Delete alt locs: access violation

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.3rc202111182158 (2021-11-18 21:58:36 UTC)
Description
Running `delete_alt_locs()` on 5eih causes an access violation.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3rc202111182158 (2021-11-18)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Registration

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requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  

> open 3g2i structureFactors true

Summary of feedback from opening 3g2i fetched from pdb  
---  
warnings | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
intensity_meas, intensity_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
No free flags detected in this dataset! Automatically generated a new random
set with 2071 free from 62878 observed reflections. You should save your data
to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Fetching compressed mmCIF 3g2i from
http://files.rcsb.org/download/3g2i.cif  
Fetching CCD RUG from http://ligand-expo.rcsb.org/reports/R/RUG/RUG.cif  
Fetching CCD LLP from http://ligand-expo.rcsb.org/reports/L/LLP/LLP.cif  
Fetching compressed 3g2i structure factors from
http://files.rcsb.org/download/3g2i-sf.cif  
Resolution: 1.9993483783884805  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 40,40,38, pixel
0.663,0.663,0.654, shown at level 0.483, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 40,40,38, pixel
0.663,0.663,0.654, shown at level -0.154,0.154, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_15 as #1.1.1.4, grid size 40,40,38, pixel
0.663,0.663,0.654, shown at level 0.379, step 1, values float32  
3g2i title:  
Crystal structure of 1-(beta-D-glucopyranosyl)-4-substituted-1,2,3-triazole
[more info...]  
  
Chain information for 3g2i  
---  
Chain | Description | UniProt  
1.2/A | Glycogen phosphorylase, muscle form | PYGM_RABIT  
  
Non-standard residues in 3g2i #1.2  
---  
RUG — 1-beta-D-glucopyranosyl-4-(hydroxymethyl)-1H-1,2,3-triazole  
  
3g2i mmCIF Assemblies  
---  
1| author_defined_assembly  
2| software_defined_assembly  
  

> view :RUG

> addh

Summary of feedback from adding hydrogens to 3g2i #1.2  
---  
notes | Termini for 3g2i (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLN 12, /A GLY 261,
/A THR 324  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A LEU 254, /A SER 314, /A
ALA 836  
1742 hydrogen bonds  
Adding 'H' to /A GLN 12  
Adding 'H' to /A GLY 261  
Adding 'H' to /A THR 324  
/A ALA 836 is not terminus, removing H atom from 'C'  
7126 hydrogens added  
  

> select /A:998@N1

1 atom, 1 residue, 1 model selected  

> select up

33 atoms, 34 bonds, 1 residue, 1 model selected  

> show sel

> close #1

Deleting Crystallographic maps (3g2i-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_15  

> open 6cdy structureFactors true

Summary of feedback from opening 6cdy fetched from pdb  
---  
notes | Fetching compressed mmCIF 6cdy from
http://files.rcsb.org/download/6cdy.cif  
Fetching CCD EY1 from http://ligand-expo.rcsb.org/reports/E/EY1/EY1.cif  
Fetching compressed 6cdy structure factors from
http://files.rcsb.org/download/6cdy-sf.cif  
Resolution: 2.320114427937553  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,34,38, pixel
0.765,0.77,0.745, shown at level 0.4, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,34,38, pixel 0.765,0.77,0.745,
shown at level -0.149,0.149, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_8 as #1.1.1.4, grid size 50,34,38, pixel
0.765,0.77,0.745, shown at level 0.359, step 1, values float32  
6cdy title:  
Crystal structure of TEAD complexed with its inhibitor [more info...]  
  
