Opened 3 years ago

Closed 3 years ago

#7256 closed defect (fixed)

Crash in swapaa

Reported by: afrance2@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc: Tom Goddard
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: 1.5.dev202206100131 (2022-06-10 01:31:06 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007000130d5000 (most recent call first):
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00000001095c2600 (most recent call first):
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/clashes/clashes.py", line 120 in find_clashes
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/swap_res.py", line 739 in process_clashes
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/swap_res.py", line 97 in swap_aa
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/cmd.py", line 45 in swap_aa
  File "/Users/amandaghilardi/Desktop/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
  File "/Users/amandaghilardi/Desktop/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
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 332 in event_loop
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in 
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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{
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  "procLaunch" : "2022-07-10 15:01:50.9925 -0400",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 504,
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  "incident" : "5082318E-B788-4D55-9C10-EF9BFCCF5CA3",
  "bug_type" : "309",
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  "procName" : "ChimeraX",
  "procPath" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "B648F3E9-3C05-5922-1609-51E501149E1F",
  "bridgeVersion" : {"build":"19P549","train":"6.0"},
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  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4425338880\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      107c55000-107c56000    [    4K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
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  "exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
  "ktriageinfo" : "VM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\n",
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=2.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               640K        5 \nActivity Tracing                   256K        1 \nCG backing stores                 3840K        4 \nCG image                          1708K       69 \nColorSync                          244K       29 \nCoreAnimation                     7288K      102 \nCoreGraphics                        12K        2 \nCoreUI image data                 5240K       38 \nFoundation                          36K        2 \nKernel Alloc Once                   12K        2 \nMALLOC                             1.5G     6548 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        32K        6 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        116K       29 \nStack                            165.7M       30 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      262.1M      354 \nVM_ALLOCATE (reserved)           320.0M        4         reserved VM address space (unallocated)\n__DATA                            58.1M      736 \n__DATA_CONST                      30.3M      350 \n__DATA_DIRTY                      1639K      219 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       675.4M      206 \n__OBJC_RO                         81.5M        1 \n__OBJC_RW                         3120K        2 \n__TEXT                           856.3M      733 \n__UNICODE                          588K        1 \ndyld private memory               1280K        3 \nmapped file                      556.6M       78 \nshared memory                     2976K       25 \n===========                     =======  ======= \nTOTAL                              4.7G     9596 \nTOTAL, minus reserved VM space     4.2G     9596 \n",
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.5.dev202206100131 (2022-06-10)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/amandaghilardi/Desktop/sdf/py145.sdf format sdf

> close session

> open /Users/amandaghilardi/Desktop/Docking/AHR/py108/py108_test1.pdbqt

Summary of feedback from opening
/Users/amandaghilardi/Desktop/Docking/AHR/py108/py108_test1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -10.445 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -11.764  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -11.390  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -0.375  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -0.098  
  
139 messages similar to the above omitted  
  
Opened py108_test1.pdbqt containing 9 structures (180 atoms, 198 bonds)  

> open /Users/amandaghilardi/Desktop/Docking/AHR/py108/hAhR_49.pdbqt

Chain information for hAhR_49.pdb #2  
---  
Chain | Description  
? | No description available  
  
Opened hAhR_49.pdbqt containing 1 structures (1146 atoms, 1165 bonds)  

> hide #1.9 models

> hide #1.8 models

> hide #1.7 models

> hide #1.6 models

> hide #1.5 models

> hide #1.4 models

> hide #1.3 models

> hide #1.2 models

> select ::name="UNL"

180 atoms, 198 bonds, 9 residues, 9 models selected  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.  

> select clear

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.  

> ui tool show ViewDockX

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> ZOOM

Unknown command: ZOOM  

> zoom

Pixel size at center of rotation is 0.0695  

> zoom

Pixel size at center of rotation is 0.0695  

> zoom

Pixel size at center of rotation is 0.0695  

> color bfactor #2#1.1

1166 atoms, 114 residues, atom bfactor range 0 to 0  

> color bfactor #2#1.1

1166 atoms, 114 residues, atom bfactor range 0 to 0  

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

1146 atoms, 1165 bonds, 113 residues, 1 model selected  

> color bfactor sel

1146 atoms, 113 residues, atom bfactor range 0 to 0  

> color bfactor sel

1146 atoms, 113 residues, atom bfactor range 0 to 0  

> mlp sel

Map values for surface "hAhR_49.pdb_ SES surface": minimum -25.13, mean
-2.884, maximum 26.25  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp sel

Map values for surface "hAhR_49.pdb_ SES surface": minimum -25.13, mean
-2.884, maximum 26.25  
To also show corresponding color key, enter the above mlp command and add key
true  

> select clear

> mlp #1.1#!2

Map values for surface "hAhR_49.pdb_ SES surface": minimum -25.13, mean
-2.884, maximum 26.25  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp #1.1#!2

Map values for surface "hAhR_49.pdb_ SES surface": minimum -25.13, mean
-2.884, maximum 26.25  
To also show corresponding color key, enter the above mlp command and add key
true  

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

1146 atoms, 1165 bonds, 113 residues, 1 model selected  

> mlp sel

Map values for surface "hAhR_49.pdb_ SES surface": minimum -25.13, mean
-2.884, maximum 26.25  
To also show corresponding color key, enter the above mlp command and add key
true  

> rainbow sel

> color sel bypolymer

> color sel byhetero

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 1146 atom styles  

> style sel sphere

Changed 1146 atom styles  

> hide sel surfaces

> show sel cartoons

> show sel atoms

> hide sel atoms

> close session

> open /Users/amandaghilardi/Desktop/Docking/AHR/py108/complex.pdb

Chain information for complex.pdb #1  
---  
Chain | Description  
? | No description available  
  

> color bfactor

1166 atoms, 114 residues, atom bfactor range 0 to 0  

> close session

> open /Users/amandaghilardi/Desktop/Docking/AHR/py108/hAhR_49.pdb

Chain information for hAhR_49.pdb #1  
---  
Chain | Description  
? | No description available  
  

> close session

> open
> /Users/amandaghilardi/Desktop/Docking/Practice/practice-2_basic/1iep.pdb

1iep.pdb title:  
Crystal structure of the C-abl kinase domain In complex with sti-571. [more
info...]  
  
