Opened 3 years ago

Closed 2 years ago

#9003 closed defect (can't reproduce)

Crash in removeRow() when Modeller Comparative tool shown again

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000070000f225000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700005554000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700019243000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700018240000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001723d000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001623a000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700015237000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700014234000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700013231000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001222e000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001122b000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700010228000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070000e222000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007ff84bb96680 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/modeller/tool.py", line 340 in _update_sequence_menus
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seqalign/widgets.py", line 34 in _items_change
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/item_chooser.py", line 79 in showEvent
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2454 in shown
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2197 in _mw_set_shown
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1891 in _tool_window_request_shown
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2100 in shown
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 793 in set_tool_shown
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 350 in set_tool_shown
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 175 in 
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 368 in thread_safe
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 174 in display
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/cmd.py", line 210 in ui_tool_show
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1656 in 
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


{"app_name":"ChimeraX","timestamp":"2023-05-12 11:49:32.00 -0400","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.2.1 (22D68)","roots_installed":0,"name":"ChimeraX","incident_id":"0D79F755-8C46-4989-A99B-83B9D094C0AE"}
{
  "uptime" : 4000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,2",
  "coalitionID" : 565,
  "osVersion" : {
    "train" : "macOS 13.2.1",
    "build" : "22D68",
    "releaseType" : "User"
  },
  "captureTime" : "2023-05-12 11:49:29.7308 -0400",
  "incident" : "0D79F755-8C46-4989-A99B-83B9D094C0AE",
  "pid" : 492,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-05-12 10:41:52.2364 -0400",
  "procStartAbsTime" : 18569821246,
  "procExitAbsTime" : 4076083049706,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"3E438169-16F6-591F-8656-2489DFFEB8E2","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "3223F3F7-D3F2-3BE2-1352-3B6C6784B010",
  "throttleTimeout" : 2147483647,
  "bridgeVersion" : {"build":"20P3045","train":"7.2"},
  "sip" : "enabled",
  "vmRegionInfo" : "0xf8 is not in any region.  Bytes before following region: 140737487187720\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      shared memory            7fffffee3000-7fffffee4000 [    4K] r-x\/r-x SM=SHM  ",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000f8","rawCodes":[1,248],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000f8"},
  "ktriageinfo" : "VM - Waiting on busy page was interrupted\n",
  "vmregioninfo" : "0xf8 is not in any region.  Bytes before following region: 140737487187720\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      shared memory            7fffffee3000-7fffffee4000 [    4K] r-x\/r-x SM=SHM  ",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/pierceherbert/Desktop/Research/Group 1/Tam I/6XA2.pdb" format
> pdb

6XA2.pdb title:  
Structure of the tirandamycin C-bound P450 monooxygenase tami [more info...]  
  
Chain information for 6XA2.pdb #1  
---  
Chain | Description | UniProt  
A B E F G H | TAMI | D3Y1J3_9ACTN 2-413  
C | TAMI | D3Y1J3_9ACTN 2-413  
D | TAMI | D3Y1J3_9ACTN 2-413  
  
Non-standard residues in 6XA2.pdb #1  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
V0A —
(3E)-3-{(2E,4E,6R)-1-hydroxy-4-methyl-6-[(1R,3R,4S,5R)-1,4,8-trimethyl-2,9-dioxabicyclo[3.3.1]non-7-en-3-yl]hepta-2,4-dien-1-ylidene}-2H-pyrrole-2,4(3H)-dione
(tirandamycin C)  
  

> open /Users/pierceherbert/Desktop/Research/CYP168A1.fasta

Summary of feedback from opening
/Users/pierceherbert/Desktop/Research/CYP168A1.fasta  
---  
note | Alignment identifier is CYP168A1.fasta  
  
Opened 1 sequences from CYP168A1.fasta  

> open "/Users/pierceherbert/Desktop/Research/Models/TAMI/TAM I:tirandamycin
> C.fasta"

