id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6333 Show AlphaFold predicted aligned error (PAE) for selected residues Tristan Croll Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Had to give a talk on AlphaFold today (to an actual member of the AlphaFold team - quite nerve-wracking!), which got me thinking more about the PAE matrix. It's a really important source of information - potentially as if not more valuable than the pLDDT values, but currently is really hard for the average user to understand. The attached session contains a case where it's particularly important (might need ISOLDE installed to open it - in any case it's the AlphaFold-DB prediction for P0C7U0, looking at a site where three alpha-helices sit across the face of the N-terminal leucine-rich repeat domain). The pLDDT values for the helices are admittedly at the low end (in the 50-70 range), but the unwary user could easily be fooled into thinking there's a real interaction here. But if you look at the PAE values between residue pairs across the interfaces it becomes immediately obvious it's all spurious - the predicted errors are all above 20 angstroms. Anyway, here's what I was thinking about how to use this: what about a command with a syntax something like ""color pae {selection} relativeTo {residue}""? Then, if {residue} is in position i in the chain, for each residue j in {selection}, color it according to PAE[i,j]. Or probably better, min{PAE[i,j],PAE[j,i]) - if residue i has a reasonably well-defined position but poorly-defined orientation but residue j is well-defined in both, then PAE[i,j] will be large while PAE[j,i] is small. The best analogy I've heard (courtesy of Randy) is a boat in heavy seas vs. the lighthouse - a person on the boat trying to view the lighthouse through a telescope will report a huge error in the position of the lighthouse, but a person in the lighthouse will be able to locate the boat quite precisely. Apart from this scenario, I think it would also be useful for inferring range of mobility around hinges etc. Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open ""/Users/tic20/OneDrive - University of > Cambridge/Documents/Grants/2021_Phenix_R01/P0C7U0_questionable_interface/P0C7U0_questionable_interface.cxs"" Log from Sat Jan 15 14:16:26 2022 > 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: 1.3rc202112030319 (2021-12-03) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > alphafold fetch R01 AI141707 Expected a keyword > alphafold fetch P0C7U0 Fetching compressed AlphaFold P0C7U0 from https://alphafold.ebi.ac.uk/files/AF-P0C7U0-F1-model_v1.cif Chain information for AlphaFold P0C7U0 #1 --- Chain | Description | UniProt A | Protein ELFN1 | ELFN1_HUMAN > show > color byhetero > select @@bfactor<60 3192 atoms, 3276 bonds, 429 residues, 1 model selected > select @@bfactor<50 2702 atoms, 2767 bonds, 362 residues, 1 model selected > style sel sphere Changed 2702 atom styles > style sel stick Changed 2702 atom styles > select @@bfactor<40 2028 atoms, 2043 bonds, 270 residues, 1 model selected > select @@bfactor<50 2702 atoms, 2767 bonds, 362 residues, 1 model selected > select clear > set bgColor white > cofr centerOfView showPivot true > hbonds 474 hydrogen bonds found > ~cartoon @@bfactor<40 > hide @@bfactor<40 > cartoon > show > ui tool show ""Side View"" > camera mono > camera ortho > color lightgrey > color byhetero > ~hbonds > hbonds sideonly 168 hydrogen bonds found > color tan target ar > color byhetero > addh Summary of feedback from adding hydrogens to AlphaFold P0C7U0 #1 --- notes | Termini for AlphaFold P0C7U0 (#1) chain A determined from SEQRES records Chain-initial residues that are actual N termini: /A MET 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A SER 828 Chain-final residues that are not actual C termini: 474 hydrogen bonds 6328 hydrogens added > hide HC > ~hbonds > hbonds 453 hydrogen bonds found > ~hobnds Unknown command: ~hobnds > ~hbonds > hbonds sidechain 145 hydrogen bonds found > select add /A:64@OD2 1 atom, 1 bond, 1 residue, 1 model selected > select up 3 atoms, 1 bond, 2 residues, 1 model selected > select up 36 atoms, 34 bonds, 2 residues, 1 model selected > select add /A:812@CG 37 atoms, 34 bonds, 3 residues, 1 model selected > select add /A:40@CZ2 38 atoms, 35 bonds, 4 residues, 1 model selected > select add /A:43@CG2 39 atoms, 35 bonds, 5 residues, 1 model selected > select add /A:813@CE1 40 atoms, 35 bonds, 6 residues, 1 model selected > select add /A:32@CG1 41 atoms, 35 bonds, 7 residues, 1 model selected > select add /A:816@CG 42 atoms, 35 bonds, 8 residues, 1 model selected > select add /A:30@CE2 43 atoms, 35 bonds, 9 residues, 1 model selected > select add /A:114@NE2 44 atoms, 35 bonds, 10 residues, 1 model selected > select add /A:693@CD 45 atoms, 35 bonds, 11 residues, 1 model selected > select add /A:88@OH 46 atoms, 35 bonds, 12 residues, 1 model selected > select add /A:90@HD22 47 atoms, 35 bonds, 13 residues, 1 model selected > select add /A:93@CD 48 atoms, 35 bonds, 14 residues, 1 model selected > select add /A:689@CB 49 atoms, 35 bonds, 15 residues, 1 model selected > select add /A:690@CG 50 atoms, 35 bonds, 16 residues, 1 model selected > select add /A:686@CB 51 atoms, 35 bonds, 17 residues, 1 model selected > select add /A:138@OH 52 atoms, 35 bonds, 18 residues, 1 model selected > select add /A:117@OH 53 atoms, 35 bonds, 19 residues, 1 model selected > select add /A:700@CE1 54 atoms, 35 bonds, 20 residues, 1 model selected > select up 56 atoms, 35 bonds, 21 residues, 1 model selected > select up 393 atoms, 384 bonds, 21 residues, 1 model selected > hide ~sel > show > hde H Unknown command: hde H > hide H > select add /A:804@CG2 394 atoms, 384 bonds, 22 residues, 1 model selected > select up 409 atoms, 399 bonds, 22 residues, 1 model selected > select up 411 atoms, 400 bonds, 23 residues, 1 model selected > select up 426 atoms, 416 bonds, 23 residues, 1 model selected > select add /A:801@NE 427 atoms, 416 bonds, 24 residues, 1 model selected > select up 450 atoms, 439 bonds, 24 residues, 1 model selected > select add /A:35@OD1 451 atoms, 439 bonds, 25 residues, 1 model selected > select up 462 atoms, 450 bonds, 25 residues, 1 model selected > select up 464 atoms, 451 bonds, 26 residues, 1 model selected > select up 483 atoms, 471 bonds, 26 residues, 1 model selected > select add /A:111@OE1 484 atoms, 471 bonds, 27 residues, 1 model selected > select up 500 atoms, 487 bonds, 27 residues, 1 model selected > select add /A:809@CB 501 atoms, 487 bonds, 28 residues, 1 model selected > select up 512 atoms, 498 bonds, 28 residues, 1 model selected > select add /A:696@CE 513 atoms, 498 bonds, 29 residues, 1 model selected > select up 534 atoms, 519 bonds, 29 residues, 1 model selected > select subtract /A:700@CZ 533 atoms, 519 bonds, 29 residues, 1 model selected > select up 534 atoms, 519 bonds, 29 residues, 1 model selected > hide ~sel > select clear > cd ""C:/Users/tristan/OneDrive - University of > Cambridge/Documents/Grants/2021_Phenix_R01/P0C7U0_questionable_interface"" Current working directory is: C:\Users\tristan\OneDrive - University of Cambridge\Documents\Grants\2021_Phenix_R01\P0C7U0_questionable_interface > hbonds sideonly 145 hydrogen bonds found > select @@display=True 273 atoms, 258 bonds, 29 residues, 1 model selected > show sel&~HC > select up 534 atoms, 519 bonds, 29 residues, 1 model selected > show sel&~HC > select clear > rainbow > color tan target a > color byhetero > cofr showPivot false > select /A:819 24 atoms, 25 bonds, 1 residue, 1 model selected > select /A:817 12 atoms, 11 bonds, 1 residue, 1 model selected > select /A:809@CB 1 atom, 1 residue, 1 model selected > select /A:818 21 atoms, 21 bonds, 1 residue, 1 model selected > label sel > ~label > select /A:816@CB 1 atom, 1 residue, 1 model selected > label sel [Repeated 1 time(s)] > select /A:804@CB 1 atom, 1 residue, 1 model selected > label sel > ~label > select clear > save P0C7U0_apparent_interface.jpg > alphafold fetch P0C7U0 Chain information for AlphaFold P0C7U0 #2 --- Chain | Description | UniProt A | Protein ELFN1 | ELFN1_HUMAN > hide #!1 models > color bfactor #2 palette alphafold 6368 atoms, 828 residues, atom bfactor range 25.1 to 98.2 > select #2@@bfactor<50 