Chain information for 1iep.pdb #1  
---  
Chain | Description | UniProt  
A B | proto-oncogene tyrosine-protein kinase abl | ABL1_MOUSE  
  
Non-standard residues in 1iep.pdb #1  
---  
CL — chloride ion  
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571;imatinib)  
  

> color bfactor

4710 atoms, 728 residues, atom bfactor range 23.6 to 114  

> select ::name="STI"

74 atoms, 82 bonds, 2 residues, 1 model selected  

> mlp sel

mlp: no amino acids specified  

> mlp sel

mlp: no amino acids specified  

> mlp sel

mlp: no amino acids specified  

> style sel sphere

Changed 74 atom styles  

> select /B:225-498

2229 atoms, 2288 bonds, 274 residues, 1 model selected  

> select /B:225-498

2229 atoms, 2288 bonds, 274 residues, 1 model selected  

> select clear

> color bfactor

4710 atoms, 728 residues, atom bfactor range 23.6 to 114  

> ui tool show "Side View"

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62,
maximum 9.00  
Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57,
maximum 11.58  
To also show corresponding color key, enter the above coulombic command and
add key true  

> undo

> coulombic

Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62,
maximum 9.00  
Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57,
maximum 11.58  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62,
maximum 9.00  
Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57,
maximum 11.58  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62,
maximum 9.00  
Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57,
maximum 11.58  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62,
maximum 9.00  
Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57,
maximum 11.58  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62,
maximum 9.00  
Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57,
maximum 11.58  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> open
> /Users/amandaghilardi/Desktop/Docking/Practice/practice-2_basic/1iep.pdb

1iep.pdb title:  
Crystal structure of the C-abl kinase domain In complex with sti-571. [more
info...]  
  
Chain information for 1iep.pdb #1  
---  
Chain | Description | UniProt  
A B | proto-oncogene tyrosine-protein kinase abl | ABL1_MOUSE  
  
Non-standard residues in 1iep.pdb #1  
---  
CL — chloride ion  
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571;imatinib)  
  

> select :CL

6 atoms, 6 residues, 1 model selected  

> delete

Missing or invalid "atoms" argument: empty atom specifier  

> delete CL

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete 'CL'

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete "CL"

Missing or invalid "atoms" argument: invalid atoms specifier  

> select :CL

6 atoms, 6 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> color bfactor

4704 atoms, 722 residues, atom bfactor range 23.6 to 114  

> open 1iep fromDatabase Database eds

Invalid "fromDatabase" argument: Should be one of 'alphafold', 'ccd',
'cellpack', 'eds', 'edsdiff', 'emdb', 'emdb_china', 'emdb_europe',
'emdb_japan', 'emdb_us', 'ftp', 'help', 'http', 'https', 'pdb', 'pdbdev',
'pdbe', 'pdbe_bio', 'pdbj', 'pubchem', 'rcsb_bio', 'smiles', or 'uniprot'  

> ui tool show "Side View"

> ui tool show "Volume Viewer"

> modelcol white

Unknown command: modelcol white  

> open 1iep fromDatabse eds

'fromDatabse' has no suffix  

> open 1iep fromDatabase eds

Summary of feedback from opening 1iep fetched from eds  
---  
note | Fetching map 1iep from
http://www.ebi.ac.uk/pdbe/coordinates/files/1iep.ccp4  
  
Opened eds 1iep as #2, grid size 93,142,147, pixel 0.706,0.709,0.697, shown at
level 0.514, step 1, values float32  

> volume #2 level 0.4502

> volume #2 level 0.3734

> volume #2 color #2700d7

> undo

> volume #2 color #d77692

> color bfactor

4704 atoms, 722 residues, atom bfactor range 23.6 to 114  

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> volume #2 level 0.5849

> hide #!2 models

> delete /A

> combine #1

> rename #ligand

Missing or invalid "models" argument: invalid models specifier  

> rename #1 ligand

> hide #3 models

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

4458 atoms, 4576 bonds, 548 residues, 2 models selected  

> delete atoms (#1 & sel)

> delete bonds (#1 & sel)

> select ::name="HOH"

146 atoms, 146 residues, 2 models selected  

> delete atoms (#1 & sel)

> delete bonds (#1 & sel)

> show #3 models

> hide #1 models

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

2229 atoms, 2288 bonds, 274 residues, 1 model selected  

> select ~sel

147 atoms, 82 bonds, 75 residues, 4 models selected  

> delete atoms (#3 & sel)

> delete bonds (#3 & sel)

> show #1 models

> select ::name="STI"

37 atoms, 41 bonds, 1 residue, 1 model selected  

> color sel magenta

> color sel byhetero

> select clear

> select ligand

37 atoms, 41 bonds, 1 residue, 1 model selected  

> select zone

Missing or invalid "near" argument: empty atom specifier  

> select Zone...

