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#14836 closed defect (fixed)
Residue addition problem
| Reported by: | Tristan Croll | Owned by: | Eric Pettersen |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC)
Description
Looks like something has changed in the way residue addition is handled, breaking ISOLDE's "isolde add aa" command (aliased as simply "aa {residue ID}" here). The new residues are going in with garbled (and contradictory) order...
The residue that triggered the traceback was added to the model, but in a somewhat bizarre location well away from the others. After deleting that, if I select the two new residues and the two preceding, then do in the log:
m = session.isolde.selected_model
from chimerax.atomic import selected_residues
m.residues.indices(selected_residues(session))
array([55, 56, 59, 58])
m.atoms.selecteds=False
m.residues[57].atoms.selected=True
m.residues.indices(selected_residues(session))
array([58])
... so the last added residue is somehow both index 57 and 58 in `m.residues`
For what it's worth, the code I'm using to add the residues is at https://github.com/tristanic/isolde/blob/ead1b3f7d64869b42efe9b6f2720675656d720e1/isolde/src/atomic/building/build_utils.py#L131 (which calls https://github.com/tristanic/isolde/blob/ead1b3f7d64869b42efe9b6f2720675656d720e1/isolde/src/atomic/building/place_ligand.py#L159 to add the new residue).
As far as I can tell, this seems to work correctly in ChimeraX 1.7.
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: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6zp4
Summary of feedback from opening 6zp4 fetched from pdb
---
note | Fetching compressed mmCIF 6zp4 from http://files.rcsb.org/download/6zp4.cif
6zp4 title:
SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
[more info...]
Chain information for 6zp4 #1
---
Chain | Description | UniProt
1 | tRNA |
2 | 18S ribosomal RNA |
4 | Eukaryotic translation initiation factor 2 subunit 2 | IF2B_HUMAN 1-333
A | Eukaryotic translation initiation factor 3 subunit A | EIF3A_HUMAN 1-1406
B | Eukaryotic translation initiation factor 3 subunit B | EIF3B_HUMAN 1-814
C | Eukaryotic translation initiation factor 3 subunit C | EIF3C_HUMAN 1-913
D | 40S ribosomal protein S15a | RS15A_HUMAN 1-130
E | Eukaryotic translation initiation factor 3 subunit E | EIF3E_HUMAN 1-445
F | Eukaryotic translation initiation factor 3 subunit F | EIF3F_HUMAN 1-357
G | Eukaryotic translation initiation factor 1A, X-chromosomal | IF1AX_HUMAN 1-144
H | Eukaryotic translation initiation factor 3 subunit H | EIF3H_HUMAN 1-352
I | Eukaryotic translation initiation factor 3 subunit I | EIF3I_HUMAN 1-325
J | Non-structural protein 1 | R1AB_SARS2 1-180
K | Eukaryotic translation initiation factor 3 subunit K | EIF3K_HUMAN 1-218
L | Eukaryotic translation initiation factor 3 subunit L | EIF3L_HUMAN 1-564
M | Eukaryotic translation initiation factor 3 subunit M | EIF3M_HUMAN 1-374
N | Eukaryotic translation initiation factor 3 subunit D | EIF3D_HUMAN 1-548
O | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 0-314
P | 40S ribosomal protein S25 | RS25_HUMAN 1-125
Q | 40S ribosomal protein S26 | RS26_HUMAN 1-115
R | 40S ribosomal protein S27 | RS27_HUMAN 1-84
S | 40S ribosomal protein S28 | RS28_HUMAN 1-69
T | 40S ribosomal protein S30 | RS30_HUMAN 1-59
U | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 1-156
V | Receptor of activated protein C kinase 1 | RACK1_HUMAN 1-317
W | 60S ribosomal protein L41 | RL41_HUMAN 1-25