Summary of feedback from opening
/Users/pierceherbert/Desktop/Research/Models/TAMI/TAM I:tirandamycin C.fasta  
---  
notes | Illegal ':' character in alignment identifier replaced with '/'  
Alignment identifier is TAM I/tirandamycin C.fasta  
Associated 6XA2.pdb chain A to 6XA2_1|Chains A, B, C, D, E, F, G,
H|TamI|Streptomyces sp. 307-9 (529089) with 0 mismatches  
Associated 6XA2.pdb chain B to 6XA2_1|Chains A, B, C, D, E, F, G,
H|TamI|Streptomyces sp. 307-9 (529089) with 0 mismatches  
Associated 6XA2.pdb chain E to 6XA2_1|Chains A, B, C, D, E, F, G,
H|TamI|Streptomyces sp. 307-9 (529089) with 0 mismatches  
Associated 6XA2.pdb chain F to 6XA2_1|Chains A, B, C, D, E, F, G,
H|TamI|Streptomyces sp. 307-9 (529089) with 0 mismatches  
Associated 6XA2.pdb chain G to 6XA2_1|Chains A, B, C, D, E, F, G,
H|TamI|Streptomyces sp. 307-9 (529089) with 0 mismatches  
3 messages similar to the above omitted  
Showing conservation header ("seq_conservation" residue attribute) for
alignment TAM I/tirandamycin C.fasta  
  
Opened 2 sequences from TAM I:tirandamycin C.fasta  

> select all

25091 atoms, 25438 bonds, 40 pseudobonds, 3422 residues, 3 models selected  

> hide sel atoms

> select #1/A

3166 atoms, 3199 bonds, 5 pseudobonds, 440 residues, 3 models selected  

> show sel cartoons

> ui tool show "Modeller Comparative"

> modeller comparative "TAM I/tirandamycin C.fasta:2" numModels 10 fast false
> multichain true hetPreserve true hydrogens false waterPreserve false

Cannot preserve water/het with more than one template per target; not
preserving  

Webservices job id: 531O745PHT3ICK2A  

> ui mousemode right select

Drag select of 399 residues, 1 pseudobonds  

> select clear

Drag select of 399 residues, 1 pseudobonds  

> select clear

Drag select of 27 residues  

> select clear

> ui mousemode right translate

Modeller job (ID 531O745PHT3ICK2A) finished  
Parameters  
---  
Chain pairing | ss  
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 6XA2.pdb, chain A (#1) with cyp168a1, chain A (#), sequence
alignment score = 790.3  
Matchmaker 6XA2.pdb, chain B (#1) with cyp168a1, chain B (#), sequence
alignment score = 812.6  
Matchmaker 6XA2.pdb, chain C (#1) with cyp168a1, chain C (#), sequence
alignment score = 788.4  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain D (#), sequence
alignment score = 804  
Matchmaker 6XA2.pdb, chain E (#1) with cyp168a1, chain E (#), sequence
alignment score = 815.2  
Matchmaker 6XA2.pdb, chain F (#1) with cyp168a1, chain F (#), sequence
alignment score = 825  
Matchmaker 6XA2.pdb, chain G (#1) with cyp168a1, chain G (#), sequence
alignment score = 788  
Matchmaker 6XA2.pdb, chain H (#1) with cyp168a1, chain H (#), sequence
alignment score = 812  
RMSD between 2859 pruned atom pairs is 1.029 angstroms; (across all 3137
pairs: 2.540)  
  
Parameters  
---  
Chain pairing | ss  
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 6XA2.pdb, chain A (#1) with cyp168a1, chain A (#), sequence
alignment score = 796.8  
Matchmaker 6XA2.pdb, chain B (#1) with cyp168a1, chain B (#), sequence
alignment score = 803.4  
Matchmaker 6XA2.pdb, chain C (#1) with cyp168a1, chain C (#), sequence
alignment score = 779.4  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain D (#), sequence
alignment score = 807.8  
Matchmaker 6XA2.pdb, chain E (#1) with cyp168a1, chain E (#), sequence
alignment score = 788.5  
Matchmaker 6XA2.pdb, chain F (#1) with cyp168a1, chain F (#), sequence
alignment score = 808.6  
Matchmaker 6XA2.pdb, chain G (#1) with cyp168a1, chain G (#), sequence
alignment score = 812.6  
Matchmaker 6XA2.pdb, chain H (#1) with cyp168a1, chain H (#), sequence
alignment score = 809.7  
RMSD between 2759 pruned atom pairs is 0.985 angstroms; (across all 3137
pairs: 2.557)  
  