Expected an objects specifier or a keyword  

> select sel @ show sel atoms

> hbonds sel reveal true

16 hydrogen bonds found  

> select clear

> hbonds reveal true

251 hydrogen bonds found  

> hide #4 models

> ui tool show H-Bonds

> hbonds intraModel false intraMol false intraRes false select true reveal
> true

5 hydrogen bonds found  

> show #4 models

> select clear

> select ligand

37 atoms, 41 bonds, 1 residue, 1 model selected  

> select invert

Expected an objects specifier or a keyword  

> invert

Unknown command: invert  

> select ~sel

2229 atoms, 2288 bonds, 274 residues, 3 models selected  

> show sel surfaces

> select clear

> mlp

Map values for surface "copy of 1iep.pdb_B SES surface": minimum -26.69, mean
-3.94, maximum 23.19  
To also show corresponding color key, enter the above mlp command and add key
true  

> select ::name="STI"

37 atoms, 41 bonds, 1 residue, 1 model selected  

> mlp sel

mlp: no amino acids specified  

> ui tool show "Surface Color"

> transparency sel 50

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

2229 atoms, 2288 bonds, 274 residues, 1 model selected  

> transparency (#!3 & sel) 60

> select clear

Alignment identifier is 3/B  

> select
> #3/B:238-240,249-252,263-265,279-291,322-330,336-357,365-367,373-375,383-387,402-414,417-434,444-454,465-476,479-483,485-496

1099 atoms, 1109 bonds, 136 residues, 1 model selected  

> select clear

> select #3/B:302-303

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #3/B:302-303

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select clear

> select ::name="STI"

37 atoms, 41 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 37 atom styles  

> style sel sphere

Changed 37 atom styles  

> style sel ball

Changed 37 atom styles  

> show sel surfaces

> hide sel surfaces

Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 0 maps.  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.  

> volume show

> volume hide

> ui mousemode right "mark surface"

> ui mousemode right "mark point"

> ui mousemode right "link markers"

> ui mousemode right distance

> show sel surfaces

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> view sel

> side view

Unknown command: side view  

> sideview

Unknown command: sideview  

> ui tool show "Side View"

> distance #3/B:326@CA #3/B:260@CB

Distance between copy of 1iep.pdb #3/B TYR 326 CA and VAL 260 CB: 23.969Å  

> distance #3/B:317@CE2 #3/B:258@OE1

Distance between copy of 1iep.pdb #3/B PHE 317 CE2 and GLU 258 OE1: 6.675Å  

> distance #3/B:258@CG #3/B:312@OH

Distance between copy of 1iep.pdb #3/B GLU 258 CG and TYR 312 OH: 12.629Å  

> distance #3/B:250@CA #3/B:266@CD2

Distance between copy of 1iep.pdb #3/B GLY 250 CA and LEU 266 CD2: 19.784Å  

> distance #3/B:317@CZ #3/B:258@CD

Distance between copy of 1iep.pdb #3/B PHE 317 CZ and GLU 258 CD: 4.712Å  

> slect ligand

Unknown command: slect ligand  

> hide sel surfaces

> hide #!5 models

> hide #4 models

> hide #!3 models

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-3.1412,0,1,0,0.85101,0,0,1,0.10614

> view matrix models #1,1,0,0,-5.6603,0,1,0,1.7873,0,0,1,-0.10158

> view matrix models #1,1,0,0,-8.7063,0,1,0,1.4387,0,0,1,-1.8774

> view matrix models #1,1,0,0,-6.0654,0,1,0,-0.87088,0,0,1,-3.027

> view matrix models #1,1,0,0,-6.1034,0,1,0,-1.4409,0,0,1,-3.9743

> show #!3 models

> slect ligand

Unknown command: slect ligand  

> slect clear

Unknown command: slect clear  

> mlp sel

mlp: no amino acids specified  

> hide sel surfaces

> select ligand

37 atoms, 41 bonds, 1 residue, 1 model selected  

> select ~sel

2229 atoms, 2288 bonds, 5 pseudobonds, 274 residues, 7 models selected  

> mlp sel

Map values for surface "copy of 1iep.pdb_B SES surface": minimum -26.69, mean
-3.94, maximum 23.19  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> view matrix models
> #2,1,0,0,0.16969,0,1,0,2.5458,0,0,1,4.112,#3,1,0,0,0.16969,0,1,0,2.5458,0,0,1,4.112,#1.1.1,1,0,0,0.16969,0,1,0,2.5458,0,0,1,4.112,#5,1,0,0,0,0,1,0,0,0,0,1,0

> undo

> select clear

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> close session

> open
> /Users/amandaghilardi/Desktop/Docking/Practice/practice-2_basic/1iep.pdb
> format pdb

1iep.pdb title:  
Crystal structure of the C-abl kinase domain In complex with sti-571. [more
info...]  
  
Chain information for 1iep.pdb #1  
---  
Chain | Description | UniProt  
A B | proto-oncogene tyrosine-protein kinase abl | ABL1_MOUSE  
  
Non-standard residues in 1iep.pdb #1  
---  
CL — chloride ion  
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571;imatinib)  
  

> select ::name="CL"

6 atoms, 6 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select ::name="HOH"

172 atoms, 172 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> delecte /B

Unknown command: delecte /B  

> delete /B

> combina #1

Unknown command: combina #1  

> combine #1

> rename #2 ligand

> hide #2 models

> select ::name="STI"

74 atoms, 82 bonds, 2 residues, 2 models selected  

> delete atoms (#1 & sel)

> delete bonds (#1 & sel)

> show #2 models

> hide #1 models

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

4458 atoms, 4576 bonds, 548 residues, 2 models selected  

> delete atoms (#2 & sel)

> delete bonds (#2 & sel)

> show #1 models

> select clear

> select ligand

Nothing selected  

> style ball

Changed 2266 atom styles  

> color light sea green

> undo

> select ligand

Nothing selected  

> color cyan

> select clear

> select ::name="STI"

37 atoms, 41 bonds, 1 residue, 1 model selected  

> color sel light sea green

> color sel byhetero

> select clear

> select ::name="STI"

37 atoms, 41 bonds, 1 residue, 1 model selected  

> select sel @ show sel atoms

> style sel stick

Changed 149 atom styles  

> color sel byhetero

> select clear

> ui tool show H-Bonds

> hbonds intraModel false intraMol false intraRes false select true reveal
> true

