measure sasa: crash in spheres_surface_area

[miyovan@…]

The following bug report has been submitted:
Platform:        macOS-12.6.8-x86_64-i386-64bit
ChimeraX Version: 1.10rc202506052252 (2025-06-05 22:52:41 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00000001186be600 (most recent call first):
  File "/Applications/ChimeraX-1.10-rc2025.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/surface/sasa.py", line 493 in spheres_surface_area
  File "/Applications/ChimeraX-1.10-rc2025.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/surface/measure_sasacmd.py", line 46 in measure_sasa
  File "/Applications/ChimeraX-1.10-rc2025.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3219 in run
  File "/Applications/ChimeraX-1.10-rc2025.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
  File "/Applications/ChimeraX-1.10-rc2025.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
  File "/Applications/ChimeraX-1.10-rc2025.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
  File "/Applications/ChimeraX-1.10-rc2025.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
  File "/Applications/ChimeraX-1.10-rc2025.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath (total: 56)


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{
  "uptime" : 210000,
  "procLaunch" : "2025-06-08 21:51:28.8677 -0700",
  "procRole" : "Foreground",
  "version" : 2,
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  "deployVersion" : 210,
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  "procStartAbsTime" : 218145088320842,
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    "build" : "21G725",
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  "captureTime" : "2025-06-08 22:00:19.9959 -0700",
  "incident" : "CBAD7D9B-DCB1-4AB7-A4D4-91E0CE9FF810",
  "bug_type" : "309",
  "pid" : 30547,
  "procExitAbsTime" : 218675804043945,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.10-rc2025.06.06.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "9E4F77A0-CDF5-D7FC-81F7-B4BBF031DE61",
  "wakeTime" : 4656,
  "sleepWakeUUID" : "5B40B64C-5A11-4655-840A-2A53D2FD5060",
  "sip" : "enabled",
  "vmRegionInfo" : "0x7ff7b4af1ff8 is in 0x7ff7b12f2000-0x7ff7b4af2000;  bytes after start: 58720248  bytes before end: 7\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_LARGE             7feee7eae000-7feee7ed2000 [  144K] rw-\/rwx SM=PRV  \n      GAP OF 0x8c9420000 BYTES\n--->  Stack Guard              7ff7b12f2000-7ff7b4af2000 [ 56.0M] ---\/rwx SM=NUL  \n      Stack                    7ff7b4af2000-7ff7b52f2000 [ 8192K] rw-\/rwx SM=PRV  ",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000002, 0x00007ff7b4af1ff8","rawCodes":[2,140701865025528],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_PROTECTION_FAILURE at 0x00007ff7b4af1ff8"},
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  "faultingThread" : 0,
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    "path" : "\/usr\/lib\/system\/libsystem_malloc.dylib",
    "name" : "libsystem_malloc.dylib"
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    "size" : 90112,
    "uuid" : "a99f1fb2-fd31-3cf4-be4d-a9fccf219974",
    "path" : "\/usr\/lib\/libc++abi.dylib",
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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=9.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=9.3G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG backing stores                  544K        4 \nCG image                            72K       11 \nColorSync                          224K       26 \nCoreAnimation                       92K       18 \nCoreGraphics                        12K        2 \nCoreUI image data                 1868K       26 \nDispatch continuations            32.0M        1 \nFoundation                          16K        1 \nIOKit                             7940K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                             8.8G    35660 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            732K        2         reserved VM address space (unallocated)\nMach message                        24K        3 \nObjC additional data                15K        1 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        136K       34 \nStack                            257.8M       35 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      202.6M      230 \n__CTF                               756        1 \n__DATA                            42.5M      718 \n__DATA_CONST                      41.7M      449 \n__DATA_DIRTY                      1805K      239 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       676.4M      152 \n__TEXT                           867.6M      717 \n__UNICODE                          592K        1 \ndyld private memory               1104K        3 \nmapped file                      184.2M       46 \nshared memory                     3100K       27 \n===========                     =======  ======= \nTOTAL                             11.2G    38426 \nTOTAL, minus reserved VM space    11.2G    38426 \n",
  "legacyInfo" : {
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  "trialInfo" : {
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.10rc202506052252 (2025-06-05)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/admin/Downloads/Liu2025_top1k_ampc_poses.cxs