Chain information for 6cdy  
---  
Chain | Description | UniProt  
1.2/A 1.2/B | Transcriptional enhancer factor TEF-4 | TEAD2_HUMAN  
  
Non-standard residues in 6cdy #1.2  
---  
EY1 —
2-[(4H-1,2,4-triazol-3-yl)sulfanyl]-N-{4-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]phenyl}acetamide  
  
6cdy mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> view :EY1

> view /A:EY1

> close #1

Deleting Crystallographic maps (6cdy-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_8  

> open 6iqn structureFactors true

Summary of feedback from opening 6iqn fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
intensity_meas, intensity_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 6iqn from
http://files.rcsb.org/download/6iqn.cif  
Fetching CCD AQ6 from http://ligand-expo.rcsb.org/reports/A/AQ6/AQ6.cif  
Fetching compressed 6iqn structure factors from
http://files.rcsb.org/download/6iqn-sf.cif  
Resolution: 2.5356356434398193  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 32,32,30, pixel
0.841,0.841,0.821, shown at level 0.234, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 32,32,30, pixel
0.841,0.841,0.821, shown at level -0.0977,0.0977, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_6 as #1.1.1.4, grid size 32,32,30, pixel
0.841,0.841,0.821, shown at level 0.393, step 1, values float32  
6iqn title:  
Crystal structure of TrkA kinase with ligand [more info...]  
  
Chain information for 6iqn  
---  
Chain | Description | UniProt  
1.2/A 1.2/B | High affinity nerve growth factor receptor | NTRK1_HUMAN  
  
Non-standard residues in 6iqn #1.2  
---  
AQ6 —
4-[[4-azanyl-3-(4-cyclohexylpiperazin-1-yl)-9,10-bis(oxidanylidene)anthracen-1-yl]amino]benzoic
acid  
  

> view :AQ6

> view /A:AQ6

> view /B:AQ6

> close #1

Deleting Crystallographic maps (6iqn-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_6  

> open 6nbw structureFactors true

Summary of feedback from opening 6nbw fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
intensity_meas, intensity_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 6nbw from
http://files.rcsb.org/download/6nbw.cif  
Fetching CCD LAB from http://ligand-expo.rcsb.org/reports/L/LAB/LAB.cif  
Fetching CCD SOP from http://ligand-expo.rcsb.org/reports/S/SOP/SOP.cif  
Fetching CCD MES from http://ligand-expo.rcsb.org/reports/M/MES/MES.cif  
Fetching compressed 6nbw structure factors from
http://files.rcsb.org/download/6nbw-sf.cif  
Resolution: 2.496084344340796  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 32,32,30, pixel
0.816,0.803,0.826, shown at level 0.353, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 32,32,30, pixel
0.816,0.803,0.826, shown at level -0.126,0.126, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_1 as #1.1.1.4, grid size 32,32,30, pixel
0.816,0.803,0.826, shown at level 0.521, step 1, values float32  
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.5, grid size 32,32,30,
pixel 0.816,0.803,0.826, shown at level -0.315,0.315, step 1, values float32  
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.6, grid size 32,32,30, pixel
0.816,0.803,0.826, shown at level -0.912,0.912, step 1, values float32  
6nbw title:  
Ternary Complex of Beta/Gamma-Actin with Profilin and AnCoA-NAA80 [more
info...]  
  
Chain information for 6nbw  
---  
Chain | Description | UniProt  
1.2/A | Actin, cytoplasmic 1 | ACTB_HUMAN  
1.2/N | N-alpha-acetyltransferase 80 | NAA80_HUMAN  
1.2/P | Profilin-1 | PROF1_HUMAN  
  
Non-standard residues in 6nbw #1.2  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
LAB — latrunculin B  
MES — 2-(N-morpholino)-ethanesulfonic acid  
SOP —
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl
(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-{[3-oxo-3-({2-[(2-oxopropyl)thio]ethyl}amino)propyl]amino}butyl
dihydrogen diphosphate (S-(2-oxopropyl)-coenzyme A)  
  

> addh template true

Summary of feedback from adding hydrogens to 6nbw #1.2  
---  
notes | Termini for 6nbw (#1.2) chain A determined from SEQRES records  
Termini for 6nbw (#1.2) chain N determined from SEQRES records  
Termini for 6nbw (#1.2) chain P determined from SEQRES records  
Chain-initial residues that are actual N termini: /A ASP 2  
Chain-initial residues that are not actual N termini: /A GLY 48, /N HIS 76, /N
PRO 140, /N LEU 263, /N PRO 300, /P GLY 2  
Chain-final residues that are actual C termini: /A PHE 375, /N ILE 308, /P TYR
139  
Chain-final residues that are not actual C termini: /A HIS 40, /N HIS 133, /N
LEU 230, /N GLU 271  
1132 hydrogen bonds  
Adding 'H' to /A GLY 48  
Adding 'H' to /N HIS 76  
Adding 'H' to /N LEU 263  
Adding 'H' to /P GLY 2  
424 hydrogens added  
  