5 hydrogen bonds found  

> hbonds intraModel false intraMol false intraRes false select true reveal
> true

5 hydrogen bonds found  

> view matrix models
> #1,1,0,0,-3.6848,0,1,0,0.023014,0,0,1,1.3471,#2,1,0,0,-3.6848,0,1,0,0.023014,0,0,1,1.3471

> view matrix models
> #1,1,0,0,-4.5413,0,1,0,-0.011304,0,0,1,1.7374,#2,1,0,0,-4.5413,0,1,0,-0.011304,0,0,1,1.7374

> close session

> open /Users/amandaghilardi/Desktop/Docking/AHR/py108/py108_test1.pdbqt

Summary of feedback from opening
/Users/amandaghilardi/Desktop/Docking/AHR/py108/py108_test1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -10.445 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -11.764  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -11.390  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -0.375  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -0.098  
  
139 messages similar to the above omitted  
  
Opened py108_test1.pdbqt containing 9 structures (180 atoms, 198 bonds)  

> open /Users/amandaghilardi/Desktop/Docking/AHR/py108/hAhR_49.pdbqt

Chain information for hAhR_49.pdb #2  
---  
Chain | Description  
? | No description available  
  
Opened hAhR_49.pdbqt containing 1 structures (1146 atoms, 1165 bonds)  

> hide #1.9 models

> hide #1.8 models

> hide #1.7 models

> hide #1.6 models

> hide #1.5 models

> hide #1.4 models

> hide #1.3 models

> hide #1.2 models

> hide #2 models

> show #2 models

> ui tool show ViewDockX

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.2 models

> hide #1.2 models

> show #1.1 models

> hide #1.1 models

> show #1.2 models

> hide #1.2 models

> show #1.3 models

> hide #1.3 models

> show #1.4 models

> hide #1.4 models

> show #1.5 models

> hide #1.5 models

> show #1.6 models

> hide #1.6 models

> show #1.7 models

> hide #1.7 models

> show #1.8 models

> hide #1.8 models

> show #1.9 models

> hide #1.9 models

> show #1.8 models

> hide #1.8 models

> show #1.7 models

> hide #1.7 models

> show #1.6 models

> hide #1.6 models

> show #1.5 models

> hide #1.5 models

> show #1.4 models

> hide #1.4 models

> show #1.3 models

> hide #1.3 models

> show #1.2 models

> hide #1.2 models

> show #1.1 models

> Add H

Unknown command: Add H  

> hide #2 models

> select ::name="UNL"

180 atoms, 198 bonds, 9 residues, 9 models selected  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
No usable SEQRES records for hAhR_49.pdb (#2) chain (blank); guessing termini
instead  
Chain-initial residues that are actual N termini: hAhR_49.pdb #2/? GLU 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: hAhR_49.pdb #2/? GLY 113  
Chain-final residues that are not actual C termini:  
80 hydrogen bonds  
774 hydrogens added  
  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> close session

> open help:user/tutorial/binding-sites.html

Opened help:user/tutorial/binding-sites.html  
No help found for 'help:user/tutorial/binding-sites.html'  

> open help:user/tutorials/binding-sites.html

Opened help:user/tutorials/binding-sites.html  

> open help:user/tutorials/binding-sites.html

Opened help:user/tutorials/binding-sites.html  

> open help:user/tutorials/binding-sites.html

Opened help:user/tutorials/binding-sites.html  

> open help:user/tutorials/binding-sites.html

Opened help:user/tutorials/binding-sites.html  

> open help:user/tutorials/binding-sites.html

Opened help:user/tutorials/binding-sites.html  

> open help:user/tutorials/binding-sites.html

Opened help:user/tutorials/binding-sites.html  

> open 2hyy

Summary of feedback from opening 2hyy fetched from pdb  
---  
notes | Fetching compressed mmCIF 2hyy from
http://files.rcsb.org/download/2hyy.cif  
Fetching CCD STI from http://ligand-expo.rcsb.org/reports/S/STI/STI.cif  
  
2hyy title:  
Human Abl kinase domain in complex with imatinib (STI571, Glivec) [more
info...]  
  
Chain information for 2hyy #1  
---  
Chain | Description | UniProt  
A B C D | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_HUMAN  
  
Non-standard residues in 2hyy #1  
---  
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571;imatinib)  
  
2hyy mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  

> panel

Unknown command: modeller panel  

> close session

> log clear

> open 1fpp

Summary of feedback from opening 1fpp fetched from pdb  
---  
notes | Fetching compressed mmCIF 1fpp from
http://files.rcsb.org/download/1fpp.cif  
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif  
Fetching CCD PO4 from http://ligand-expo.rcsb.org/reports/P/PO4/PO4.cif  
Fetching CCD FPP from http://ligand-expo.rcsb.org/reports/F/FPP/FPP.cif  
  
1fpp title:  
Protein farnesyltransferase complex with farnesyl diphosphate [more info...]  
  
Chain information for 1fpp #1  
---  
Chain | Description | UniProt  
A | protein farnesyltransferase | PFTA_RAT  
B | protein farnesyltransferase | PFTB_RAT  
  
Non-standard residues in 1fpp #1  
---  
FPP — farnesyl diphosphate  
PO4 — phosphate ion  
ZN — zinc ion  
  

> mlp

Map values for surface "1fpp_A SES surface": minimum -28.46, mean -4.976,
maximum 24.73  
Map values for surface "1fpp_B SES surface": minimum -27.83, mean -4.111,
maximum 22.2  

> surface zone #1 nearAtoms :fpp distance 8 maxComponents 1

> hide ~:fpp target ar

> close

> open 4xt3

Summary of feedback from opening 4xt3 fetched from pdb  
---  
notes | Fetching compressed mmCIF 4xt3 from
http://files.rcsb.org/download/4xt3.cif  
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif  
Fetching CCD PCA from http://ligand-expo.rcsb.org/reports/P/PCA/PCA.cif  
  
4xt3 title:  
Structure of a viral GPCR bound to human chemokine CX3CL1 [more info...]  
  