Parameters  
---  
Chain pairing | ss  
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 6XA2.pdb, chain A (#1) with cyp168a1, chain A (#), sequence
alignment score = 821.4  
Matchmaker 6XA2.pdb, chain B (#1) with cyp168a1, chain B (#), sequence
alignment score = 804.7  
Matchmaker 6XA2.pdb, chain C (#1) with cyp168a1, chain C (#), sequence
alignment score = 796.9  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain D (#), sequence
alignment score = 800.4  
Matchmaker 6XA2.pdb, chain E (#1) with cyp168a1, chain E (#), sequence
alignment score = 794.8  
Matchmaker 6XA2.pdb, chain F (#1) with cyp168a1, chain F (#), sequence
alignment score = 798.7  
Matchmaker 6XA2.pdb, chain G (#1) with cyp168a1, chain G (#), sequence
alignment score = 798.2  
Matchmaker 6XA2.pdb, chain H (#1) with cyp168a1, chain H (#), sequence
alignment score = 795.7  
RMSD between 2425 pruned atom pairs is 1.140 angstroms; (across all 3137
pairs: 2.759)  
  
Parameters  
---  
Chain pairing | ss  
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 6XA2.pdb, chain A (#1) with cyp168a1, chain A (#), sequence
alignment score = 789.6  
Matchmaker 6XA2.pdb, chain B (#1) with cyp168a1, chain B (#), sequence
alignment score = 823.4  
Matchmaker 6XA2.pdb, chain C (#1) with cyp168a1, chain C (#), sequence
alignment score = 795.6  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain D (#), sequence
alignment score = 804  
Matchmaker 6XA2.pdb, chain E (#1) with cyp168a1, chain E (#), sequence
alignment score = 808  
Matchmaker 6XA2.pdb, chain F (#1) with cyp168a1, chain F (#), sequence
alignment score = 805.3  
Matchmaker 6XA2.pdb, chain G (#1) with cyp168a1, chain G (#), sequence
alignment score = 791.1  
Matchmaker 6XA2.pdb, chain H (#1) with cyp168a1, chain H (#), sequence
alignment score = 812  
RMSD between 2128 pruned atom pairs is 1.117 angstroms; (across all 3137
pairs: 3.340)  
  
Parameters  
---  
Chain pairing | ss  
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 6XA2.pdb, chain A (#1) with cyp168a1, chain A (#), sequence
alignment score = 796.8  
Matchmaker 6XA2.pdb, chain B (#1) with cyp168a1, chain B (#), sequence
alignment score = 801  
Matchmaker 6XA2.pdb, chain C (#1) with cyp168a1, chain C (#), sequence
alignment score = 777.6  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain D (#), sequence
alignment score = 830  
Matchmaker 6XA2.pdb, chain E (#1) with cyp168a1, chain E (#), sequence
alignment score = 798.7  
Matchmaker 6XA2.pdb, chain F (#1) with cyp168a1, chain F (#), sequence
alignment score = 815.2  
Matchmaker 6XA2.pdb, chain G (#1) with cyp168a1, chain G (#), sequence
alignment score = 801.8  
Matchmaker 6XA2.pdb, chain H (#1) with cyp168a1, chain H (#), sequence
alignment score = 812  
RMSD between 2315 pruned atom pairs is 1.231 angstroms; (across all 3137
pairs: 2.929)  
  
Parameters  
---  
Chain pairing | ss  
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 6XA2.pdb, chain A (#1) with cyp168a1, chain A (#), sequence
alignment score = 796.1  
Matchmaker 6XA2.pdb, chain B (#1) with cyp168a1, chain B (#), sequence
alignment score = 810.6  
Matchmaker 6XA2.pdb, chain C (#1) with cyp168a1, chain C (#), sequence
alignment score = 788.4  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain D (#), sequence
alignment score = 793.3  
Matchmaker 6XA2.pdb, chain E (#1) with cyp168a1, chain E (#), sequence
alignment score = 813.7  
Matchmaker 6XA2.pdb, chain F (#1) with cyp168a1, chain F (#), sequence
alignment score = 803.5  
Matchmaker 6XA2.pdb, chain G (#1) with cyp168a1, chain G (#), sequence
alignment score = 805.4  
Matchmaker 6XA2.pdb, chain H (#1) with cyp168a1, chain H (#), sequence
alignment score = 830  
RMSD between 2234 pruned atom pairs is 0.993 angstroms; (across all 3137
pairs: 2.967)  
  
