charge estimation: 'Ring' object has no attribute '_c_pointer_ref'

[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
I've seen this in two different cases now (this one is residue A1901 of 6fzm): the first call to estimate_net_charge() on a ligand with rings fails with "AttributeError: 'Ring' object has no attribute '_c_pointer_ref'". Repeating the call with nothing else changed leads to success.

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.
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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.

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

[pett]

The code "isolde parameterise sel" is actually running is at ​https://github.com/tristanic/isolde/blob/90224f43b8f8e7e8d97a067e98f4db68a36edafc/isolde/src/openmm/amberff/parameterise.py#L36.

[pett]

Okay, though I was never able to reproduce it, have committed what I believe is a fix for it. Hoping you can check it out some tomorrow...

[pett]

Sorry it's been a bit of a wait before I could properly test this... my daughter had a positive PCR test for COVID early last week (she's fine as is everyone else, but it messed up a lot of plans and put me way behind on my fellowship application). Anyway, I'm afraid this still happened to me in today's release candidate (on my Linux machine this time, so at least we know it's not platform-specific). Same behaviour - first call fails, second works. This time it was the ligand named H96 in 7dl6.

A bit of extra probing suggests that it's only happening when the model was opened via "open 7dl6 structureFactors true", suggesting models loaded that way are missing some step that estimate_net_charge() expects to have already happened. Does that give any clues?

[pett]

I think I know the cause (at the very least, I can reliably avoid it now). Basically, Clipper goes out of its way to avoid any use of idatm_types - there's a discussion of that in an old ticket, but the upshot is that it was making things slow when adding new atoms/residues to really big structures with lots of heterocycles*. Anyway, the exception is triggered when I (a) load a model into Clipper's framework; (b) addh (invalidating the old idatm_types and rings); (c) do the call to "isolde parameterise" which calls estimate_charge(), which in turn apparently expects the rings to be current. If after adding hydrogens I go into the shell and just do m.atoms.idatm_types and *then* do "isolde parameterise" then it works fine.

• That might have been partly my fault - the AMBER templates for hemes and chlorophylls treat the metal ion as explicitly bonded to the surrounding nitrogens so to avoid adding extra complication to the template-assignment code in ISOLDE I make those metal-coordination pseudobonds into real ones, which I suppose would complicate those multi-ring structures considerably.

[pett]

Is your code looping through rings? My changes should have prevented this error in estimate_net_charge(). Is the stack trace different than before -- is the error coming from a different part of the code?

At any rate, I have decided that this behavior is too error prone. The fact that rings are ephemeral on the C++ is too baked in to change, but I can have the Python side cache all relevant info (atoms, bonds, aromaticity) at construction time so that it does not need to refer back to the C++ side, which may have disappeared. This change will only be going into the 1.4 branch though.

[pett]

Could this have something to do with my last comment on #5619? The cygwin libraries you added disappeared in the latest rc (along with gaff2.dat)... did some commits get rolled back, perhaps?

[pett]

Original ticket got corrupted; reconstituted description and comments.

[pett]

Rings now cache C++ info at construction time. 1.4 branch only.