2702 atoms, 2767 bonds, 362 residues, 1 model selected > show sel > hide sel > select #2@@bfactor<60 3192 atoms, 3276 bonds, 429 residues, 1 model selected > show sel > hide sel > select clear > select #2@@bfactor<60 3192 atoms, 3276 bonds, 429 residues, 1 model selected > show sel > hide sel > ~cartoon sel > select clear > cartoon sel > select #2@@bfactor<60 3192 atoms, 3276 bonds, 429 residues, 1 model selected > cartoon sel > color sel red > color bfactor #2 palette red-white-blue 6368 atoms, 828 residues, atom bfactor range 25.1 to 98.2 > color bfactor #2 palette red-white-blue range 50,100 6368 atoms, 828 residues, atom bfactor range 25.1 to 98.2 > select clear > save P0C7U0_apparent_interface_color_by_pLDDT_RWB_range_50-100.jpg > alphafold fetch P0C7U0 Chain information for AlphaFold P0C7U0 #3 --- Chain | Description | UniProt A | Protein ELFN1 | ELFN1_HUMAN > hide #2 models > ui tool show Shell Fetching compressed Alphafold P0C7U0 PAE from https://alphafold.ebi.ac.uk/files/AF-P0C7U0-F1-predicted_aligned_error_v1.json > color byattribute r:isolde_domain #3 target ra palette paired-12 range 0,12 6368 atoms, 828 residues, atom isolde_domain range 0 to 7 > select #3/A:693 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:810 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select #3/A:808 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #3/A:689 16 atoms, 14 bonds, 2 residues, 1 model selected > color byattribute r:isolde_domain #3 target ra palette paired-12 range 0,12 6368 atoms, 828 residues, atom isolde_domain range 0 to 12 > select clear > hide #3 models > show #!1 models > save P0C7U0_apparent_interface.jpg > hide #!1 models > show #2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > save P0C7U0_apparent_interface_color_by_pLDDT_RWB_range_50-100.jpg > hide #2 models > show #3 models > save P0C7U0_apparent_interface_PAE_domains.jpg > select #3/A:813 10 atoms, 10 bonds, 1 residue, 1 model selected > select add #3/A:43 18 atoms, 17 bonds, 2 residues, 1 model selected > select sel@@CA Expected an objects specifier or a keyword > select sel&@CA 2 atoms, 2 residues, 1 model selected > show sel > label sel text ""PAE = 23.7 "" > select #3/A:697 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #3/A:161 12 atoms, 10 bonds, 2 residues, 1 model selected > select sel&@CA 2 atoms, 2 residues, 1 model selected > show sel [Repeated 1 time(s)] > select sel&@CA 2 atoms, 1 pseudobond, 2 residues, 2 models selected > select sel&@CA 2 atoms, 1 pseudobond, 2 residues, 2 models selected > show sel > select up 12 atoms, 10 bonds, 1 pseudobond, 2 residues, 2 models selected > show sel > select clear > label sel text ""PAE = 27.5 "" > select #3/A:693 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:692 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #3/A:808 14 atoms, 12 bonds, 2 residues, 1 model selected > select sel&@CA 2 atoms, 2 residues, 1 model selected > show sel > hide sel > show sel > select clear [Repeated 1 time(s)] > label sel text ""PAE = 26.9 "" > hide #!3 models > show #!1 models > hide #!1 models > show #2 models > hide #2 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > show #!3 models > label sel text ""PAE = 26.9 "" offset -2,0 Invalid ""offset"" argument: Need exactly 3 ','-separated numbers > usage label label [objects] [objectType] [text text] [offset offset] [color color] [bgColor bgColor] [size size] [height height] [defaultHeight a number] [font a text string] [attribute a text string] [onTop true or false] — Create atom labels objects: an objects specifier or nothing objectType: one of atoms, bonds, pseudobonds, or residues text: default or a text string offset: default or some numbers color: one of auto or default or a color bgColor: none or a color size: default or an integer height: fixed or a number label delete [objects] [objectType] — Delete atom labels objects: an objects specifier or nothing objectType: one of atoms, bonds, pseudobonds, or residues label listfonts — List available fonts label orient [orient] — Set label orientation updating orient: a number > label sel text ""PAE = 26.9 "" offset 0,-5,0 > label sel text ""PAE = 26.9 "" offset 0,2,0 > label sel text ""PAE = 26.9 "" offset 0,1,0 > label sel text ""PAE = 26.9 "" offset -0.5,1,0 > label sel text ""PAE = 26.9 "" offset -1,1,0 > select clear > show #!1 models > hide #!3 models > save P0C7U0_apparent_interface_ribbon_color_by_rainbow_N-C.jpg > hide #!1 models > show #2 models > save P0C7U0_apparent_interface_color_by_pLDDT_RWB_range_50-100.jpg > hide #2 models > show #!3 models > save P0C7U0_apparent_interface_PAE_domains.jpg > save P0C7U0_questionable_interface.cxs > hide #!3 models > show #!1 models > save P0C7U0_apparent_interface_ribbon_color_by_rainbow_N-C.jpg > hide #!1 models > show #2 models > save P0C7U0_apparent_interface_color_by_pLDDT_RWB_range_50-100.jpg > hide #2 models > show #!3 models > hide #!3 models > show #!1 models > show #!3 models > hide #!3 models > save P0C7U0_apparent_interface_ribbon_color_by_rainbow_N-C.jpg > hide #!1 models > show #2 models > save P0C7U0_apparent_interface_color_by_pLDDT_RWB_range_50-100.jpg > hide #2 models > show #!3 models > save P0C7U0_apparent_interface_PAE_domains.jpg > usage label label [objects] [objectType] [text text] [offset offset] [color color] [bgColor bgColor] [size size] [height height] [defaultHeight a number] [font a text string] [attribute a text string] [onTop true or false] — Create atom labels objects: an objects specifier or nothing objectType: one of atoms, bonds, pseudobonds, or residues text: default or a text string offset: default or some numbers color: one of auto or default or a color bgColor: none or a color size: default or an integer height: fixed or a number label delete [objects] [objectType] — Delete atom labels objects: an objects specifier or nothing objectType: one of atoms, bonds, pseudobonds, or residues label listfonts — List available fonts label orient [orient] — Set label orientation updating orient: a number > label size 20 > label size 40 > label size 80 > label size 1 > label size 2 > label size 3 > label size 4 > label size 20 > label size 40 > label height 2 > label height 1 > label height 1.5 > label height 1.5 size 50 > label sel offset -5,0,0 > label sel offset -7,0,0 > select clear > hide #!3 models > show #!1 models > show #!3 models > hide #!3 models > save P0C7U0_apparent_interface_ribbon_color_by_rainbow_N-C.jpg > hide #!1 models > show #2 models > save P0C7U0_apparent_interface_color_by_pLDDT_RWB_range_50-100.jpg > hide #2 models > show #!3 models > save P0C7U0_apparent_interface_PAE_domains.jpg > label sel text ""PAE = 23.7 Å "" > label sel text ""PAE = 26.9 Å "" > label sel text ""PAE = 27.5 Å "" > select clear > save P0C7U0_apparent_interface_PAE_domains.jpg > save P0C7U0_questionable_interface.cxs ——— End of log from Sat Jan 15 14:16:26 2022 ——— opened ChimeraX session > ui tool show ""Selection Inspector"" > select #3/A:813 10 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:693 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:689 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:803 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:800 8 atoms, 7 bonds, 1 residue, 1 model selected OpenGL version: 4.1 INTEL-16.4.5 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir7,2 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1.6 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 427.0.0.0.0 SMC Version (system): 2.27f2 Software: System Software Overview: System Version: macOS 11.4 (20F71) Kernel Version: Darwin 20.5.0 Time since boot: 213 days 9:37 Graphics/Displays: Intel HD Graphics 6000: Chipset Model: Intel HD Graphics 6000 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1626 Revision ID: 0x0009 Metal Family: Supported, Metal GPUFamily macOS 1 Displays: Color LCD: Display Type: LCD Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus) UI Looks like: 1440 x 900 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.3 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 File attachment: P0C7U0_questionable_interface.cxs }}} [attachment:""P0C7U0_questionable_interface.cxs""] " enhancement assigned normal Structure Prediction Eric Pettersen phil.cruz@… all ChimeraX