Chain information for 4xt3 #1  
---  
Chain | Description | UniProt  
A | G-protein coupled receptor homolog US28 | US28_HCMVA  
B | Fractalkine | X3CL1_HUMAN  
  
Non-standard residues in 4xt3 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
PO4 — phosphate ion  
UNL — unknown ligand  
  

> mlp

Map values for surface "4xt3_A SES surface": minimum -28.71, mean 1.122,
maximum 23.28  
Map values for surface "4xt3_B SES surface": minimum -25.15, mean -4.785,
maximum 22.04  

> close

> open 1g74

Summary of feedback from opening 1g74 fetched from pdb  
---  
notes | Fetching compressed mmCIF 1g74 from
http://files.rcsb.org/download/1g74.cif  
Fetching CCD OLA from http://ligand-expo.rcsb.org/reports/O/OLA/OLA.cif  
  
1g74 title:  
Toward changing specificity: adipocyte lipid binding protein mutant, oleic
acid bound form [more info...]  
  
Chain information for 1g74 #1  
---  
Chain | Description | UniProt  
A | adipocyte lipid-binding protein | FABPA_MOUSE  
  
Non-standard residues in 1g74 #1  
---  
OLA — oleic acid  
PO4 — phosphate ion  
  

> surface

> cliup

Unknown command: cliup  

> clip

> volume planes z style image imageMode "full region"

No volumes specified  

> ui mousemode right clip

> ui mousemode right "clip rotate"

> ui mousemode right translate

> ui mousemode right rotate

> ui mousemode right "clip rotate"

> ui mousemode right clip

> ui mousemode right "clip rotate"

> ui mousemode right translate

> clip model #!1 false

> hide ~:ola target ar

> color :ola & C green

> mlp

Map values for surface "1g74_A SES surface": minimum -27.91, mean -5.662,
maximum 22.39  

> mlp protein surfaces #1.1.1

Map values for surface "cap front": minimum -53.62, mean 0.8646, maximum 49.31  

> transparency #1.1.1 30

> coulombic protein

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 1g74_A SES surface #1.1: minimum, -11.34, mean -0.02,
maximum 10.80  

> coulombic protein surfaces #1.1.1 offset 0

Coulombic values for cap front #1.1.1: minimum, -2199.36, mean 4.92, maximum
1486.74  

> close session

> open 3d6y fromDatabase rcsb_bio maxAssemblies 1

Summary of feedback from opening 3d6y fetched from rcsb_bio  
---  
notes | Fetching compressed 3d6y bioassembly 1 from
https://files.rcsb.org/download/3d6y-assembly1.cif  
Fetching CCD BER from http://ligand-expo.rcsb.org/reports/B/BER/BER.cif  
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif  
  
3d6y bioassembly 1 title:  
Crystal structure of R275E mutant of BMRR bound to DNA and berberine [more
info...]  
  
Chain information for 3d6y bioassembly 1 #1  
---  
Chain | Description  
A A-2 | Multidrug-efflux transporter 1 regulator  
B B-2 | BMR promoter DNA  
  
Non-standard residues in 3d6y bioassembly 1 #1  
---  
BER — berberine  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
Opened 1 biological assemblies for 3d6y  

> select :BER

50 atoms, 58 bonds, 2 residues, 1 model selected  

> select :BER

50 atoms, 58 bonds, 2 residues, 1 model selected  

> select :BER

50 atoms, 58 bonds, 2 residues, 1 model selected  

> select :BER

50 atoms, 58 bonds, 2 residues, 1 model selected  

> select :GOL

24 atoms, 20 bonds, 4 residues, 1 model selected  

> hide :gol

> hide solvent

> hide protein

> select clear

> coulombic protein

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 3d6y bioassembly 1_A SES surface #1.1: minimum, -16.84,
mean -2.11, maximum 14.59  
Coulombic values for 3d6y bioassembly 1_A-2 SES surface #1.2: minimum, -16.17,
mean -2.12, maximum 15.04  

> color nucleic tan

> cartoon style nucleic xsection round width 1.5 thickness 1.5

> nucleotides tubs

Missing or invalid "representation" argument: Should be one of 'atoms',
'fill', 'ladder', 'slab', 'stubs', or 'tube/slab'  

> nucleotides stubs

> nucleotides tube/slab shape muffler

> nucleotides tube/slab shape ellipsoid

> nucleotides tube/slab shape box

> nucleotides slab

> style nucleic stick

Changed 976 atom styles  

> nucleotides fill

> style nucleic stick

Changed 976 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 976 atom styles  

> nucleotides stubs

> size :ber stickRadius .7

Changed 58 bond radii  

> color C & :ber limegreen

> set bgColor white

> set bgColor gray

> set bgColor black

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting shadows true

> lighting full

> lighting soft

> lighting simple

> graphics silhouettes false

> coulombic protein key true

Coulombic values for 3d6y bioassembly 1_A SES surface #1.1: minimum, -16.84,
mean -2.11, maximum 14.59  
Coulombic values for 3d6y bioassembly 1_A-2 SES surface #1.2: minimum, -16.17,
mean -2.12, maximum 15.04  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> 2dlabels text "electrostatic potential"