> view name session-start

opened ChimeraX session  

> measure sasa :1 #2.9 setAttribute

Missing "setAttribute" keyword's argument  

> measure sasa :1 #2.9 setAttribute true


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

Log:
UCSF ChimeraX version: 1.10rc202506052252 (2025-06-05)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/admin/Downloads/Liu2025_top1k_ampc_poses.cxs

Log from Sun Jun 8 15:43:02 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/katieholland/Desktop/ampc_inhibs.cxs

Log from Fri Jun 6 14:18:08 2025 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle  
  
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/katieholland/Downloads/ampc_inhibitors.pyc

Failed opening file /Users/katieholland/Downloads/ampc_inhibitors.pyc:  
Python code was compiled for a different version of Python  

> open /Users/katieholland/Downloads/ampc_inhibitors.py

ChimeraX cannot open a regular Chimera session. An exporter from Chimera  
to ChimeraX is being worked on but only handles molecules and molecular
surfaces  
(not volumes) at this time. If that is sufficient, use the latest Chimera  
daily build and its File->Export Scene menu item, and change the resulting  
dialog's "File Type" to ChimeraX.  

> open /Users/katieholland/Downloads/7aue.pdb format pdb

7aue.pdb title:  
Melanocortin receptor 4 (MC4R) GS protein complex [more info...]  
  
Chain information for 7aue.pdb #1  
---  
Chain | Description | UniProt  
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 32-373  
B | transducin β chain 1 | GBB1_HUMAN 19-357  
C | aminoserine |   
G | G γ-I | GBG2_HUMAN 1-71  
R | MC4-R | MC4R_HUMAN 1-332  
S | SCFV16 |   
  
Non-standard residues in 7aue.pdb #1  
---  
ACE — acetyl group  
CA — calcium ion  
CY3 — 2-amino-3-mercapto-propionamide  
DAL — D-alanine  
DPN — D-phenylalanine  
  

> measure sasa

Solvent accessible area for all atoms (8755 atoms) = 51692  

> select /R:288@CD1

1 atom, 1 residue, 1 model selected  

> select clear

> select /R:288@CD2

1 atom, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

78 atoms, 82 bonds, 9 residues, 1 model selected  

> measure sasa

Solvent accessible area for all atoms (8755 atoms) = 51692  

> measure sasa sel

Solvent accessible area for sel (78 atoms) = 1328.6  

> measure sasa sel H

Expected a keyword  

> measure sasa sel hydrogen

Expected a keyword  

> ui tool show "Add Hydrogens"

> addh #!1

Summary of feedback from adding hydrogens to 7aue.pdb #1  
---  
warnings | Not adding hydrogens to /R TYR 41 CB because it is missing heavy-atom bond partners  
Not adding hydrogens to /R GLU 49 CG because it is missing heavy-atom bond
partners  
Not adding hydrogens to /R ASN 108 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /R ASP 189 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /R SER 191 CB because it is missing heavy-atom bond
partners  
31 messages similar to the above omitted  
notes | Termini for 7aue.pdb (#1) chain A determined from SEQRES records  
Termini for 7aue.pdb (#1) chain B determined from SEQRES records  
Termini for 7aue.pdb (#1) chain C determined from SEQRES records  
Termini for 7aue.pdb (#1) chain G determined from SEQRES records  
Termini for 7aue.pdb (#1) chain R determined from SEQRES records  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /C ACE 1  
Chain-initial residues that are not actual N termini: /A CYS 3, /A GLY 185, /A
ARG 207, /A ASN 243, /B GLU 20, /G ALA 7, /R CYS 40, /R SER 116, /R ASN 240,
/S VAL 2, /S SER 124  
Chain-final residues that are actual C termini: /A LEU 373, /B ASN 357, /C CY3
9  
Chain-final residues that are not actual C termini: /A ILE 55, /A GLY 204, /A
VAL 235, /G GLU 63, /R ASN 108, /R GLY 231, /R ILE 317, /S SER 121, /S LEU 235  
Missing OXT added to C-terminal residue /A LEU 373  
Missing OXT added to C-terminal residue /B ASN 357  
785 hydrogen bonds  
Adding 'H' to /A CYS 3  
Adding 'H' to /A GLY 185  
Adding 'H' to /A ARG 207  
Adding 'H' to /A ASN 243  
Adding 'H' to /B GLU 20  
6 messages similar to the above omitted  
/G GLU 63 is not terminus, removing H atom from 'C'  
/R ILE 317 is not terminus, removing H atom from 'C'  
/S LEU 235 is not terminus, removing H atom from 'C'  
8627 hydrogens added  
  