> isolde start

> set selectionWidth 4

Removed all altlocs in #1.2 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 28 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.7, grid size 32,32,30, pixel
0.816,0.803,0.826, shown at level 0.351, step 1, values float32  
Done loading forcefield  
Loading residue template for ATP from internal database  
Loading residue template for GOL from internal database  
Loading residue template for LAB from internal database  
Loading residue template for MES from internal database  

> view :HIC

Deleted the following atoms from residue HIC A73: O, H2, H3  

> setattr sel atom name O

Assigning name attribute to 1 item  

> close #1

Deleting Crystallographic maps (6nbw-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_1  
Deleting (LIVE) MDFF potential  

> open 6hkx structureFactors true

Summary of feedback from opening 6hkx fetched from pdb  
---  
warnings | Cannot find consistent set of bond orders for ring system
containing atom C13 in residue GCE /A:602  
Cannot find consistent set of bond orders for ring system containing atom C10
in residue GCE /B:602  
WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma,  
intensity_meas, intensity_sigma,  
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 6hkx from
http://files.rcsb.org/download/6hkx.cif  
Fetching CCD GCE from http://ligand-expo.rcsb.org/reports/G/GCE/GCE.cif  
Fetching CCD PEG from http://ligand-expo.rcsb.org/reports/P/PEG/PEG.cif  
Fetching compressed 6hkx structure factors from
http://files.rcsb.org/download/6hkx-sf.cif  
Resolution: 2.800019462853161  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 30,32,30, pixel
0.861,0.835,0.849, shown at level 0.39, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 30,32,30, pixel
0.861,0.835,0.849, shown at level -0.16,0.16, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_22 as #1.1.1.4, grid size 30,32,30, pixel
0.861,0.835,0.849, shown at level 0.836, step 1, values float32  
6hkx title:  
Eg5-inhibitor complex [more info...]  
  
Chain information for 6hkx  
---  
Chain | Description | UniProt  
1.2/A 1.2/B | Kinesin-like protein KIF11 | KIF11_HUMAN  
  
Non-standard residues in 6hkx #1.2  
---  
ADP — adenosine-5'-diphosphate  
GCE —
(2~{S})-2-(3-azanylpropyl)-5-[2,5-bis(fluoranyl)phenyl]-~{N}-methoxy-~{N}-methyl-2-phenyl-1,3,4-thiadiazole-3-carboxamide  
MG — magnesium ion  
PEG — di(hydroxyethyl)ether  
  
Removed all altlocs in #1.2 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 55 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 30,32,30, pixel
0.861,0.835,0.849, shown at level 0.454, step 1, values float32  

> view #1

> addh template true

Summary of feedback from adding hydrogens to 6hkx #1.2  
---  
warnings | Not adding hydrogens to /A ARG 47 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LYS 146 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ASP 149 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 153 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 191 CB because it is missing heavy-atom bond
partners  
15 messages similar to the above omitted  
notes | Termini for 6hkx (#1.2) chain A determined from SEQRES records  
Termini for 6hkx (#1.2) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A LYS 17, /A HIS 38, /A
LEU 255, /A ASN 287, /B LYS 17, /B HIS 38, /B SER 61, /B ASN 287  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ASN 29, /A THR 249, /A
ASN 271, /A GLU 364, /B ALA 31, /B GLY 56, /B ASN 271, /B GLU 364  
1177 hydrogen bonds  
Adding 'H' to /A LYS 17  
Adding 'H' to /A HIS 38  
Adding 'H' to /A LEU 255  
Adding 'H' to /A ASN 287  
Adding 'H' to /B LYS 17  
3 messages similar to the above omitted  
/A GLU 364 is not terminus, removing H atom from 'C'  
/B GLU 364 is not terminus, removing H atom from 'C'  
5451 hydrogens added  
  
