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Opened 8 months ago
Closed 7 months ago
#17277 closed defect (fixed)
D-amino acids assigned wrong atom types
| Reported by: | Tristan Croll | Owned by: | Eric Pettersen |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.8.0-51-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Looks like AddH gets a bit confused by D-amino acids... adding hydrogens to 9f01, and I see multiple issues:
- D-Arg NE atom does not get protonated
- backbone nitrogens get doubly protonated (or singly D-Pro)... or they did *the first time* - strangely I can't replicate that either on the same model or a freshly-downloaded copy.
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
Running command "isolde shorthand"
> 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: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 9f01
Summary of feedback from opening 9f01 fetched from pdb
---
notes | Fetching compressed mmCIF 9f01 from http://files.rcsb.org/download/9f01.cif
Fetching CCD DAL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/DAL/DAL.cif
Fetching CCD DAR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/DAR/DAR.cif
Fetching CCD DAS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/DAS/DAS.cif
Fetching CCD DCY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/DCY/DCY.cif
Fetching CCD DGL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/DGL/DGL.cif
Fetching CCD DGN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/DGN/DGN.cif
Fetching CCD DHI from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/DHI/DHI.cif
Fetching CCD DIL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/DIL/DIL.cif
Fetching CCD DLY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/DLY/DLY.cif
Fetching CCD DPN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/DPN/DPN.cif
Fetching CCD DSG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/DSG/DSG.cif
Fetching CCD DSN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/DSN/DSN.cif
Fetching CCD DTH from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/DTH/DTH.cif
Fetching CCD DTR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/DTR/DTR.cif
Fetching CCD DTY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/DTY/DTY.cif
Fetching CCD DVA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/DVA/DVA.cif
9f01 title:
Complex between D-SH2 domain of ABL with monobody 'DAM21 [more info...]
Chain information for 9f01 #1
---
Chain | Description
A B C D | synthetic D-SH2 domain NS1-10
E F G H | nanobody DAM21.3
Non-standard residues in 9f01 #1
---
CL — chloride ion
9f01 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
> cartoon
> hide
> isolde select #1
Running command "set selectionWidth 4"
> set selectionWidth 4
Done loading forcefield
Running command "isolde set simFidelityMode "Highest/Slowest""
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #1 to IUPAC-IUB
standards.
9f01 title:
Complex between D-SH2 domain of ABL with monobody 'DAM21 [more info...]
Chain information for 9f01
---
Chain | Description
1.2/A 1.2/B 1.2/C 1.2/D | synthetic D-SH2 domain NS1-10
1.2/E 1.2/F 1.2/G 1.2/H | nanobody DAM21.3
Non-standard residues in 9f01 #1.2
---
CL — chloride ion
9f01 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
> addh
Summary of feedback from adding hydrogens to 9f01 #1.2
---
notes | Termini for 9f01 (#1.2) chain A determined from SEQRES records
Termini for 9f01 (#1.2) chain B determined from SEQRES records
Termini for 9f01 (#1.2) chain C determined from SEQRES records
Termini for 9f01 (#1.2) chain D determined from SEQRES records
Termini for 9f01 (#1.2) chain E determined from SEQRES records
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A DGL 142, /B DGL 142, /C
DGL 142, /D DGL 142
Chain-initial residues that are not actual N termini: /E SER 6, /F SER 6, /G
SER 6, /H SER 6
Chain-final residues that are actual C termini: /A DSG 240, /B DSG 240, /C DSG
240, /D DSG 240, /E THR 98, /F THR 98, /G THR 98, /H THR 98
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /A DSG 240
Missing OXT added to C-terminal residue /B DSG 240
Missing OXT added to C-terminal residue /C DSG 240
Missing OXT added to C-terminal residue /D DSG 240
891 hydrogen bonds
Adding 'H' to /E SER 6
Adding 'H' to /F SER 6
Adding 'H' to /G SER 6
Adding 'H' to /H SER 6
5934 hydrogens added
Running command "select clear"
> select clear
Running command "isolde sim start /A:220"
> isolde sim start /A:220
"isolde sim" called with command start
Sim termination reason: None
Running command "clipper spot #1.2"
ISOLDE: stopped sim
> addh template true
Summary of feedback from adding hydrogens to 9f01 #1.2
---
notes | Termini for 9f01 (#1.2) chain A determined from SEQRES records
Termini for 9f01 (#1.2) chain B determined from SEQRES records
Termini for 9f01 (#1.2) chain C determined from SEQRES records
Termini for 9f01 (#1.2) chain D determined from SEQRES records
Termini for 9f01 (#1.2) chain E determined from SEQRES records
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A DGL 142, /B DGL 142, /C
DGL 142, /D DGL 142
Chain-initial residues that are not actual N termini: /E SER 6, /F SER 6, /G
SER 6, /H SER 6
Chain-final residues that are actual C termini: /A DSG 240, /B DSG 240, /C DSG
240, /D DSG 240, /E THR 98, /F THR 98, /G THR 98, /H THR 98
Chain-final residues that are not actual C termini:
746 hydrogen bonds
367 hydrogens added
Deleted the following atoms from residue DAR A153: H2
Running command "select clear"
> select clear
> cd /home/tcroll/Desktop
Current working directory is: /home/tcroll/Desktop
> cd /home/tcroll/Desktop/random
Current working directory is: /home/tcroll/Desktop/random
> open 9f01
9f01 title:
Complex between D-SH2 domain of ABL with monobody 'DAM21 [more info...]