> ui tool show "Measure Volume and Area"

> measure sasa sel & element H sum

Expected a keyword  

> measure sasa sel

Solvent accessible area for sel (78 atoms) = 1318.9  

> select /R:291@CG2

1 atom, 1 residue, 1 model selected  

> select /C:1@HH32

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

148 atoms, 152 bonds, 9 residues, 1 model selected  

> select /R:51@CE2

1 atom, 1 residue, 1 model selected  

> select clear

> select H

8627 atoms, 1133 residues, 1 model selected  

> split ligands

Split 7aue.pdb (#1) into 2 models  
Chain information for 7aue.pdb #1.1  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
R | No description available  
S | No description available  
  
Chain information for 7aue.pdb ACE #1.2  
---  
Chain | Description  
C | No description available  
  

> select H #1.2

Expected a keyword  

> select H

8627 atoms, 1133 residues, 2 models selected  

> hide #!1.1 models

> show #!1.1 models

> hide #1.2 models

> show #1.2 models

> select clear

> select #1.2/C:9@N

1 atom, 1 residue, 1 model selected  

> select up

13 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

148 atoms, 152 bonds, 9 residues, 1 model selected  

> measure sasa sel & sum @H

Expected a keyword  

> select clear

[Repeated 1 time(s)]

> select H model #1.2

Expected a keyword  

> measure sasa sel & sel sum @H

No atoms specified by sel & sel  

> select #1.2/C:3@C

1 atom, 1 residue, 1 model selected  

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

148 atoms, 152 bonds, 9 residues, 1 model selected  

> measure sasa sel & sel sum @H

Solvent accessible area for sel & sel (148 atoms) = 1361.4  
Solvent accessible area for @H (1099 atoms) of sel & sel (148 atoms) = 45.616  

> measure sasa sel sum @H

Solvent accessible area for sel (148 atoms) = 1361.4  
Solvent accessible area for @H (1099 atoms) of sel (148 atoms) = 45.616  

> measure sasa sel sum @H

Solvent accessible area for sel (148 atoms) = 1361.4  
Solvent accessible area for @H (1099 atoms) of sel (148 atoms) = 45.616  

> measure sasa sel sum @C

Solvent accessible area for sel (148 atoms) = 1361.4  
Solvent accessible area for @C (1132 atoms) of sel (148 atoms) = 15.071  

> select clear

[Repeated 1 time(s)]

> select #1.2/C:4@N

1 atom, 1 residue, 1 model selected  

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

148 atoms, 152 bonds, 9 residues, 1 model selected  

> measure sasa sel

Solvent accessible area for sel (148 atoms) = 1361.4  

> measure sasa sel @ sel sum @N

Expected a keyword  

> measure sasa sel & sel sum @N

Solvent accessible area for sel & sel (148 atoms) = 1361.4  
Solvent accessible area for @N (1131 atoms) of sel & sel (148 atoms) = 12.674  

> measure sasa sel & sel sum @C

Solvent accessible area for sel & sel (148 atoms) = 1361.4  
Solvent accessible area for @C (1132 atoms) of sel & sel (148 atoms) = 15.071  

> measure sasa sel & sel sum @H

Solvent accessible area for sel & sel (148 atoms) = 1361.4  
Solvent accessible area for @H (1099 atoms) of sel & sel (148 atoms) = 45.616  

