id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6224	Crash deleting structure	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open BIR-jellyroll_conservation-electrostatic.cxc

> open coulomb-cons/BRUCE-full.pdb coulomb-cons/SMAC-4J46_1.pdb coulomb-
> cons/SMAC-4J46_2.pdb coulomb-cons/SMAC-4TX5.pdb

Summary of feedback from opening coulomb-cons/BRUCE-full.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 9 9 ARG A
1398 ILE A 1412 1 15  
Start residue of secondary structure not found: HELIX 10 10 PHE A 1424 ALA A
1441 1 18  
Start residue of secondary structure not found: HELIX 11 11 GLY A 1445 GLU A
1461 1 17  
Start residue of secondary structure not found: HELIX 12 12 LEU A 1463 ARG A
1484 1 22  
Start residue of secondary structure not found: HELIX 13 13 PRO A 1487 TYR A
1496 1 10  
935 messages similar to the above omitted  
  
Summary of feedback from opening coulomb-cons/SMAC-4J46_1.pdb  
---  
warnings | CONECT record for nonexistent atom: 1084  
Start residue of secondary structure not found: HELIX 6 6 GLU C 163 PHE C 170
1 8  
Start residue of secondary structure not found: HELIX 7 7 PRO C 181 SER C 186
1 6  
Start residue of secondary structure not found: HELIX 8 8 ALA C 216 HIS C 223
1 8  
Start residue of secondary structure not found: HELIX 9 9 PHE C 228 ARG C 233
1 6  
Start residue of secondary structure not found: SHEET 5 5 1 LEU C 189 TYR C
191 0  
1 messages similar to the above omitted  
Cannot find LINK/SSBOND residue HIS (220 )  
Cannot find LINK/SSBOND residue CYS (227 )  
Cannot find LINK/SSBOND residue CYS (203 )  
Cannot find LINK/SSBOND residue CYS (200 )  
  
Summary of feedback from opening coulomb-cons/SMAC-4J46_2.pdb  
---  
warnings | CONECT record for nonexistent atom: 1084  
Start residue of secondary structure not found: HELIX 6 6 GLU C 163 PHE C 170
1 8  
Start residue of secondary structure not found: HELIX 7 7 PRO C 181 SER C 186
1 6  
Start residue of secondary structure not found: HELIX 8 8 ALA C 216 HIS C 223
1 8  
Start residue of secondary structure not found: HELIX 9 9 PHE C 228 ARG C 233
1 6  
Start residue of secondary structure not found: SHEET 5 5 1 LEU C 189 TYR C
191 0  
1 messages similar to the above omitted  
Cannot find LINK/SSBOND residue HIS (220 )  
Cannot find LINK/SSBOND residue CYS (227 )  
Cannot find LINK/SSBOND residue CYS (203 )  
Cannot find LINK/SSBOND residue CYS (200 )  
  
Chain information for BRUCE-full.pdb  
---  
Chain | Description  
1.1/A | No description available  
1.2/A 1.3/A | No description available  
1.4/A 1.5/A | No description available  
1.1/B | No description available  
  
SMAC-4J46_1.pdb title:  
Crystal structure of xiap-BIR2 domain with AVPI bound [more info...]  
  
Chain information for SMAC-4J46_1.pdb #2  
---  
Chain | Description  
A | E3 ubiquitin-protein ligase xiap  
B | peptide (ala-val-pro-ile)  
  
Non-standard residues in SMAC-4J46_1.pdb #2  
---  
ZN — zinc ion  
  
SMAC-4J46_2.pdb title:  
Crystal structure of xiap-BIR2 domain with AVPI bound [more info...]  
  
Chain information for SMAC-4J46_2.pdb #3  
---  
Chain | Description  
A | E3 ubiquitin-protein ligase xiap  
B | peptide (ala-val-pro-ile)  
  
Non-standard residues in SMAC-4J46_2.pdb #3  
---  
ZN — zinc ion  
  
SMAC-4TX5.pdb title:  
Crystal structure of smac-diablo (In space group P65) [more info...]  
  
Chain information for SMAC-4TX5.pdb #4  
---  
Chain | Description  
A B | diablo homolog, mitochondrial  
  
Non-standard residues in SMAC-4TX5.pdb #4  
---  
ACT — acetate ion  
MPD — (4S)-2-methyl-2,4-pentanediol  
  