Chain information for 9f01 #2
---
Chain | Description
A B C D | synthetic D-SH2 domain NS1-10
E F G H | nanobody DAM21.3
Non-standard residues in 9f01 #2
---
CL — chloride ion
9f01 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
> save d_protein_test.pdb #2
> open d_protein_test.pdb
Chain information for d_protein_test.pdb #3
---
Chain | Description
A B C D | No description available
E F G H | No description available
Running command "hide #2 models"
> hide #2 models
Running command "style #3#!1.2 stick"
> style #3#!1.2 stick
Changed 18509 atom styles
Running command "hide #!1 models"
> hide #!1 models
> color #3 byhetero
> cartoon #3
> ~cartoon #3
> addh #3
Summary of feedback from adding hydrogens to d_protein_test.pdb #3
---
notes | Termini for d_protein_test.pdb (#3) chain A determined from SEQRES records
Termini for d_protein_test.pdb (#3) chain B determined from SEQRES records
Termini for d_protein_test.pdb (#3) chain C determined from SEQRES records
Termini for d_protein_test.pdb (#3) chain D determined from SEQRES records
Termini for d_protein_test.pdb (#3) chain E determined from SEQRES records
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: d_protein_test.pdb #3/A DGL
142, d_protein_test.pdb #3/B DGL 142, d_protein_test.pdb #3/C DGL 142,
d_protein_test.pdb #3/D DGL 142
Chain-initial residues that are not actual N termini: d_protein_test.pdb #3/E
SER 6, d_protein_test.pdb #3/F SER 6, d_protein_test.pdb #3/G SER 6,
d_protein_test.pdb #3/H SER 6
Chain-final residues that are actual C termini: d_protein_test.pdb #3/A DSG
240, d_protein_test.pdb #3/B DSG 240, d_protein_test.pdb #3/C DSG 240,
d_protein_test.pdb #3/D DSG 240, d_protein_test.pdb #3/E THR 98,
d_protein_test.pdb #3/F THR 98, d_protein_test.pdb #3/G THR 98,
d_protein_test.pdb #3/H THR 98
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue d_protein_test.pdb #3/A DSG 240
Missing OXT added to C-terminal residue d_protein_test.pdb #3/B DSG 240
Missing OXT added to C-terminal residue d_protein_test.pdb #3/C DSG 240
Missing OXT added to C-terminal residue d_protein_test.pdb #3/D DSG 240
889 hydrogen bonds
Adding 'H' to d_protein_test.pdb #3/E SER 6
Adding 'H' to d_protein_test.pdb #3/F SER 6
Adding 'H' to d_protein_test.pdb #3/G SER 6
Adding 'H' to d_protein_test.pdb #3/H SER 6
5924 hydrogens added
> save d_protein_test.cif #2
> open d_protein_test.cif
Chain information for d_protein_test.cif #4
---
Chain | Description
A B C D | synthetic D-SH2 domain NS1-10
E F G H | nanobody DAM21.3
d_protein_test.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
Running command "hide #3 models"
> hide #3 models
> cartoon #4
Running command "style #4 stick"
> style #4 stick
Changed 6102 atom styles
Running command "select clear"
> select clear
> color byhetero
> ~cartoon #4
> addh #4
Summary of feedback from adding hydrogens to d_protein_test.cif #4
---
notes | Termini for d_protein_test.cif (#4) chain A determined from SEQRES records
Termini for d_protein_test.cif (#4) chain B determined from SEQRES records
Termini for d_protein_test.cif (#4) chain C determined from SEQRES records
Termini for d_protein_test.cif (#4) chain D determined from SEQRES records
Termini for d_protein_test.cif (#4) chain E determined from SEQRES records
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: d_protein_test.cif #4/A DGL