> addh H

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Not adding hydrogens to 7aue.pdb #1.1/R TYR 41 CB because it is missing heavy-atom bond partners  
Not adding hydrogens to 7aue.pdb #1.1/R GLU 49 CG because it is missing heavy-
atom bond partners  
Not adding hydrogens to 7aue.pdb #1.1/R ASN 108 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to 7aue.pdb #1.1/R ASP 189 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to 7aue.pdb #1.1/R SER 191 CB because it is missing
heavy-atom bond partners  
31 messages similar to the above omitted  
notes | No usable SEQRES records for 7aue.pdb (#1.1) chain A; guessing termini instead  
No usable SEQRES records for 7aue.pdb (#1.1) chain B; guessing termini instead  
No usable SEQRES records for 7aue.pdb (#1.1) chain G; guessing termini instead  
No usable SEQRES records for 7aue.pdb (#1.1) chain R; guessing termini instead  
No usable SEQRES records for 7aue.pdb (#1.1) chain S; guessing termini instead  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 7aue.pdb #1.1/A CYS 3,
7aue.pdb #1.1/A GLY 185, 7aue.pdb #1.1/A ARG 207, 7aue.pdb #1.1/A ASN 243,
7aue.pdb #1.1/B GLU 20, 7aue.pdb #1.1/G ALA 7, 7aue.pdb #1.1/R CYS 40,
7aue.pdb #1.1/R SER 116, 7aue.pdb #1.1/R ASN 240, 7aue.pdb #1.1/S VAL 2,
7aue.pdb #1.1/S SER 124  
Chain-final residues that are actual C termini: 7aue.pdb #1.1/A LEU 373,
7aue.pdb #1.1/B ASN 357  
Chain-final residues that are not actual C termini: 7aue.pdb #1.1/A ILE 55,
7aue.pdb #1.1/A GLY 204, 7aue.pdb #1.1/A VAL 235, 7aue.pdb #1.1/G GLU 63,
7aue.pdb #1.1/R ILE 317, 7aue.pdb #1.1/R ASN 108, 7aue.pdb #1.1/R GLY 231,
7aue.pdb #1.1/S LEU 235, 7aue.pdb #1.1/S SER 121  
729 hydrogen bonds  
7aue.pdb #1.1/G GLU 63 is not terminus, removing H atom from 'C'  
7aue.pdb #1.1/R ILE 317 is not terminus, removing H atom from 'C'  
7aue.pdb #1.1/S LEU 235 is not terminus, removing H atom from 'C'  
No usable SEQRES records for 7aue.pdb ACE (#1.2) chain C; guessing termini
instead  
Chain-initial residues that are actual N termini: 7aue.pdb ACE #1.2/C ACE 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: 7aue.pdb ACE #1.2/C CY3 9  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
1 hydrogens added  
  

> select clear

> select H model#1.2

Expected a keyword  

> select H #1.2

Expected a keyword  

> select H #1.2]

Expected a keyword  

> select H #1.2]

Expected a keyword  

> select H #1.2

Expected a keyword  

> select H 1.2

Expected a keyword  

> select #1.2 & element.H

Expected a keyword  

> measure sasa @H #1.2

Solvent accessible area for @H#1.2 (1239 atoms) = 51892  

> hide #1.2 models

> show #1.2 models

> open /Users/katieholland/Desktop/ampc/rec.crg.pdb

Chain information for rec.crg.pdb #2  
---  
Chain | Description  
R | No description available  
  

> close #1.2#1#1.1

> close

> open /Users/katieholland/Desktop/ampc/ampc_rec.crg.pdb

Summary of feedback from opening
/Users/katieholland/Desktop/ampc/ampc_rec.crg.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
585 messages similar to the above omitted  
  
Chain information for ampc_rec.crg.pdb #1  
---  
Chain | Description  
B | No description available  
  

> show atoms

> hide cartoons

> show cartoons

> style stick

Changed 3350 atom styles  

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> open /Users/katieholland/Desktop/test_compounds.mol2

Opened test_compounds.mol2 containing 189 structures (7832 atoms, 8222 bonds)  

