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 , 7 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 , 6 months ago
Resolution: | → fixed |
---|---|
Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
Chimera gets the NE atoms correct (Ng+) whereas ChimeraX assigns N2.