142, d_protein_test.cif #4/B DGL 142, d_protein_test.cif #4/C DGL 142,
d_protein_test.cif #4/D DGL 142
Chain-initial residues that are not actual N termini: d_protein_test.cif #4/E
SER 6, d_protein_test.cif #4/F SER 6, d_protein_test.cif #4/G SER 6,
d_protein_test.cif #4/H SER 6
Chain-final residues that are actual C termini: d_protein_test.cif #4/A DSG
240, d_protein_test.cif #4/B DSG 240, d_protein_test.cif #4/C DSG 240,
d_protein_test.cif #4/D DSG 240, d_protein_test.cif #4/E THR 98,
d_protein_test.cif #4/F THR 98, d_protein_test.cif #4/G THR 98,
d_protein_test.cif #4/H THR 98
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue d_protein_test.cif #4/A DSG 240
Missing OXT added to C-terminal residue d_protein_test.cif #4/B DSG 240
Missing OXT added to C-terminal residue d_protein_test.cif #4/C DSG 240
Missing OXT added to C-terminal residue d_protein_test.cif #4/D DSG 240
886 hydrogen bonds
Adding 'H' to d_protein_test.cif #4/E SER 6
Adding 'H' to d_protein_test.cif #4/F SER 6
Adding 'H' to d_protein_test.cif #4/G SER 6
Adding 'H' to d_protein_test.cif #4/H SER 6
5923 hydrogens added
Running command "show #!1 models"
> show #!1 models
Running command "hide #4 models"
> hide #4 models
> delete #1&H
> addh #1
Summary of feedback from adding hydrogens to 9f01 #1.2
---
notes | Termini for 9f01 (#1.2) chain A determined from SEQRES records
Termini for 9f01 (#1.2) chain B determined from SEQRES records
Termini for 9f01 (#1.2) chain C determined from SEQRES records
Termini for 9f01 (#1.2) chain D determined from SEQRES records
Termini for 9f01 (#1.2) chain E determined from SEQRES records
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: 9f01 #1.2/A DGL 142, 9f01
#1.2/B DGL 142, 9f01 #1.2/C DGL 142, 9f01 #1.2/D DGL 142
Chain-initial residues that are not actual N termini: 9f01 #1.2/E SER 6, 9f01
#1.2/F SER 6, 9f01 #1.2/G SER 6, 9f01 #1.2/H SER 6
Chain-final residues that are actual C termini: 9f01 #1.2/A DSG 240, 9f01
#1.2/B DSG 240, 9f01 #1.2/C DSG 240, 9f01 #1.2/D DSG 240, 9f01 #1.2/E THR 98,
9f01 #1.2/F THR 98, 9f01 #1.2/G THR 98, 9f01 #1.2/H THR 98
Chain-final residues that are not actual C termini:
887 hydrogen bonds
Adding 'H' to 9f01 #1.2/E SER 6
Adding 'H' to 9f01 #1.2/F SER 6
Adding 'H' to 9f01 #1.2/G SER 6
Adding 'H' to 9f01 #1.2/H SER 6
5934 hydrogens added
> addh #1
Summary of feedback from adding hydrogens to 9f01 #1.2
---
notes | Termini for 9f01 (#1.2) chain A determined from SEQRES records
Termini for 9f01 (#1.2) chain B determined from SEQRES records
Termini for 9f01 (#1.2) chain C determined from SEQRES records
Termini for 9f01 (#1.2) chain D determined from SEQRES records
Termini for 9f01 (#1.2) chain E determined from SEQRES records
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: 9f01 #1.2/A DGL 142, 9f01
#1.2/B DGL 142, 9f01 #1.2/C DGL 142, 9f01 #1.2/D DGL 142
Chain-initial residues that are not actual N termini: 9f01 #1.2/E SER 6, 9f01
#1.2/F SER 6, 9f01 #1.2/G SER 6, 9f01 #1.2/H SER 6
Chain-final residues that are actual C termini: 9f01 #1.2/A DSG 240, 9f01
#1.2/B DSG 240, 9f01 #1.2/C DSG 240, 9f01 #1.2/D DSG 240, 9f01 #1.2/E THR 98,
9f01 #1.2/F THR 98, 9f01 #1.2/G THR 98, 9f01 #1.2/H THR 98
Chain-final residues that are not actual C termini:
683 hydrogen bonds
0 hydrogens added
Running command "show #2 models"
> show #2 models
Running command "hide #!1 models"
> hide #!1 models
