"Direct" modeling doesn't handle target deletion relative to template

[Eric Pettersen]

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:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
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    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
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    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202311080002
    ChimeraX-CoreFormats: 1.2
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    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
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    ChimeraX-EMDB-SFF: 1.0
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    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
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    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
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    ChimeraX-Mole: 1.0
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    ChimeraX-TapeMeasure: 1.0
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    ChimeraX-UI: 1.33.3
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    ChimeraX-UnitCell: 1.0.1
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    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
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    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

alignment.ali​

[Eric Pettersen]

Added by email2trac

[Eric Pettersen]

Fix in next daily build.

Fix: ​https://github.com/RBVI/ChimeraX/commit/60e2494fda5f8f56c93d1f1fe1a07b3034f7d88a