> set bgColor white

> graphics silhouettes true

> coulombic #2-4

Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for SMAC-4J46_1.pdb_A SES surface #2.2: minimum, -14.74, mean
0.28, maximum 11.28  
Coulombic values for SMAC-4J46_1.pdb_B SES surface #2.3: minimum, -10.29, mean
-0.56, maximum 8.29  
Coulombic values for SMAC-4J46_2.pdb_A SES surface #3.2: minimum, -15.29, mean
0.26, maximum 11.21  
Coulombic values for SMAC-4J46_2.pdb_B SES surface #3.3: minimum, -10.20, mean
-0.58, maximum 8.36  
Coulombic values for SMAC-4TX5.pdb_A SES surface #4.1: minimum, -23.10, mean
-4.09, maximum 9.78  
Coulombic values for SMAC-4TX5.pdb_B SES surface #4.2: minimum, -25.00, mean
-3.97, maximum 10.44  

> select #1/*:2875-2883,3158-3311

2389 atoms, 2439 bonds, 321 residues, 1 model selected  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
BRUCE-full.pdb #1.1/A GLU 1091  
BRUCE-full.pdb #1.1/A PHE 1108  
BRUCE-full.pdb #1.1/A LEU 1110  
BRUCE-full.pdb #1.1/A PHE 1173  
BRUCE-full.pdb #1.1/A LEU 1194  
BRUCE-full.pdb #1.1/A GLN 1297  
BRUCE-full.pdb #1.1/A GLU 1298  
BRUCE-full.pdb #1.1/A ARG 1304  
BRUCE-full.pdb #1.1/A HIS 1347  
BRUCE-full.pdb #1.1/A LYS 1637  
BRUCE-full.pdb #1.1/A GLU 2326  
BRUCE-full.pdb #1.1/A ARG 2327  
BRUCE-full.pdb #1.1/A PHE 2883  
BRUCE-full.pdb #1.1/A PHE 2887  
BRUCE-full.pdb #1.1/A MET 3006  
BRUCE-full.pdb #1.1/A LYS 3675  
BRUCE-full.pdb #1.1/A TYR 4489  
BRUCE-full.pdb #1.1/B GLU 1091  
BRUCE-full.pdb #1.1/B PHE 1108  
BRUCE-full.pdb #1.1/B LEU 1110  
BRUCE-full.pdb #1.1/B PHE 1173  
BRUCE-full.pdb #1.1/B LEU 1194  
BRUCE-full.pdb #1.1/B GLN 1297  
BRUCE-full.pdb #1.1/B GLU 1298  
BRUCE-full.pdb #1.1/B ARG 1304  
BRUCE-full.pdb #1.1/B HIS 1347  
BRUCE-full.pdb #1.1/B LYS 1637  
BRUCE-full.pdb #1.1/B GLU 2326  
BRUCE-full.pdb #1.1/B ARG 2327  
BRUCE-full.pdb #1.1/B PHE 2883  
BRUCE-full.pdb #1.1/B PHE 2887  
BRUCE-full.pdb #1.1/B MET 3006  
BRUCE-full.pdb #1.1/B LYS 3675  
BRUCE-full.pdb #1.1/B TYR 4489  

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.2.5.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/wp/vv45m0h50mn_649xdntwx59c0000gn/T/tmpj8x8jv8i/ante.in.mol2 -fi
mol2 -o
/var/folders/wp/vv45m0h50mn_649xdntwx59c0000gn/T/tmpj8x8jv8i/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
(HIS) ``  
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`  
(HIS) ``  
(HIS) `Info: Finished reading file
(/var/folders/wp/vv45m0h50mn_649xdntwx59c0000gn/T/tmpj8x8jv8i/ante.in.mol2);
atoms read (19), bonds read (18).`  
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(HIS) `Running:
/Applications/ChimeraX-1.2.5.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HIS) ``  
(HIS) ``  
(HIS) `Running:
/Applications/ChimeraX-1.2.5.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(HIS) `Info: Total number of electrons: 78; net charge: -3`  
(HIS) ``  
(HIS) `Running: /Applications/ChimeraX-1.2.5.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`  
(HIS) `/Applications/ChimeraX-1.2.5.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(HIS) `Cannot properly run
""/Applications/ChimeraX-1.2.5.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out"".`  
Failure running ANTECHAMBER for residue HIS  
Check reply log for details  




OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0)
      OS Loader Version: 540.80.2~11

Software:

    System Software Overview:

      System Version: macOS 12.2 (21D49)
      Kernel Version: Darwin 21.3.0
      Time since boot: 24 days 21:47

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
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          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
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          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP P203:
          Resolution: 1600 x 900
          UI Looks like: 1600 x 900
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: CNC8220HPX  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: Apple USB-C VGA Adapter
          Automatically Adjust Brightness: Yes
          Adapter Firmware Version: 1.91

Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    ChimeraX-PubChem: 2.0.1
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    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
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    ChimeraX-SDF: 2.0
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    ChimeraX-SeqView: 2.3
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    ChimeraX-Shell: 1.0
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    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
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    wheel: 0.36.0
    wheel-filename: 1.3.0

}}}
"	defect	closed	normal		Core		duplicate						all	ChimeraX