Loading residue template for ADP from internal database  
Loading residue template for PEG from internal database  

> close #1

Deleting Crystallographic maps (6hkx-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_22  
Deleting (LIVE) MDFF potential  

> open 6hv0 structureFactors true

Summary of feedback from opening 6hv0 fetched from pdb  
---  
notes | Fetching compressed mmCIF 6hv0 from
http://files.rcsb.org/download/6hv0.cif  
Fetching CCD GUK from http://ligand-expo.rcsb.org/reports/G/GUK/GUK.cif  
Fetching compressed 6hv0 structure factors from
http://files.rcsb.org/download/6hv0-sf.cif  
Resolution: 2.7252848595389296  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 40,32,30, pixel 0.9,0.822,0.899,
shown at level 0.319, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 40,32,30, pixel 0.9,0.822,0.899,
shown at level -0.139,0.139, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_19 as #1.1.1.4, grid size 40,32,30, pixel
0.9,0.822,0.899, shown at level 0.633, step 1, values float32  
6hv0 title:  
IRE1 kinase/RNase in complex with imidazo[1,2-b]pyridazin-8-amine compound 33
[more info...]  
  
Chain information for 6hv0  
---  
Chain | Description | UniProt  
1.2/A | Serine/threonine-protein kinase/endoribonuclease IRE1 | ERN1_HUMAN  
  
Non-standard residues in 6hv0 #1.2  
---  
GUK — 6-chloranyl-3-(2~{H}-indazol-5-yl)-~{N}-propan-2-yl-
imidazo[1,2-b]pyridazin-8-amine  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 31 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 40,32,30, pixel
0.9,0.822,0.899, shown at level 0.344, step 1, values float32  

> addh template true

Summary of feedback from adding hydrogens to 6hv0 #1.2  
---  
warnings | Not adding hydrogens to /A LYS 633 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LEU 718 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A VAL 720 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 864 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 887 CB because it is missing heavy-atom bond
partners  
4 messages similar to the above omitted  
notes | Termini for 6hv0 (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A SER 562  
Chain-initial residues that are not actual N termini: /A SER 619, /A GLY 662,
/A ASN 750, /A ARG 890  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A CYS 605, /A PHE 658, /A
MET 742, /A ARG 887, /A HIS 963  
442 hydrogen bonds  
Adding 'H' to /A SER 619  
Adding 'H' to /A GLY 662  
Adding 'H' to /A ASN 750  
Adding 'H' to /A ARG 890  
/A HIS 963 is not terminus, removing H atom from 'C'  
3077 hydrogens added  
  

> close #1

Deleting Crystallographic maps (6hv0-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_19  
Deleting (LIVE) MDFF potential  

> open 6fzm structureFactors true

Summary of feedback from opening 6fzm fetched from pdb  
---  
notes | Fetching compressed mmCIF 6fzm from
http://files.rcsb.org/download/6fzm.cif  
Fetching CCD EE5 from http://ligand-expo.rcsb.org/reports/E/EE5/EE5.cif  
Fetching compressed 6fzm structure factors from
http://files.rcsb.org/download/6fzm-sf.cif  
Resolution: 2.670303299218495  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 46,34,30, pixel
0.874,0.874,0.854, shown at level 0.301, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 46,34,30, pixel
0.874,0.874,0.854, shown at level -0.139,0.139, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_16 as #1.1.1.4, grid size 46,34,30, pixel
0.874,0.874,0.854, shown at level 0.538, step 1, values float32  
6fzm title:  
Human PARP14 (ARTD8), catalytic fragment in complex with inhibitor ITK6 [more
info...]  
  
