Bug in matchmaker secondary structure code revamp

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202209281710 (2022-09-28 17:10:28 UTC)
Description
morph AttributeError: 'set' object has no attribute 'items'

open 2gbp
open 2fw0
mm #2 to #1
morph #1,2

.... gives traceback.  This same set of commands works fine in version 1.4.

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start toolshed show $1

> alias whereprefs info path user unversioned config

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> http://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias segtest open 0557 from emdb; vol threshold #1 min 0; vol scale #2
> value uint8; open 6nzk

executed startup.cxc  
UCSF ChimeraX version: 1.5.dev202209281710 (2022-09-28)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> usage save format mmcif

save name [allCoordsets true or false] [displayedOnly true or false] [models a
models specifier] [relModel a model specifier] [selectedOnly true or false]
[fixedWidth true or false] [bestGuess true or false] [computedSheets true or
false]  
— save data to mmcif format  
names: name of a file to save/write; a name of 'browse' will bring up a file
browser  

> open 2gbp

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #1  
---  
Chain | Description | UniProt  
A | D-GALACTOSE/D-GLUCOSE BINDING PROTEIN | DGAL_ECOLI  
  
Non-standard residues in 2gbp #1  
---  
BGC — β-D-glucose  
CA — calcium ion  
  

> open 2fw0

2fw0 title:  
Apo Open Form of Glucose/Galactose Binding Protein [more info...]  
  
Chain information for 2fw0 #2  
---  
Chain | Description | UniProt  
A | D-galactose-binding periplasmic protein | DGAL_ECOLI  
  
Non-standard residues in 2fw0 #2  
---  
CA — calcium ion  
CIT — citric acid  
MLA — malonic acid (dicarboxylic acid C3; propanediolic acid;
methanedicarboxylic acid)  
NA — sodium ion  
  

> mmaker #2 to #1

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 2gbp, chain A (#1) with 2fw0, chain A (#2), sequence alignment
score = 1563.6  
RMSD between 147 pruned atom pairs is 0.425 angstroms; (across all 305 pairs:
7.702)  
  

> morph #1,2

Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/morph/motion.py", line 111, in segment_and_pair_atoms  
results = segmentHingeExact(sm, m, cf, mhs, log=log)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/morph/segment.py", line 109, in segmentHingeExact  
raise AtomPairingError('%s chain %s (%d) and %s chain %s (%d) have different
number of residues'  
chimerax.morph.segment.AtomPairingError: Morph - 2gbp chain A (525) and 2fw0
chain A (661) have different number of residues  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/morph/morph.py", line 73, in morph  
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/morph/motion.py", line 24, in compute_morph  
res_groups, atom_map, trimmed = motion.segment_and_pair_atoms(mol)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/morph/motion.py", line 114, in segment_and_pair_atoms  
results = segmentHingeApproximate(sm, m, cf, mhs, log=log)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/morph/segment.py", line 190, in segmentHingeApproximate  
score, gapped0, gapped1 = align(session, seq0, seq1,  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
AttributeError: 'set' object has no attribute 'items'  
  
AttributeError: 'set' object has no attribute 'items'  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-14.0.32 355.11.11.10.10.143
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac13,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 8 GB
      Boot ROM Version: 429.0.0.0.0
      SMC Version (system): 2.11f16

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2026)
      Kernel Version: Darwin 19.6.0
      Time since boot: 20 days 23:46

Graphics/Displays:

    NVIDIA GeForce GTX 675MX:

      Chipset Model: NVIDIA GeForce GTX 675MX
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 1 GB
      Vendor: NVIDIA (0x10de)
      Device ID: 0x11a2
      Revision ID: 0x00a2
      ROM Revision: 3707
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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[Eric Pettersen]

Duplicate of #7695 -- adding Elaine to recipient list for that ticket.