Parameters  
---  
Chain pairing | ss  
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 6XA2.pdb, chain A (#1) with cyp168a1, chain A (#), sequence
alignment score = 803.3  
Matchmaker 6XA2.pdb, chain B (#1) with cyp168a1, chain B (#), sequence
alignment score = 776.6  
Matchmaker 6XA2.pdb, chain C (#1) with cyp168a1, chain C (#), sequence
alignment score = 781.2  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain D (#), sequence
alignment score = 804  
Matchmaker 6XA2.pdb, chain E (#1) with cyp168a1, chain E (#), sequence
alignment score = 788.5  
Matchmaker 6XA2.pdb, chain F (#1) with cyp168a1, chain F (#), sequence
alignment score = 798.7  
Matchmaker 6XA2.pdb, chain G (#1) with cyp168a1, chain G (#), sequence
alignment score = 797.6  
Matchmaker 6XA2.pdb, chain H (#1) with cyp168a1, chain H (#), sequence
alignment score = 825.8  
RMSD between 2809 pruned atom pairs is 0.938 angstroms; (across all 3137
pairs: 2.605)  
  
Parameters  
---  
Chain pairing | ss  
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 6XA2.pdb, chain A (#1) with cyp168a1, chain A (#), sequence
alignment score = 808.2  
Matchmaker 6XA2.pdb, chain B (#1) with cyp168a1, chain B (#), sequence
alignment score = 798.7  
Matchmaker 6XA2.pdb, chain C (#1) with cyp168a1, chain C (#), sequence
alignment score = 774  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain D (#), sequence
alignment score = 804  
Matchmaker 6XA2.pdb, chain E (#1) with cyp168a1, chain E (#), sequence
alignment score = 787.3  
Matchmaker 6XA2.pdb, chain F (#1) with cyp168a1, chain F (#), sequence
alignment score = 797.5  
Matchmaker 6XA2.pdb, chain G (#1) with cyp168a1, chain G (#), sequence
alignment score = 754.4  
Matchmaker 6XA2.pdb, chain H (#1) with cyp168a1, chain H (#), sequence
alignment score = 811.4  
RMSD between 2778 pruned atom pairs is 1.059 angstroms; (across all 3137
pairs: 2.615)  
  
Parameters  
---  
Chain pairing | ss  
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 6XA2.pdb, chain A (#1) with cyp168a1, chain A (#), sequence
alignment score = 812.4  
Matchmaker 6XA2.pdb, chain B (#1) with cyp168a1, chain B (#), sequence
alignment score = 808.8  
Matchmaker 6XA2.pdb, chain C (#1) with cyp168a1, chain C (#), sequence
alignment score = 791.4  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain D (#), sequence
alignment score = 832.8  
Matchmaker 6XA2.pdb, chain E (#1) with cyp168a1, chain E (#), sequence
alignment score = 807.7  
Matchmaker 6XA2.pdb, chain F (#1) with cyp168a1, chain F (#), sequence
alignment score = 795.7  
Matchmaker 6XA2.pdb, chain G (#1) with cyp168a1, chain G (#), sequence
alignment score = 791.6  
Matchmaker 6XA2.pdb, chain H (#1) with cyp168a1, chain H (#), sequence
alignment score = 820  
RMSD between 2708 pruned atom pairs is 1.005 angstroms; (across all 3137
pairs: 2.597)  
  
Parameters  
---  
Chain pairing | ss  
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 6XA2.pdb, chain A (#1) with cyp168a1, chain A (#), sequence
alignment score = 803.3  
Matchmaker 6XA2.pdb, chain B (#1) with cyp168a1, chain B (#), sequence
alignment score = 810.6  
Matchmaker 6XA2.pdb, chain C (#1) with cyp168a1, chain C (#), sequence
alignment score = 782.9  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain D (#), sequence
alignment score = 807.6  
Matchmaker 6XA2.pdb, chain E (#1) with cyp168a1, chain E (#), sequence
alignment score = 786.7  
Matchmaker 6XA2.pdb, chain F (#1) with cyp168a1, chain F (#), sequence
alignment score = 788.5  
Matchmaker 6XA2.pdb, chain G (#1) with cyp168a1, chain G (#), sequence
alignment score = 804.8  
Matchmaker 6XA2.pdb, chain H (#1) with cyp168a1, chain H (#), sequence
alignment score = 823.5  
RMSD between 2528 pruned atom pairs is 1.049 angstroms; (across all 3137
pairs: 2.833)  
  
