Opened 2 years ago
Closed 23 months ago
#10244 closed defect (fixed)
"Direct" modeling doesn't handle target deletion relative to template
Reported by: | Eric Pettersen | Owned by: | Eric Pettersen |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Structure Prediction | Version: | |
Keywords: | Cc: | Elaine Meng | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-12.7.1-x86_64-i386-64bit ChimeraX Version: 1.7.dev202311080002 (2023-11-08 00:02:18 UTC) Description If the template is directly assocated with target, then modeling fails where the target has a deletion relative to the sequence. Log: UCSF ChimeraX version: 1.7.dev202311080002 (2023-11-08) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/pett/rm/alignment.ali Summary of feedback from opening /Users/pett/rm/alignment.ali --- note | Alignment identifier is alignment.ali Opened 1 sequences from alignment.ali > open /Users/pett/rm/EOGG2KP8FQQJNC4G/2Q7Y_clean_format.pdb_1.pdb Chain information for 2Q7Y_clean_format.pdb_1.pdb #1 --- Chain | Description C | No description available D | No description available > sequence associate /C Associated 2Q7Y_clean_format.pdb_1.pdb chain C to chain_C with 87 mismatches and/or gaps > ui tool show "Modeller Comparative" > modeller comparative alignment.ali:1 numModels 3 fast false multichain true > hetPreserve false hydrogens false waterPreserve false directory > /Users/pett/rm Webservices job id: GCVVGQW9762J1460 Modeller job (ID GCVVGQW9762J1460) finished Modeller error output Traceback (most recent call last): File "ModellerModelling.py", line 72, in <module> a.make() File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 141, in make self.homcsr(exit_stage) File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 625, in homcsr self.check_alignment(aln) File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 578, in check_alignment aln.check() File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in check self.check_structure_structure(io=io) File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : Modeller run output MODELLER 10.4, 2022/10/28, r12463 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2022 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux wilkins.cgl.ucsf.edu 4.18.0-477.21.1.el8_8.x86_64 x86_64 Date and time of compilation : 2022/10/28 21:02:55 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2023/11/28 11:24:13 environ____W> The class 'environ' is deprecated; use 'Environ' instead openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL10v4}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL10v4}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592 0.183 openf___224_> Open ${MODINSTALL10v4}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053 0.230 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL10v4}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041 0.242 openf___224_> Open ${MODINSTALL10v4}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL10v4}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL10v4}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL10v4}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL10v4}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL10v4}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead openf___224_> Open alignment.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282425 275.806 0.269 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297517 290.544 0.284 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 312917 305.583 0.298 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343717 335.661 0.328 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405317 395.817 0.387 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405345 395.845 0.387 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405373 395.872 0.387 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 406829 397.294 0.388 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 407913 398.353 0.389 Read the alignment from file : alignment.ali Total number of alignment positions: 370 # Code #_Res #_Segm PDB_code Name \------------------------------------------------------------------------------- 1 2Q7Y_clea 365 2 2Q7Y_clean_ 2 chain_C 272 1 chain_C check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ./2Q7Y_clean_format.pdb_1.pdb_1.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 519138 506.971 0.495 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 519138 506.971 0.495 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 519309 507.138 0.495 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 520159 507.968 0.496 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 521417 509.196 0.497 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 523321 511.056 0.499 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 526177 513.845 0.502 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 526177 513.845 0.502 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 526267 513.933 0.502 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 526267 513.933 0.502 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 526402 514.064 0.502 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 530686 518.248 0.506 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 530686 518.248 0.506 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 530884 518.441 0.506 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 537310 524.717 0.512 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 546932 534.113 0.522 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 546932 534.113 0.522 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 547229 534.403 0.522 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 547229 534.403 0.522 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 547679 534.843 0.522 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 562129 548.954 0.536 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 562129 548.954 0.536 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 562804 549.613 0.537 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 584462 570.764 0.557 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 584462 570.764 0.557 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 584462 570.764 0.557 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 584462 570.764 0.557 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 585470 571.748 0.558 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 617974 603.490 0.589 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 617974 603.490 0.589 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 619486 604.967 0.591 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 668242 652.580 0.637 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 667608 651.961 0.637 read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 82) Alignment ELVKMPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLD PDB ELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSW Match ***** * * Alignment residue type 13 (P, PRO) does not match pdb residue type 11 (M, MET), for align code 2Q7Y_clean_format.pdb_1.pdb_1 (atom file 2Q7Y_clean_format.pdb_1.pdb_1), pdb residue number " 88", chain "C" Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 1 2Q7Y_clean_format.pdb_1.pdb_1 No output models from Modeller; see log for Modeller text output. Traceback (most recent call last): File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py", line 717, in customEvent func(*args, **kw) File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/modeller/common.py", line 602, in on_finish self.caller.process_ok_models(model_info, get_pdb_model) ^^^^^^^^^^ UnboundLocalError: cannot access local variable 'model_info' where it is not associated with a value UnboundLocalError: cannot access local variable 'model_info' where it is not associated with a value File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/modeller/common.py", line 602, in on_finish self.caller.process_ok_models(model_info, get_pdb_model) ^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 INTEL-18.8.6 OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200 OpenGL vendor: Intel Inc. Python: 3.11.2 Locale: en_US.UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Memory: 16 GB System Firmware Version: 486.0.0.0.0 OS Loader Version: 540.120.3~37 SMC Version (system): 2.32f21 Software: System Software Overview: System Version: macOS 12.7.1 (21G920) Kernel Version: Darwin 21.6.0 Time since boot: 3:47 Graphics/Displays: Intel Iris Pro Graphics 6200: Chipset Model: Intel Iris Pro Graphics 6200 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1622 Revision ID: 0x000a Metal Family: Supported, Metal GPUFamily macOS 1 Displays: iMac: Display Type: LCD Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.12 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.50 ChimeraX-AtomicLibrary: 12.1.2 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: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 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.dev202311080002 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: 1.1.2 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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.1 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-MatchAlign: 1.0 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 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: 1.5.12 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-NIHPresets: 1.1.14 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.2.1 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.2 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: 1.13 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-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.1.0 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: 4.40.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2023.3.16 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.1 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 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: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.8.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.6 PyOpenGL-accelerate: 3.1.6 pyparsing: 3.1.0 pyproject-hooks: 1.0.0 PyQt6: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.1.0 qtconsole: 5.4.3 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 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: 3.8.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.2 traitlets: 5.9.0 typing-extensions: 4.6.3 tzdata: 2023.3 urllib3: 2.0.3 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 File attachment: alignment.ali
Attachments (1)
Change History (3)
by , 2 years ago
Attachment: | alignment.ali added |
---|
comment:1 by , 2 years ago
Cc: | added |
---|---|
Component: | Unassigned → Structure Prediction |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → "Direct" modeling doesn't handle target deletion relative to template |
comment:2 by , 23 months ago
Resolution: | → fixed |
---|---|
Status: | accepted → closed |
Fix in next daily build.
Fix: https://github.com/RBVI/ChimeraX/commit/60e2494fda5f8f56c93d1f1fe1a07b3034f7d88a
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