Chain information for 6fzm  
---  
Chain | Description | UniProt  
1.2/A 1.2/B | Poly [ADP-ribose] polymerase 14 | PAR14_HUMAN  
  
Non-standard residues in 6fzm #1.2  
---  
EE5 —
4-[(8-methyl-4-oxidanylidene-7-prop-1-ynyl-3~{H}-quinazolin-2-yl)methylsulfanyl]benzoic
acid  
  
6fzm mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 17 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 46,34,30, pixel
0.874,0.874,0.854, shown at level 0.329, step 1, values float32  

> addh template true

Summary of feedback from adding hydrogens to 6fzm #1.2  
---  
notes | Termini for 6fzm (#1.2) chain A determined from SEQRES records  
Termini for 6fzm (#1.2) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A MET 1612, /B LYS
1613, /B VAL 1707  
Chain-final residues that are actual C termini: /A LYS 1801, /B LYS 1801  
Chain-final residues that are not actual C termini: /B ALA 1702  
Missing OXT added to C-terminal residue /A LYS 1801  
Missing OXT added to C-terminal residue /B LYS 1801  
397 hydrogen bonds  
Adding 'H' to /A MET 1612  
Adding 'H' to /B LYS 1613  
Adding 'H' to /B VAL 1707  
2950 hydrogens added  
  

> isolde parameterise sel

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\amberff\parameterise.py", line 52, in
parameterise_cmd  
parameterise_ligand(session, residue, net_charge=net_charge)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\amberff\parameterise.py", line 23, in
parameterise_ligand  
net_charge = estimate_net_charge(residue.atoms)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 409, in estimate_net_charge  
for a in ring.atoms:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'Ring' object has no attribute '_c_pointer_ref'  
  
AttributeError: 'Ring' object has no attribute '_c_pointer_ref'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  

> isolde parameterise sel

Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\tristan\AppData\Local\Temp\tmp1xf1qnei\ante.in.mol2 -fi mol2 -o
C:\Users\tristan\AppData\Local\Temp\tmp1xf1qnei\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n  
(EE5) ``  
(EE5) `Welcome to antechamber 20.0: molecular input file processor.`  
(EE5) ``  
(EE5) `Info: Finished reading file
(C:\Users\tristan\AppData\Local\Temp\tmp1xf1qnei\ante.in.mol2); atoms read
(41), bonds read (43).`  
(EE5) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(EE5) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(EE5) `bash.exe: warning: could not find /tmp, please create!`  
(EE5) ``  
(EE5) ``  
(EE5) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(EE5) `bash.exe: warning: could not find /tmp, please create!`  
(EE5) `Info: Total number of electrons: 190; net charge: -1`  
(EE5) ``  
(EE5) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(EE5) `bash.exe: warning: could not find /tmp, please create!`  
(EE5) ``  
(EE5) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(EE5) `bash.exe: warning: could not find /tmp, please create!`  
(EE5) ``  
(EE5) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(EE5) `bash.exe: warning: could not find /tmp, please create!`  
(EE5) ``  
Charges for residue EE5 determined  
OpenMM ffXML file EE5 written to the current working directory.  
New template added to forcefield as USER_EE5. This ligand should now work in
all remaining simulations for this session. To use in future sessions, load
the ffXML file with ISOLDE's Load Residue MD Definition(s) button.  
ISOLDE: started sim  

> select clear

> set bgColor white

> hide HC

Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> close #1

Deleting Crystallographic maps (6fzm-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_16  
Deleting (LIVE) MDFF potential  

> open 5eih structureFactors true

Summary of feedback from opening 5eih fetched from pdb  
---  
notes | Fetching compressed mmCIF 5eih from
http://files.rcsb.org/download/5eih.cif  
Fetching CCD TZ2 from http://ligand-expo.rcsb.org/reports/T/TZ2/TZ2.cif  
Fetching CCD PZ5 from http://ligand-expo.rcsb.org/reports/P/PZ5/PZ5.cif  
Fetching CCD ACT from http://ligand-expo.rcsb.org/reports/A/ACT/ACT.cif  
Fetching CCD P6G from http://ligand-expo.rcsb.org/reports/P/P6G/P6G.cif  
Fetching compressed 5eih structure factors from
http://files.rcsb.org/download/5eih-sf.cif  
Resolution: 2.700006433862177  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 32,30,28, pixel
0.828,0.883,0.885, shown at level 0.264, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 32,30,28, pixel
0.828,0.883,0.885, shown at level -0.0842,0.0842, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_18 as #1.1.1.4, grid size 32,30,28, pixel
0.828,0.883,0.885, shown at level 0.522, step 1, values float32  
Opened (STATIC) F_calc, phase_calc as #1.1.1.5, grid size 32,30,28, pixel
0.828,0.883,0.885, shown at level -0.436,0.436, step 1, values float32  
5eih title:  
mAChE-TZ2/PA5 complex [more info...]  
  