Associated cyp168a1 chain A to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain B to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain C to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain D to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain E to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain F to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain G to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain H to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain A to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain B to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain C to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain D to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain E to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain F to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain G to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain H to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain A to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain B to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain C to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain D to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain E to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain F to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain G to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain H to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain A to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain B to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain C to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain D to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain E to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain F to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain G to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain H to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain A to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain B to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain C to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain D to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain E to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain F to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain G to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain H to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain A to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain B to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain C to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain D to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain E to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain F to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain G to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain H to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain A to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain B to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain C to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain D to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain E to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain F to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain G to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain H to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain A to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain B to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain C to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain D to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain E to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain F to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain G to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain H to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain A to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain B to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain C to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain D to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain E to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain F to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain G to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain H to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain A to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain B to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain C to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain D to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain E to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain F to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain G to cyp168a1 with 0 mismatches  
Associated cyp168a1 chain H to cyp168a1 with 0 mismatches  
Chain information for cyp168a1  
---  
Chain | Description  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.1/B 2.2/B 2.3/B
2.4/B 2.5/B 2.6/B 2.7/B 2.8/B 2.9/B 2.10/B 2.1/C 2.2/C 2.3/C 2.4/C 2.5/C 2.6/C
2.7/C 2.8/C 2.9/C 2.10/C 2.1/D 2.2/D 2.3/D 2.4/D 2.5/D 2.6/D 2.7/D 2.8/D 2.9/D
2.10/D 2.1/E 2.2/E 2.3/E 2.4/E 2.5/E 2.6/E 2.7/E 2.8/E 2.9/E 2.10/E 2.1/F
2.2/F 2.3/F 2.4/F 2.5/F 2.6/F 2.7/F 2.8/F 2.9/F 2.10/F 2.1/G 2.2/G 2.3/G 2.4/G
2.5/G 2.6/G 2.7/G 2.8/G 2.9/G 2.10/G 2.1/H 2.2/H 2.3/H 2.4/H 2.5/H 2.6/H 2.7/H
2.8/H 2.9/H 2.10/H | No description available  
  
Associated cyp168a1 (2.1) chain A to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.1) chain B to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.1) chain C to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.1) chain D to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.1) chain E to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.1) chain F to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.1) chain G to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.1) chain H to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.2) chain A to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.2) chain B to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.2) chain C to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.2) chain D to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.2) chain E to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.2) chain F to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.2) chain G to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.2) chain H to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.3) chain A to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.3) chain B to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.3) chain C to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.3) chain D to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.3) chain E to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.3) chain F to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.3) chain G to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.3) chain H to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.4) chain A to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.4) chain B to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.4) chain C to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.4) chain D to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.4) chain E to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.4) chain F to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.4) chain G to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.4) chain H to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.5) chain A to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.5) chain B to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.5) chain C to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.5) chain D to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.5) chain E to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.5) chain F to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.5) chain G to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.5) chain H to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.6) chain A to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.6) chain B to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.6) chain C to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.6) chain D to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.6) chain E to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.6) chain F to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.6) chain G to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.6) chain H to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.7) chain A to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.7) chain B to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.7) chain C to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.7) chain D to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.7) chain E to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.7) chain F to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.7) chain G to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.7) chain H to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.8) chain A to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.8) chain B to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.8) chain C to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.8) chain D to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.8) chain E to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.8) chain F to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.8) chain G to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.8) chain H to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.9) chain A to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.9) chain B to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.9) chain C to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.9) chain D to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.9) chain E to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.9) chain F to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.9) chain G to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.9) chain H to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.10) chain A to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.10) chain B to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.10) chain C to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.10) chain D to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.10) chain E to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.10) chain F to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.10) chain G to CYP168A1 with 0 mismatches  
Associated cyp168a1 (2.10) chain H to CYP168A1 with 0 mismatches  

> select all

303731 atoms, 310798 bonds, 40 pseudobonds, 38942 residues, 14 models selected  

> hide sel atoms

> select #2.1/A

3483 atoms, 3567 bonds, 444 residues, 1 model selected  

> show sel cartoons

> ui tool show "Modeller Comparative"

> ui tool show Matchmaker

> matchmaker #2.1-10 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 6XA2.pdb, chain D (#1) with cyp168a1, chain F (#2.1), sequence
alignment score = 830.9  
RMSD between 360 pruned atom pairs is 0.529 angstroms; (across all 392 pairs:
1.949)  
  
Matchmaker 6XA2.pdb, chain B (#1) with cyp168a1, chain G (#2.2), sequence
alignment score = 822.8  
RMSD between 346 pruned atom pairs is 0.424 angstroms; (across all 393 pairs:
2.552)  
  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain A (#2.3), sequence
alignment score = 824.9  
RMSD between 359 pruned atom pairs is 0.548 angstroms; (across all 392 pairs:
2.384)  
  