X | Unknown factor |
Y | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472
Z | Eukaryotic translation initiation factor 1 | EIF1_HUMAN 1-113
a | 40S ribosomal protein SA | RSSA_HUMAN 1-295
b | 40S ribosomal protein S3 | RS3_HUMAN 1-243
c | 40S ribosomal protein S9 | RS9_HUMAN 1-194
d | 40S ribosomal protein S2 | RS2_HUMAN 1-293
e | 40S ribosomal protein S5 | RS5_HUMAN 1-204
g | 40S ribosomal protein S16 | RS16_HUMAN 1-146
h | 40S ribosomal protein S20 | RS20_HUMAN 1-119
i | 40S ribosomal protein S14 | RS14_HUMAN 1-151
j | 40S ribosomal protein S23 | RS23_HUMAN 1-143
k | 40S ribosomal protein S18 | RS18_HUMAN 1-152
l | 40S ribosomal protein S29 | RS29_HUMAN 1-56
m | 40S ribosomal protein S13 | RS13_HUMAN 1-151
n | 40S ribosomal protein S11 | RS11_HUMAN 1-158
o | 40S ribosomal protein S15 | RS15_HUMAN 1-145
p | 40S ribosomal protein S3a | RS3A_HUMAN 1-264
q | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263
r | 40S ribosomal protein S6 | RS6_HUMAN 1-249
s | 40S ribosomal protein S7 | RS7_HUMAN 1-194
t | 40S ribosomal protein S8 | RS8_HUMAN 1-208
u | 40S ribosomal protein S10 | RS10_HUMAN 1-165
v | 40S ribosomal protein S12 | RS12_HUMAN 1-132
w | 40S ribosomal protein S17 | RS17_HUMAN 1-135
x | 40S ribosomal protein S19 | RS19_HUMAN 1-145
y | 40S ribosomal protein S21 | RS21_HUMAN 1-83
z | 40S ribosomal protein S24 | RS24_HUMAN 1-133
Non-standard residues in 6zp4 #1
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> view :GTP
> clipper init
> cofr centerOfView showPivot true
> camera ortho
> lighting simple
> cartoon
> style stick
Changed 117784 atom styles
> color byhetero
> log metadata #1
Metadata for 6zp4 #1
---
Title | SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
Citation | Thoms, M., Buschauer, R., Ameismeier, M., Koepke, L., Denk, T., Hirschenberger, M., Kratzat, H., Hayn, M., Mackens-Kiani, T., Cheng, J., Straub, J.H., Sturzel, C.M., Frohlich, T., Berninghausen, O., Becker, T., Kirchhoff, F., Sparrer, K.M.J., Beckmann, R. (2020). Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science, 369, 1249-1255. PMID: 32680882. DOI: 10.1126/science.abc8665
Non-standard residues | GTP — guanosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
Sources (natural) | Severe acute respiratory syndrome coronavirus 2 (2019-ncov)
Homo sapiens (human)
CryoEM Map | EMDB 11335 — open map
Experimental method | Electron microscopy
Resolution | 2.9Å
> open 11335 fromDatabase emdb
Summary of feedback from opening 11335 fetched from emdb
---
notes | Fetching compressed map 11335 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11335/map/emd_11335.map.gz
Fetching map header 11335 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11335/header/emd-11335.xml
Opened emdb 11335 as #2, grid size 360,360,360, pixel 1.06, shown at level
0.03, step 2, values float32, fit PDB 6zp4
> volume #2 step 1
> volume #2 level 0.0434
> close
> cd "C:/Users/Tristan Croll/Documents/Structures/anti-
> isrib/8qzz_eif2_gamma_gtp"
Current working directory is: C:\Users\Tristan
Croll\Documents\Structures\anti-isrib\8qzz_eif2_gamma_gtp
> open "C:/Users/Tristan Croll/Documents/Structures/anti-
> isrib/8qzz_eif2_gamma_gtp/8qzz_partial_rebuild.pdb"
Chain information for 8qzz_partial_rebuild.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "C:/Users/Tristan Croll/Downloads/ChimeraX/PDB-SF/8qzz-sf.cif"
Summary of feedback from opening C:/Users/Tristan
Croll/Downloads/ChimeraX/PDB-SF/8qzz-sf.cif
---
warning | No mmCIF models found.