Chain information for 5eih  
---  
Chain | Description | UniProt  
1.2/A 1.2/B | Acetylcholinesterase | ACES_MOUSE  
  
Non-standard residues in 5eih #1.2  
---  
ACT — acetate ion  
P6G — hexaethylene glycol (polyethylene glycol PEG400)  
PZ5 — 5-hept-6-ynyl-6-phenyl-phenanthridin-5-ium-3,8-diamine  
TZ2 — ~{N}-(2-azidoethyl)-1,2,3,4-tetrahydroacridin-9-amine  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 1050, in _update_model_list  
self._change_selected_model(model=current_model)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2521, in _change_selected_model  
m.delete_alt_locs()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1590, in delete_alt_locs  
f = c_function('structure_delete_alt_locs', args =
(ctypes.c_void_p,))(self._c_pointer)  
OSError: exception: access violation reading 0x0000000000000014  
  
Error processing trigger "add models":  
OSError: exception: access violation reading 0x0000000000000014  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1590, in delete_alt_locs  
f = c_function('structure_delete_alt_locs', args =
(ctypes.c_void_p,))(self._c_pointer)  
  
See log for complete Python traceback.  
  

> close #1

Deleting Crystallographic maps (5eih-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_18  

> open 5eih structureFactors true

Summary of feedback from opening 5eih fetched from pdb  
---  
notes | Resolution: 2.700006433862177  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 32,30,28, pixel
0.828,0.883,0.885, shown at level 0.263, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 32,30,28, pixel
0.828,0.883,0.885, shown at level -0.0826,0.0826, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_18 as #1.1.1.4, grid size 32,30,28, pixel
0.828,0.883,0.885, shown at level 0.522, step 1, values float32  
Opened (STATIC) F_calc, phase_calc as #1.1.1.5, grid size 32,30,28, pixel
0.828,0.883,0.885, shown at level -0.436,0.436, step 1, values float32  
5eih title:  
mAChE-TZ2/PA5 complex [more info...]  
  
Chain information for 5eih  
---  
Chain | Description | UniProt  
1.2/A 1.2/B | Acetylcholinesterase | ACES_MOUSE  
  
Non-standard residues in 5eih #1.2  
---  
ACT — acetate ion  
P6G — hexaethylene glycol (polyethylene glycol PEG400)  
PZ5 — 5-hept-6-ynyl-6-phenyl-phenanthridin-5-ium-3,8-diamine  
TZ2 — ~{N}-(2-azidoethyl)-1,2,3,4-tetrahydroacridin-9-amine  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 1050, in _update_model_list  
self._change_selected_model(model=current_model)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2521, in _change_selected_model  
m.delete_alt_locs()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1590, in delete_alt_locs  
f = c_function('structure_delete_alt_locs', args =
(ctypes.c_void_p,))(self._c_pointer)  
OSError: exception: access violation reading 0x0000000000000014  
  
Error processing trigger "add models":  
OSError: exception: access violation reading 0x0000000000000014  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1590, in delete_alt_locs  
f = c_function('structure_delete_alt_locs', args =
(ctypes.c_void_p,))(self._c_pointer)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 471.11
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    -himerax-clipper: 0.17.0
    -himerax-isolde: 1.3.dev33
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.2
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3rc202111182158
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    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-ISOLDE: 1.3.dev33
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.22
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Eric Pettersen]

Only happens on Windows, and only if directly calling delete_alt_locs() (rather than the command "altlocs clean")

[Eric Pettersen]

Have committed a fix which I will test once tomorrow's build is available.