Running command "style #2 stick"
> style #2 stick
Changed 6102 atom styles
> addh #2
Summary of feedback from adding hydrogens to 9f01 #2
---
notes | Termini for 9f01 (#2) chain A determined from SEQRES records
Termini for 9f01 (#2) chain B determined from SEQRES records
Termini for 9f01 (#2) chain C determined from SEQRES records
Termini for 9f01 (#2) chain D determined from SEQRES records
Termini for 9f01 (#2) chain E determined from SEQRES records
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: 9f01 #2/A DGL 142, 9f01 #2/B
DGL 142, 9f01 #2/C DGL 142, 9f01 #2/D DGL 142
Chain-initial residues that are not actual N termini: 9f01 #2/E SER 6, 9f01
#2/F SER 6, 9f01 #2/G SER 6, 9f01 #2/H SER 6
Chain-final residues that are actual C termini: 9f01 #2/A DSG 240, 9f01 #2/B
DSG 240, 9f01 #2/C DSG 240, 9f01 #2/D DSG 240, 9f01 #2/E THR 98, 9f01 #2/F THR
98, 9f01 #2/G THR 98, 9f01 #2/H THR 98
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue 9f01 #2/A DSG 240
Missing OXT added to C-terminal residue 9f01 #2/B DSG 240
Missing OXT added to C-terminal residue 9f01 #2/C DSG 240
Missing OXT added to C-terminal residue 9f01 #2/D DSG 240
890 hydrogen bonds
Adding 'H' to 9f01 #2/E SER 6
Adding 'H' to 9f01 #2/F SER 6
Adding 'H' to 9f01 #2/G SER 6
Adding 'H' to 9f01 #2/H SER 6
5931 hydrogens added
> addh template true
Summary of feedback from adding hydrogens to multiple structures
---
notes | Termini for 9f01 (#1.2) chain A determined from SEQRES records
Termini for 9f01 (#1.2) chain B determined from SEQRES records
Termini for 9f01 (#1.2) chain C determined from SEQRES records
Termini for 9f01 (#1.2) chain D determined from SEQRES records
Termini for 9f01 (#1.2) chain E determined from SEQRES records
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: 9f01 #1.2/A DGL 142, 9f01
#1.2/B DGL 142, 9f01 #1.2/C DGL 142, 9f01 #1.2/D DGL 142
Chain-initial residues that are not actual N termini: 9f01 #1.2/E SER 6, 9f01
#1.2/F SER 6, 9f01 #1.2/G SER 6, 9f01 #1.2/H SER 6
Chain-final residues that are actual C termini: 9f01 #1.2/A DSG 240, 9f01
#1.2/B DSG 240, 9f01 #1.2/C DSG 240, 9f01 #1.2/D DSG 240, 9f01 #1.2/E THR 98,
9f01 #1.2/F THR 98, 9f01 #1.2/G THR 98, 9f01 #1.2/H THR 98
Chain-final residues that are not actual C termini:
683 hydrogen bonds
Termini for 9f01 (#2) chain A determined from SEQRES records
Termini for 9f01 (#2) chain B determined from SEQRES records
Termini for 9f01 (#2) chain C determined from SEQRES records
Termini for 9f01 (#2) chain D determined from SEQRES records
Termini for 9f01 (#2) chain E determined from SEQRES records
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: 9f01 #2/A DGL 142, 9f01 #2/B
DGL 142, 9f01 #2/C DGL 142, 9f01 #2/D DGL 142
Chain-initial residues that are not actual N termini: 9f01 #2/E SER 6, 9f01
#2/F SER 6, 9f01 #2/G SER 6, 9f01 #2/H SER 6
Chain-final residues that are actual C termini: 9f01 #2/A DSG 240, 9f01 #2/B
DSG 240, 9f01 #2/C DSG 240, 9f01 #2/D DSG 240, 9f01 #2/E THR 98, 9f01 #2/F THR
98, 9f01 #2/G THR 98, 9f01 #2/H THR 98
Chain-final residues that are not actual C termini:
684 hydrogen bonds
Termini for d_protein_test.pdb (#3) chain A determined from SEQRES records
Termini for d_protein_test.pdb (#3) chain B determined from SEQRES records
Termini for d_protein_test.pdb (#3) chain C determined from SEQRES records
Termini for d_protein_test.pdb (#3) chain D determined from SEQRES records