> clipper open "C:/Users/Tristan Croll/Downloads/ChimeraX/PDB-SF/8qzz-sf.cif"
> structureModel #1 overSampling 2.5
Resolution: 3.350277671680785
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".
Launching live xmap mgr took 1.2190792560577393 seconds.
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 38,38,38, pixel 0.67,0.67,0.659,
shown at level 0.0823, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 38,38,38, pixel 0.67,0.67,0.659,
shown at level -0.0658,0.0658, step 1, values float32
Opened (LIVE) 2mFo-DFc_sharp_39 as #1.1.1.4, grid size 38,38,38, pixel
0.67,0.67,0.659, shown at level 0.267, step 1, values float32
Chain information for 8qzz_partial_rebuild.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/C | No description available
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 38,38,38, pixel
0.67,0.67,0.659, shown at level 0.237, step 1, values float32
Done loading forcefield
> 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
> save working.cxs
> st
> select #1
8498 atoms, 8564 bonds, 3 pseudobonds, 556 residues, 28 models selected
> isolde sim start /A-C
Loading residue template for GNP from internal database
ISOLDE: started sim
> select clear
> isolde pepflip /A:11
> st
[Repeated 1 time(s)]
> isolde sim pause
> st
[Repeated 17 time(s)]
> isolde sim resume
> isolde sim pause
> st
[Repeated 8 time(s)]
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde pepflip /A:334
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde pepflip /A:151
> isolde sim pause
> isolde sim resume
> isolde pepflip /A:334
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> st
[Repeated 2 time(s)]
> select clear
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> st
[Repeated 3 time(s)]
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 8 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> al MG
> select #1
8499 atoms, 8564 bonds, 3 pseudobonds, 557 residues, 34 models selected
> isolde sim start /A-C
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> delete sel
> aw
> isolde sim start /A:502
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> delete sel
> st
> select #1
8498 atoms, 8564 bonds, 3 pseudobonds, 556 residues, 34 models selected
> isolde sim start /A-C
ISOLDE: started sim
> select clear
> isolde sim pause
> isolde sim resume
> isolde sim pause
> st
[Repeated 16 time(s)]
> isolde sim resume
> isolde pepflip /A:65
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> sequence chain #1/A
Alignment identifier is 1.2/A
> alphafold match #1 trim false
Fetching compressed AlphaFold A0A6I9J801 from
https://alphafold.ebi.ac.uk/files/AF-A0A6I9J801-F1-model_v4.cif
Fetching compressed AlphaFold G3QTZ7 from
https://alphafold.ebi.ac.uk/files/AF-G3QTZ7-F1-model_v4.cif
3 AlphaFold models found using sequence similarity searches: A0A6I9J801 (chain
A), A0A096NVP0 (chain B), G3QTZ7 (chain C)
AlphaFold prediction matching 8qzz_partial_rebuild.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
B | A0A096NVP0 | A0A096NVP0_PAPAN | 0.99 | 315 | 113 | 100
A | A0A6I9J801 | A0A6I9J801_CHRAS | 1.86 | 472 | 433 | 100
C | G3QTZ7 | G3QTZ7_GORGO | 2.21 | 682 | 9 | 100
Opened 3 AlphaFold models
> hide #!2 models
> aa VAL
> isolde sim start #1.2/A:67
ISOLDE: started sim
> isolde pepflip #1.2/A:67
[Repeated 1 time(s)]
> isolde pepflip #1.2/A:66
[Repeated 2 time(s)]
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> aa ARG
> isolde sim start #1.2/A:65,68,134
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aa PHE
Traceback (most recent call last):
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2925, in run
result = ci.function(session, *args, optional=optional,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3464, in __call__
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Tristan Croll\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\atomic\building\cmd.py", line 132, in add_aa_cmd
add_amino_acid_residue(structure, resname.upper(), prev_res=prev_res,
next_res=next_res,
File "C:\Users\Tristan Croll\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\atomic\building\build_utils.py", line 210, in
add_amino_acid_residue
add_bond(r.find_atom('N'), prev_res.find_atom('C'))
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\atomic\struct_edit.py", line 242, in add_bond
a1.structure.reorder_residues(new_residues)
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1940, in reorder_residues
f(self._c_pointer, [r._c_pointer.value for r in new_order])
TypeError: Duplicate residue in new residue order
TypeError: Duplicate residue in new residue order
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1940, in reorder_residues
f(self._c_pointer, [r._c_pointer.value for r in new_order])
See log for complete Python traceback.