Matchmaker 6XA2.pdb, chain F (#1) with cyp168a1, chain B (#2.4), sequence
alignment score = 824  
RMSD between 364 pruned atom pairs is 0.329 angstroms; (across all 393 pairs:
2.404)  
  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain D (#2.5), sequence
alignment score = 830  
RMSD between 365 pruned atom pairs is 0.264 angstroms; (across all 392 pairs:
2.365)  
  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain H (#2.6), sequence
alignment score = 830.1  
RMSD between 355 pruned atom pairs is 0.448 angstroms; (across all 392 pairs:
2.633)  
  
Matchmaker 6XA2.pdb, chain H (#1) with cyp168a1, chain H (#2.7), sequence
alignment score = 825.8  
RMSD between 365 pruned atom pairs is 0.302 angstroms; (across all 393 pairs:
1.849)  
  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain A (#2.8), sequence
alignment score = 824.3  
RMSD between 359 pruned atom pairs is 0.519 angstroms; (across all 392 pairs:
1.919)  
  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain D (#2.9), sequence
alignment score = 832.8  
RMSD between 363 pruned atom pairs is 0.288 angstroms; (across all 392 pairs:
2.441)  
  
Matchmaker 6XA2.pdb, chain D (#1) with cyp168a1, chain H (#2.10), sequence
alignment score = 823.6  
RMSD between 357 pruned atom pairs is 0.466 angstroms; (across all 392 pairs:
2.419)  
  

> ui tool show Matchmaker

> matchmaker #2.1/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 6XA2.pdb, chain A (#1) with cyp168a1, chain A (#2.1), sequence
alignment score = 790.3  
RMSD between 375 pruned atom pairs is 0.288 angstroms; (across all 393 pairs:
1.357)  
  

> save "/Users/pierceherbert/Desktop/Research/Models/TAMI/TAMI/tirandomycin C
> models.pdb"

Cannot save
'/Users/pierceherbert/Desktop/Research/Models/TAMI/TAMI/tirandomycin C
models.pdb': Unable to open file
'/Users/pierceherbert/Desktop/Research/Models/TAMI/TAMI/tirandomycin C
models.pdb' for writing  

> save "/Users/pierceherbert/Desktop/Research/Models/TAMI/TAMI_tirandomycin
> C_models.pdb"

> close #2

> open "/Users/pierceherbert/Desktop/Research/Models/TAMI/TAM I:tirandamycin C
> chop chop.fasta"

Summary of feedback from opening
/Users/pierceherbert/Desktop/Research/Models/TAMI/TAM I:tirandamycin C chop
chop.fasta  
---  
notes | Illegal ':' character in alignment identifier replaced with '/'  
Alignment identifier is TAM I/tirandamycin C chop chop.fasta  
Associated 6XA2.pdb chain A to 6XA2_1|Chains A, B, C, D, E, F, G,
H|TamI|Streptomyces sp. 307-9 (529089) with 0 mismatches  
Associated 6XA2.pdb chain B to 6XA2_1|Chains A, B, C, D, E, F, G,
H|TamI|Streptomyces sp. 307-9 (529089) with 0 mismatches  
Associated 6XA2.pdb chain E to 6XA2_1|Chains A, B, C, D, E, F, G,
H|TamI|Streptomyces sp. 307-9 (529089) with 0 mismatches  
Associated 6XA2.pdb chain F to 6XA2_1|Chains A, B, C, D, E, F, G,
H|TamI|Streptomyces sp. 307-9 (529089) with 0 mismatches  
Associated 6XA2.pdb chain G to 6XA2_1|Chains A, B, C, D, E, F, G,
H|TamI|Streptomyces sp. 307-9 (529089) with 0 mismatches  
3 messages similar to the above omitted  
Showing conservation header ("seq_conservation" residue attribute) for
alignment TAM I/tirandamycin C chop chop.fasta  
  
Opened 2 sequences from TAM I:tirandamycin C chop chop.fasta  

> ui tool show "Modeller Comparative"


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-20.2.50
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: 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: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
      OS Loader Version: 564.40.4~66

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 1 hour, 8 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          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
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.0.2
    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: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    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: 1.1.1
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    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: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    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: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    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: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    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: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Structure Prediction
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in removeRow() when Modeller Comparative tool shown again

comment:2 by Eric Pettersen, 2 years ago

Resolution: → can't reproduce
Status: accepted → closed

Tried various scenarios of adding/deleting alignments while tool not showing; bupkis.

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