> hide #!3 models

> hide #2 models

> show #!3 models

> show #2 models

> set bgColor white

> ui mousemode right label

> label delete residues

> select clear

> label delete residues

> select clear

> label delete residues

> ui mousemode right label

> ui mousemode right select

> select //chain_id='A-2':20@NZ

1 atom, 1 residue, 1 model selected  

> select //chain_id='B-2':-5

19 atoms, 20 bonds, 1 residue, 1 model selected  

> select /A:26@O

1 atom, 1 residue, 1 model selected  

> select /A:32@CB

1 atom, 1 residue, 1 model selected  

> slect clear

Unknown command: slect clear  

> ui mousemode right label

> ui mousemode right "move label"

> 2dlabels #3.1 xpos 0.658 ypos 0.140

> ui mousemode right translate

> close session

> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html

Opened https://www.rbvi.ucsf.edu/chimerax/data/conservation-
coloring/conservation-coloring.html  

> open 121p

Summary of feedback from opening 121p fetched from pdb  
---  
notes | Fetching compressed mmCIF 121p from
http://files.rcsb.org/download/121p.cif  
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
Fetching CCD GCP from http://ligand-expo.rcsb.org/reports/G/GCP/GCP.cif  
  
121p title:  
Struktur und guanosintriphosphat-hydrolysemechanismus des C-terminal
verkuerzten menschlichen krebsproteins P21-H-ras [more info...]  
  
Chain information for 121p #1  
---  
Chain | Description | UniProt  
A | H-ras P21 protein | RASH_HUMAN  
  
Non-standard residues in 121p #1  
---  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
  
121p mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> hide solvent

> style ligand ball

Changed 32 atom styles  

> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/121p-consurf.aln

Summary of feedback from opening
//www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
fetched from https  
---  
notes | Fetching 121p-consurf.aln from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln  
Downloaded 121p-consurf.aln to
/Users/amandaghilardi/Downloads/121p-consurf.aln  
Alignment identifier is 121p-consurf.aln  
Associated 121p chain A to Input_pdb_SEQRES_A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 121p-consurf.aln  
  
Opened 150 sequences from 121p-consurf.aln  

> color byattr_conservation

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color byattribute seq_conservation

1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83  

> color byattribute seq_conservation palette cyanmaroon range -1.4,1.4

1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83  

> color byattribute seq_conservation palette blue:red:yellow

1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83  

> color byattribute seq_conservation palette cyanmaroon

1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83  

> color byattribute seq_conservation palette cyanmaroon range -1.4,1.4

1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83  

> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html

Opened https://www.rbvi.ucsf.edu/chimerax/data/conservation-
coloring/conservation-coloring.html  

> hide protein

> show ::seq_conservation>1.8

> label ::seq_conservation>1.8

> label height 1.3

> preset pub

Multiple preset names match 'pub': publication 1 (silhouettes); publication 2
(depth-cued)  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> label delete

> surface

> color fromatoms

> preset inter

Using preset: Overall Look / Interactive  
Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> close session

> open 3sn6

Summary of feedback from opening 3sn6 fetched from pdb  
---  
notes | Fetching compressed mmCIF 3sn6 from
http://files.rcsb.org/download/3sn6.cif  
Fetching CCD P0G from http://ligand-expo.rcsb.org/reports/P/P0G/P0G.cif  
  
3sn6 title:  
Crystal structure of the beta2 adrenergic receptor-Gs protein complex [more
info...]  
  
Chain information for 3sn6 #1  
---  
Chain | Description | UniProt  
A | Guanine nucleotide-binding protein G(s) subunit α isoforms short |
GNAS2_BOVIN  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_RAT  
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_BOVIN  
N | Camelid antibody VHH fragment |  
R | Endolysin,Beta-2 adrenergic receptor | ADRB2_HUMAN  
  
Non-standard residues in 3sn6 #1  
---  
P0G —
8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one  
  

> preset cylinders

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 10247 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cylinders

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> color /R yellow

> hide /N cartoons

> open /Users/amandaghilardi/Desktop/81321.ali.rtf

Unrecognized file suffix '.rtf'  

> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/81321.ali

Summary of feedback from opening
//www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/81321.ali fetched from
https  
---  
notes | Fetching 81321.ali from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/81321.ali  
Downloaded 81321.ali to /Users/amandaghilardi/Downloads/81321.ali  
Alignment identifier is 81321.ali  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 81321.ali  
  
Opened 10 sequences from 81321.ali  

> sequence associate /N 81321.ali

Associated 3sn6 chain N to d1m0ka- with 128 mismatches and/or gaps  

> sequence associate /R 81321.ali

Associated 3sn6 chain R to d2rh1a1 with 2 mismatches and/or gaps  

> sequence associate /R 81321.ali

Disassociated 3sn6 chain R from d2rh1a1  
Associated 3sn6 chain R to d2rh1a1 with 2 mismatches and/or gaps  

> color byattribute seq_conservation /R & protein range -1.5,3 noValueColor
> gray

3433 atoms, 443 residues, atom seq_conservation range -1.76 to 4.75  

> show :: seq_conversation>2

> size stickRadius .5

Changed 10478 bond radii  

> color ligand byhetero

> lighting soft

> color ligand byhetero

> lighting soft

> lighting simple

> close session

> open 1kmo

Summary of feedback from opening 1kmo fetched from pdb  
---  
notes | Fetching compressed mmCIF 1kmo from
http://files.rcsb.org/download/1kmo.cif  
Fetching CCD LDA from http://ligand-expo.rcsb.org/reports/L/LDA/LDA.cif  
Fetching CCD HTO from http://ligand-expo.rcsb.org/reports/H/HTO/HTO.cif  
  
1kmo title:  
Crystal structure of the Outer Membrane Transporter FecA [more info...]  
  