Termini for d_protein_test.pdb (#3) chain E determined from SEQRES records
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: d_protein_test.pdb #3/A DGL
142, d_protein_test.pdb #3/B DGL 142, d_protein_test.pdb #3/C DGL 142,
d_protein_test.pdb #3/D DGL 142
Chain-initial residues that are not actual N termini: d_protein_test.pdb #3/E
SER 6, d_protein_test.pdb #3/F SER 6, d_protein_test.pdb #3/G SER 6,
d_protein_test.pdb #3/H SER 6
Chain-final residues that are actual C termini: d_protein_test.pdb #3/A DSG
240, d_protein_test.pdb #3/B DSG 240, d_protein_test.pdb #3/C DSG 240,
d_protein_test.pdb #3/D DSG 240, d_protein_test.pdb #3/E THR 98,
d_protein_test.pdb #3/F THR 98, d_protein_test.pdb #3/G THR 98,
d_protein_test.pdb #3/H THR 98
Chain-final residues that are not actual C termini:
682 hydrogen bonds
Termini for d_protein_test.cif (#4) chain A determined from SEQRES records
Termini for d_protein_test.cif (#4) chain B determined from SEQRES records
Termini for d_protein_test.cif (#4) chain C determined from SEQRES records
Termini for d_protein_test.cif (#4) chain D determined from SEQRES records
Termini for d_protein_test.cif (#4) chain E determined from SEQRES records
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: d_protein_test.cif #4/A DGL
142, d_protein_test.cif #4/B DGL 142, d_protein_test.cif #4/C DGL 142,
d_protein_test.cif #4/D DGL 142
Chain-initial residues that are not actual N termini: d_protein_test.cif #4/E
SER 6, d_protein_test.cif #4/F SER 6, d_protein_test.cif #4/G SER 6,
d_protein_test.cif #4/H SER 6
Chain-final residues that are actual C termini: d_protein_test.cif #4/A DSG
240, d_protein_test.cif #4/B DSG 240, d_protein_test.cif #4/C DSG 240,
d_protein_test.cif #4/D DSG 240, d_protein_test.cif #4/E THR 98,
d_protein_test.cif #4/F THR 98, d_protein_test.cif #4/G THR 98,
d_protein_test.cif #4/H THR 98
Chain-final residues that are not actual C termini:
679 hydrogen bonds
0 hydrogens added
Running command "show #!1 models"
> show #!1 models
OpenGL version: 3.3.0 NVIDIA 535.216.03
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_GB.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: XPS 8950
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
Cache Size: 25600 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 26Gi 1.3Gi 1.8Gi 3.6Gi 2.7Gi
Swap: 2.0Gi 2.0Gi 0.0Ki
Graphics:
0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3070 Lite Hash Rate] [10de:2488] (rev a1)
Subsystem: Dell GA104 [GeForce RTX 3070 Lite Hash Rate] [1028:c903]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.24.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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
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-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
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
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
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
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
rdkit: 2024.9.6
requests: 2.32.3
scipy: 1.14.0
selfies: 2.2.0
Send2Trash: 1.8.3
SEQCROW: 1.8.17
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → D-amino acids assigned wrong atom types |
comment:2 by , 7 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Chimera gets the NE atoms correct (Ng+) whereas ChimeraX assigns N2.