Matchmaker: no reference chains

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_15/Dro_real_space_refined_013_coot1_real_space_refined_015.pdb

Summary of feedback from opening
/Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_15/Dro_real_space_refined_013_coot1_real_space_refined_015.pdb  
---  
warnings | Ignored bad PDB record found on line 475  
LINK SG CYS V1 394 FE4 SF4 V1 502  
  
Ignored bad PDB record found on line 476  
LINK SG CYS V1 400 FE1 SF4 V1 502  
  
Ignored bad PDB record found on line 477  
LINK SG CYS V1 440 FE2 SF4 V1 502  
  
Ignored bad PDB record found on line 478  
LINK SG CYS V1 397 FE3 SF4 V1 502  
  
Ignored bad PDB record found on line 479  
LINK SG CYS V2 128 FE1 FES V2 301  
  
59 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 331 331 PROA7 10 LEUA7
20 1 11  
Start residue of secondary structure not found: HELIX 332 332 TYRA7 57 ARGA7
60 5 4  
Start residue of secondary structure not found: HELIX 333 333 GLYA7 62 GLUA7
65 1 4  
Start residue of secondary structure not found: HELIX 334 334 LEUA7 72 GLNA7
78 1 7  
  
Chain information for
Dro_real_space_refined_013_coot1_real_space_refined_015.pdb #1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
4L | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
A1 | No description available  
A3 | No description available  
A5 | No description available  
A6 | No description available  
A8 | No description available  
A9 | No description available  
AB | No description available  
AC | No description available  
AL | No description available  
AM | No description available  
AN | No description available  
AO | No description available  
B1 | No description available  
B2 | No description available  
B3 | No description available  
B4 | No description available  
B5 | No description available  
B6 | No description available  
B7 | No description available  
B8 | No description available  
B9 | No description available  
BL | No description available  
BM | No description available  
C2 | No description available  
S1 | No description available  
S2 | No description available  
S3 | No description available  
S4 | No description available  
S5 | No description available  
S6 | No description available  
S7 | No description available  
S8 | No description available  
V1 | No description available  
V2 | No description available  
V3 | No description available  
  

> set bgColor white

> hide atoms

> show cartoons

> color #1 cyan

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft

> open
> /Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_16/Dro_real_space_refined_014_coot2_real_space_refined_016.pdb

Summary of feedback from opening
/Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_16/Dro_real_space_refined_014_coot2_real_space_refined_016.pdb  
---  
warnings | Ignored bad PDB record found on line 475  
LINK SG CYS V1 394 FE4 SF4 V1 502  
  
Ignored bad PDB record found on line 476  
LINK SG CYS V1 400 FE1 SF4 V1 502  
  
Ignored bad PDB record found on line 477  
LINK SG CYS V1 440 FE2 SF4 V1 502  
  
Ignored bad PDB record found on line 478  
LINK SG CYS V1 397 FE3 SF4 V1 502  
  
Ignored bad PDB record found on line 479  
LINK SG CYS V2 128 FE1 FES V2 301  
  
61 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 140 140 LEUA8 34 CYSA8
38 1 5  
Start residue of secondary structure not found: HELIX 141 141 ALAA8 41 GLUA8
51 1 11  
Start residue of secondary structure not found: HELIX 142 142 VALA8 65 LYSA8
78 1 14  
Start residue of secondary structure not found: HELIX 143 143 HISA8 81 LEUA8
91 1 11  
Start residue of secondary structure not found: HELIX 144 144 THRA8 106 PHEA8
118 1 13  
  
Chain information for
Dro_real_space_refined_014_coot2_real_space_refined_016.pdb #2  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
4L | No description available  
5 | No description available  
6 | No description available  
8 | No description available  
A1 | No description available  
A3 | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A9 | No description available  
AB | No description available  
AC | No description available  
AL | No description available  
AM | No description available  
AN | No description available  
AO | No description available  
B1 | No description available  
B2 | No description available  
B3 | No description available  
B4 | No description available  
B5 | No description available  
B6 | No description available  
B7 | No description available  
B8 | No description available  
B9 | No description available  
BL | No description available  
BM | No description available  
C2 | No description available  
S1 | No description available  
S2 | No description available  
S3 | No description available  
S4 | No description available  
S5 | No description available  
S6 | No description available  
S7 | No description available  
S8 | No description available  
V1 | No description available  
V2 | No description available  
V3 | No description available  
  

> hide atoms

> show cartoons

> mmaker #1 to #2

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 Dro_real_space_refined_014_coot2_real_space_refined_016.pdb, chain
S1 (#2) with Dro_real_space_refined_013_coot1_real_space_refined_015.pdb,
chain S1 (#1), sequence alignment score = 3315.8  
RMSD between 687 pruned atom pairs is 0.442 angstroms; (across all 693 pairs:
0.497)  
  

> mmaker #2/1 to #2/1

Traceback (most recent call last):  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2868, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 3404, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/match_maker/match.py", line 659, in cmd_match  
match_items = (refs[0], matches)  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/match_maker/match.py", line 659, in cmd_match  
match_items = (refs[0], matches)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-14.0.32 355.11.11.10.10.143
OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine
OpenGL vendor: NVIDIA CorporationHardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac14,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 432.60.3.0.0
      SMC Version (system): 2.17f7

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1615)
      Kernel Version: Darwin 19.6.0
      Time since boot: 17 days 20:48

Graphics/Displays:

    NVIDIA GeForce GT 750M:

      Chipset Model: NVIDIA GeForce GT 750M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 1 GB
      Vendor: NVIDIA (0x10de)
      Device ID: 0x0fe9
      Revision ID: 0x00a2
      ROM Revision: 3762
      Metal: Supported, feature set macOS GPUFamily1 v4
      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: No
          Connection Type: Internal
        HP VH240a:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: 6CM1160B4N  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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