Chain information for 1kmo #1  
---  
Chain | Description | UniProt  
A | Iron(III) dicitrate transport protein fecA | FECA_ECOLI  
  
Non-standard residues in 1kmo #1  
---  
HTO — heptane-1,2,3-triol  
LDA — lauryl dimethylamine-N-oxide  
  

> hide

> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/56935.ali

Summary of feedback from opening
//www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/56935.ali fetched from
https  
---  
notes | Fetching 56935.ali from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/56935.ali  
Downloaded 56935.ali to /Users/amandaghilardi/Downloads/56935.ali  
Alignment identifier is 56935.ali  
Associated 1kmo chain A to d1kmoa- with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 56935.ali  
  
Opened 13 sequences from 56935.ali  

> color byattribute attr seq_conservation

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> color byattribute seq_conservation

5862 atoms, 1066 residues, atom seq_conservation range -2.29 to 4.37  

> select ~::seq_conservation

2540 atoms, 2148 bonds, 653 residues, 1 model selected  

> sequence header conservation setting al2co_gap 0.51

> sequence header conservation setting al2co_gap 0.52

> sequence header conservation setting al2co_gap 0.6

> select ~::seq_conservation

1364 atoms, 946 bonds, 496 residues, 1 model selected  

> select clear

> color byattrseq_convservation

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color byattribute seq_convservation

No known/registered numeric attribute seq_convservation  

> color byattribute seq_conservation

5862 atoms, 1066 residues, atom seq_conservation range -1.92 to 4.18  

> color byattribute seq_conservation palette cyanmaroon range -2,3
> noValueColor silver key true

> key cyan-white-maroon :-2.0 :0.5 :3.0 showTool true

> ui mousemode right "color key"

5862 atoms, 1066 residues, atom seq_conservation range -1.92 to 4.18  

> ui mousemode right translate

> windowsize 600 600

> preset pub

Multiple preset names match 'pub': publication 1 (silhouettes); publication 2
(depth-cued)  

> ui windowfill toggle

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  

> set bgColor #ffffff00

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> set bgColor steelblue

> set bgColor #4682b400

> lighting flat

> graphics silhouettes depthJump 0.003

> graphics silhouettes depthJump 0.03

> 2dlabels text "Conservation (AL2CO entropy measure)"

> ui mousemode right "move label"

> 2dlabels #3.1 xpos 0.406 ypos 0.157

> 2dlabels #3.1 xpos 0.349 ypos 0.141

> 2dlabels #3.1 xpos 0.354 ypos 0.018

> key labelSide left/top

> key pos 0.06,0.1 size 0.3,0.04

> 2dlabels xpos 0.021 ypos 0.021

> close session

> open 6ddf

Summary of feedback from opening 6ddf fetched from pdb  
---  
notes | Fetching compressed mmCIF 6ddf from
http://files.rcsb.org/download/6ddf.cif  
Fetching CCD DAL from http://ligand-expo.rcsb.org/reports/D/DAL/DAL.cif  
Fetching CCD MEA from http://ligand-expo.rcsb.org/reports/M/MEA/MEA.cif  
Fetching CCD ETA from http://ligand-expo.rcsb.org/reports/E/ETA/ETA.cif  
  
6ddf title:  
μ Opioid Receptor-Gi Protein Complex [more info...]  
  
Chain information for 6ddf #1  
---  
Chain | Description | UniProt  
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_HUMAN  
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_HUMAN  
D | DAMGO |  
R | Mu-type opioid receptor | OPRM_MOUSE  
  
Non-standard residues in 6ddf #1  
---  
ETA — ethanolamine  
  

> set bgColor black

> set bgColor transparent

> close

> open 4n6h

Summary of feedback from opening 4n6h fetched from pdb  
---  
notes | Fetching compressed mmCIF 4n6h from
http://files.rcsb.org/download/4n6h.cif  
Fetching CCD OLC from http://ligand-expo.rcsb.org/reports/O/OLC/OLC.cif  
Fetching CCD PGE from http://ligand-expo.rcsb.org/reports/P/PGE/PGE.cif  
Fetching CCD TLA from http://ligand-expo.rcsb.org/reports/T/TLA/TLA.cif  
Fetching CCD EJ4 from http://ligand-expo.rcsb.org/reports/E/EJ4/EJ4.cif  
Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif  
  
4n6h title:  
1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target)
[more info...]  
  
Chain information for 4n6h #1  
---  
Chain | Description | UniProt  
A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein |
OPRD_HUMAN  
  
Non-standard residues in 4n6h #1  
---  
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)  
NA — sodium ion  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
PGE — triethylene glycol  
TLA — L(+)-tartaric acid  
  

> surface

> mlp

Map values for surface "4n6h_A SES surface": minimum -26.77, mean -0.8566,
maximum 23.81  

> hide solvent

> hide

> show

> lighting soft

> lighting simple

> hide surfaces

> delete :1002-1106

> hbonds

582 hydrogen bonds found  

> hide solvent

> select protein

2314 atoms, 2370 bonds, 327 pseudobonds, 303 residues, 2 models selected  

> hide

> hide sel atoms

> select clear

> hbonds :EH4

Atom specifier selects no atoms  

> hbonds :EJ4

10 hydrogen bonds found  

> select ::name="EJ4"

31 atoms, 38 bonds, 1 residue, 1 model selected  

> select sel @ show sel atoms

> select clear

> color :EJ orange

> color :EJ4 orange

> color byhetero

> hide cartoons

> clip off

> hide atoms

> show :EJ4 : addh

Summary of feedback from adding hydrogens to 4n6h #1  
---  
warnings | Not adding hydrogens to /A ARG 41 CD because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A VAL 154 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LEU 157 CG because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 166 CE because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 192 CD because it is missing heavy-atom bond
partners  
10 messages similar to the above omitted  
notes | Termini for 4n6h (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLY 36  
Chain-final residues that are actual C termini: /A GLY 338  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A GLY 338  
581 hydrogen bonds  
Adding 'H' to /A GLY 36  
3076 hydrogens added  
  