> ui tool show ViewDockX

> hide #2.1-189 models

> show #2.1 models

> select clear

> select #1/B:212

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

56 atoms, 57 bonds, 7 residues, 1 model selected  

> select up

3350 atoms, 3430 bonds, 358 residues, 1 model selected  

> select up

3350 atoms, 3430 bonds, 358 residues, 2 models selected  

> select down

3350 atoms, 3430 bonds, 358 residues, 1 model selected  

> select down

56 atoms, 57 bonds, 7 residues, 1 model selected  

> select up

3350 atoms, 3430 bonds, 358 residues, 1 model selected  

> surface sel

> transparency (#!1 & sel) 80

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> select clear

> select #1/B:212@OG

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 2 models selected  

> select up

56 atoms, 57 bonds, 7 residues, 2 models selected  

> select up

3350 atoms, 3430 bonds, 358 residues, 2 models selected  

> select up

3350 atoms, 3430 bonds, 358 residues, 2 models selected  

> select clear

> surface hidePatches #1#2.1#!2

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

17 atoms, 16 bonds, 1 residue, 2 models selected  

> select up

36 atoms, 36 bonds, 3 residues, 2 models selected  

> select up

3350 atoms, 3430 bonds, 358 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select #2.1/?:1@N2

1 atom, 1 residue, 1 model selected  

> select up

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

> select #1 & protein & zone sel<5

Expected a keyword  

> select sel @< 5

7760 atoms, 8104 bonds, 215 residues, 190 models selected  

> show sel & #2.1#!1 atoms

> hide sel & #2.1#!1 cartoons

> show sel & #2.1#!1 cartoons

> select sel @< 20

11182 atoms, 10942 bonds, 547 residues, 190 models selected  

> show sel & #2.1#!1 atoms

> show sel & #2.1#!1 cartoons

> select clear

[Repeated 1 time(s)]

> hide #2.1#!1 atoms

> show #2.1#!1 atoms

> select #1/B:210

13 atoms, 13 bonds, 1 residue, 1 model selected  

> select up

56 atoms, 57 bonds, 7 residues, 2 models selected  

> select up

3350 atoms, 3430 bonds, 358 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> select sel @< 10

8310 atoms, 8681 bonds, 261 residues, 190 models selected  

> show sel & #2.1#!1 cartoons

> show sel & #2.1#!1 atoms

> select clear

> surface #1#2.1#!2

> save /Users/katieholland/Desktop/ampc_inhibs.cxs

——— End of log from Fri Jun 6 14:18:08 2025 ———

opened ChimeraX session  

> close #2

> open /Users/katieholland/Desktop/fangyu_poses_filtered.mol2

Opened fangyu_poses_filtered.mol2 containing 1113 structures (44416 atoms,
46281 bonds)  

> ui tool show ViewDockX

[Repeated 1 time(s)]

> hide #2.1-1113 models

> show #2.1 models

> hbonds #2.1-1113 restrict #!1 reveal true interSubmodel true

4882 hydrogen bonds found  

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.2 models

> hide #2.2 models

> show #2.3 models

> hide #2.3 models

> show #2.4 models

> hide #2.4 models

> show #2.5 models

> hide #2.5 models

> show #2.6 models

> hide #2.6 models

> show #2.7 models

> hide #2.7 models

> show #2.8 models

> hide #2.8 models

> show #2.9 models

> save /Users/katieholland/Desktop/Liu2025_top1k_ampc_poses.cxs

——— End of log from Sun Jun 8 15:43:02 2025 ———

> view name session-start

opened ChimeraX session  




OpenGL version: 4.1 INTEL-18.8.6
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir7,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1.8 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 481.0.0.0.0
      OS Loader Version: 540.120.3~22
      SMC Version (system): 2.27f2

Software:

    System Software Overview:

      System Version: macOS 12.6.8 (21G725)
      Kernel Version: Darwin 21.6.0
      Time since boot: 11 days 15:44

Graphics/Displays:

    Intel HD Graphics 6000:

      Chipset Model: Intel HD Graphics 6000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1626
      Revision ID: 0x0009
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
          UI Looks like: 1440 x 900
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.4
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10rc202506052252
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.8.2
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.1
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.0
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 26.4.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[pett]

Reported by Milena Yovanovich

[Tom Goddard]

Looks like the measure sasa crash happened with this data file and command

open /Users/katieholland/Desktop/fangyu_poses_filtered.mol2
measure sasa :1 #2.9 setAttribute true

I would need the mol2 file to be able to debug this crash. Very likely something is strange about residue 1 of model #2.9, perhaps multiple atoms at exactly the same position.

I am not sure why you typed the measure sasa command like this instead of the more typical

measure sasa #2.9:1 setAttribute true

That won't make any difference in the crash.