 2 of Nuclear autoantigenic sperm protein | NASP-2_HUMAN 30-100 160-323 7v1m mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > open 3av2 3av2 title: The human nucleosome structure containing the histone variant H3.3 [more info...] Chain information for 3av2 #2 --- Chain | Description | UniProt A E | Histone H3.3 | H33_HUMAN 0-135 B F | Histone H4 | H4_HUMAN 0-102 C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129 D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125 I J | 146-MER DNA | > matchmaker #2 to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7v1m, chain A (#1) with 3av2, chain A (#2), sequence alignment score = 580.7 RMSD between 69 pruned atom pairs is 0.899 angstroms; (across all 75 pairs: 1.338) > hide #2&~protein > cartoon #2 > ~cartoon #2&nucleic > hide #2 > select #1/A,E 1188 atoms, 1202 bonds, 153 residues, 1 model selected > surface sel > select #1/A,E,B,F 3087 atoms, 3144 bonds, 393 residues, 1 model selected > surface sel > select clear > select #1/A,E,B,F 3087 atoms, 3144 bonds, 393 residues, 1 model selected > surface close > select #1/A,B,C,E 2487 atoms, 2516 bonds, 319 residues, 1 model selected > surface sel > select clear > lighting soft > cartoon #2&nucleic > hide #!1 models > color #1/A,B|#2/A,E red > color #1/C,E|#2/B,F orange > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > roll y > lighting simple [Repeated 1 time(s)] > movie record size 1920, 1080 > movie stop > pwd Current working directory is: C:\Users\Tristan Croll\Desktop > movie encode rotation_test.mp4 Movie saved to rotation_test.mp4 > stop > roll > stop > roll > stop > windowsize size Expected an integer >= 1 or a keyword > windowsize window size 1341 829 OpenGL version: 3.3.0 NVIDIA 529.19 OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: en_GB.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: HP Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC OS: Microsoft Windows 11 Pro (Build 22631) Memory: 34,007,068,672 MaxProcessMemory: 137,438,953,344 CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz OSLanguage: en-GB Installed Packages: -himerax-clipper: 0.22.2 alabaster: 0.7.16 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 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: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 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: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 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: 1.1.3 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: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.7.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-QScore: 1.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 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: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-XMAS: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 comtypes: 1.1.14 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 et-xmlfile: 1.1.0 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openpyxl: 3.1.2 openvr: 1.23.701 packaging: 23.2 pandas: 2.0.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 pprintpp: 0.4.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynmrstar: 3.3.2 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pywin32: 305 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 QtRangeSlider: 0.1.5 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 seaborn: 0.12.2 Send2Trash: 1.8.2 SEQCROW: 1.7.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1 File attachment: 2024-02-07 14-54-23.mkv }}} [attachment:""2024-02-07 14-54-23.mkv""] " defect closed normal Graphics nonchimerax Greg Couch all ChimeraX