> open 4n6h fromDatabase eds

Summary of feedback from opening 4n6h fetched from eds  
---  
note | Fetching map 4n6h from
http://www.ebi.ac.uk/pdbe/coordinates/files/4n6h.ccp4  
  
Opened eds 4n6h as #2, grid size 114,100,190, pixel 0.599,0.607,0.603, shown
at level 0.799, step 1, values float32  

> volume #2 level 1.201

> volume zone #2 nearAtoms :EJ4 range 6 newMap false

> volume #2 level 0.7072

> delete H

> volume level .5

> close #2

> style :EJ4 sphere

Changed 31 atom styles  

> surface :EJ4 : ui mousemode right translate

> transparency 50

> close session

> open 6pt2

Summary of feedback from opening 6pt2 fetched from pdb  
---  
notes | Fetching compressed mmCIF 6pt2 from
http://files.rcsb.org/download/6pt2.cif  
Fetching CCD CLR from http://ligand-expo.rcsb.org/reports/C/CLR/CLR.cif  
Fetching CCD DI7 from http://ligand-expo.rcsb.org/reports/D/DI7/DI7.cif  
Fetching CCD DAR from http://ligand-expo.rcsb.org/reports/D/DAR/DAR.cif  
Fetching CCD SAR from http://ligand-expo.rcsb.org/reports/S/SAR/SAR.cif  
Fetching CCD OXJ from http://ligand-expo.rcsb.org/reports/O/OXJ/OXJ.cif  
  
6pt2 title:  
Crystal structure of the active δ opioid receptor in complex with the peptide
agonist KGCHM07 [more info...]  
  
Chain information for 6pt2 #1  
---  
Chain | Description  
A B | δ opioid receptor  
C D | Peptide agonist KGCHM07  
  
Non-standard residues in 6pt2 #1  
---  
CLR — cholesterol  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
OXJ — 1-[3,5-bis(trifluoromethyl)phenyl]-N-methylmethanamine  
  

> hide #1 models

> view

> open 4n6h

4n6h title:  
1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target)
[more info...]  
  
Chain information for 4n6h #2  
---  
Chain | Description | UniProt  
A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein |
OPRD_HUMAN  
  
Non-standard residues in 4n6h #2  
---  
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)  
NA — sodium ion  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
PGE — triethylene glycol  
TLA — L(+)-tartaric acid  
  

> open 4pt2

Summary of feedback from opening 4pt2 fetched from pdb  
---  
note | Fetching compressed mmCIF 4pt2 from
http://files.rcsb.org/download/4pt2.cif  
  
4pt2 title:  
Myxococcus xanthus encapsulin protein (EncA) [more info...]  
  
Chain information for 4pt2 #3  
---  
Chain | Description | UniProt  
A B P | Encapsulin protein | Q1D6H4_MYXXD  
  
4pt2 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  

> hide #1 models

> hide #!2 models

> view

> delete /B,D

> delete :999-1106

> color #2:73,90,95,108,131,143,268,309,323 red

> show #1 models

> matchmaker #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 4n6h, chain A (#2) with 6pt2, chain A (#1), sequence alignment
score = 1850  
RMSD between 198 pruned atom pairs is 1.026 angstroms; (across all 289 pairs:
3.234)  
  

> show #!2 models

> hide #3 models

> show #1 cartoons

> style stick

Changed 9427 atom styles  

> hide surfaces

> morph #1,2 same true

Computed 51 frame morph #4  

> coordset #4 1,51

> morph #1,2 same true

Computed 51 frame morph #5  

> coordset #5 1,51

> morph #1,2 same true

Computed 51 frame morph #6  

> coordset #6 1,51

> hide #3

> hide #3 models

> show #2 models

> show :128

> color :128 & C yellow

> color /C & C pink

> hbonds /C distSlop 0.6

47 hydrogen bonds found  

> swapaa #2:128 ASN

Using Dunbrack library  
4n6h #2/A ASP 128: phi -58.3, psi -44.7 trans  


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

Log:
UCSF ChimeraX version: 1.5.dev202206100131 (2022-06-10)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-4.7.29
OpenGL renderer: AMD Radeon Pro 5500 XT OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac20,1
      Processor Name: 8-Core Intel Core i7
      Processor Speed: 3.8 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1715.40.15.0.0 (iBridge: 19.16.10549.0.0,0)
      OS Loader Version: 540.40.4~45

Software:

    System Software Overview:

      System Version: macOS 12.0.1 (21A559)
      Kernel Version: Darwin 21.1.0
      Time since boot: 19 days 4:30

Graphics/Displays:

    AMD Radeon Pro 5500 XT:

      Chipset Model: AMD Radeon Pro 5500 XT
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0041
      ROM Revision: 113-D3220I-231
      VBIOS Version: 113-D322A1XT-011
      Option ROM Version: 113-D322A1XT-011
      EFI Driver Version: 01.01.231
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.7.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.2
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.5.dev202206100131
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.6
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.20.4
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.12.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Attachments (1)

cmds.cxc (740 bytes ) - added by Eric Pettersen 3 years ago.
command script to reproduce the crash

Download all attachments as: .zip

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: UnassignedStructure Editing
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionCrash in swapaa

Hi Amanda,

Thanks for reporting this problem. Using the commands from your log I was able to reproduce the crash. We hope to have a fix soon.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

by Eric Pettersen, 3 years ago

Attachment: cmds.cxc added

command script to reproduce the crash

comment:2 by Eric Pettersen, 3 years ago

Resolution: fixed
Status: acceptedclosed

Hi Amanda,

I have committed a fix for this and the fix will be in the next daily build:

--Eric

fix: https://github.com/RBVI/ChimeraX/commit/ab113bb8f8bfb588e217670b7d8160800e81a0a1

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