Opened 7 months ago

Closed 6 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 Eric Pettersen, 7 months ago

Component: UnassignedStructure Analysis
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionD-amino acids assigned wrong atom types

Chimera gets the NE atoms correct (Ng+) whereas ChimeraX assigns N2.

comment:2 by Eric Pettersen, 6 months ago

Resolution: fixed
Status: acceptedclosed
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