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> delete sel
> sequence chain #1/A
Alignment identifier is 1.2/A
> st
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1.2/A
Alignment identifier is 1.2/A
> sequence chain #2/A
Alignment identifier is 2.1/A
> cartoon #1
> ui tool show Shell
0.00s - Debugger warning: It seems that frozen modules are being used, which
may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to
disable this validation.
> select clear
OpenGL version: 3.3.0 NVIDIA 529.19
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: windows
Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.5.1
build: 1.1.1
certifi: 2024.2.2
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
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: 2.2.4
ChimeraX-Clipper: 0.23.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403220040
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.3.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.0
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.9.2
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
WMI: 1.5.1
Change History (12)
comment:2 by , 19 months ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Residue addition problem |
There definitely have been some intricate additions to residue addition that could be to blame.
comment:3 by , 18 months ago
| Status: | accepted → feedback |
|---|
Hi Tristan,
Though I have no doubt this is a real problem, I think I'm going to need a straightforward recipe to reproduce it. If I open 1gcn and select residue 29 and then "isolde add aa VAL sel" and then select the new valine and "isolde add aa PHE sel", there are no errors. If I then examine structure.residues and chain.residues, they both look fine.
Maybe some kind of recipe where you open a structure and issue a series of commands that result in the error or in the bad residue order...?
--Eric
comment:4 by , 18 months ago
Sorry for the slow response - things got a bit piled up and I missed this. This seems reproducible to me: open 8qzz sel /A:66 isolde add aa VAL sel sel /A:80;#other end of the gap isolde add aa ILE sel;#Things seem to start going off the rails here - cartoon doesn't go through the first VAL any more, gap pseudobond connects to 66 rather than 66 sel /A:67 isolde add aa ARG sel;#Things get *really* messy here - residues 67-68 appear to be starting their own chain with a different cartoon colour; multiple missing-structure pseudobonds pointing off to other gaps. On Wed, Apr 24, 2024 at 10:28 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > > > > >
comment:5 by , 18 months ago
Using today's 1.8 release candidate I cannot reproduce this. Everything looks fine. What version are you using?
comment:7 by , 18 months ago
This was Windows. Either the rc or a few weeks old… will check tomorrow. On Tue, 14 May 2024 at 01:03, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > >
comment:8 by , 18 months ago
Hmm... definitely using the release candidate. After a bunch of attempts to figure out what triggers it, I'm forced to conclude that it's non-deterministic. In a fresh session, repeatedly using the one-liner (closing the model in between): open 8qzz;sel #1/A:66;wait 1;isolde add aa VAL sel; sel #1/A:80;wait 1; isolde add aa ILE sel ... then sometimes it comes out fine, sometimes it's broken (with VAL67 not included in the cartoon). Under these circumstances I'm seeing it broken about one time in 5. On Tue, May 14, 2024 at 3:10 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > > > >
comment:10 by , 18 months ago
| Resolution: | → fixed |
|---|---|
| Status: | feedback → closed |
Fixed in daily build and 1.8 release branch. I had the backbone-atom-order comparison backward when updating missing-structure pseudobonds as backbone atoms got added to residues.
Fix: https://github.com/RBVI/ChimeraX/commit/08ff82dbfd83417ce0fd142b3c0a3c30813967cd
comment:11 by , 18 months ago
Thank goodness. Trying to figure out how to reproduce that one had me feeling like I was going mad. :) On Tue, May 14, 2024 at 9:29 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > > > > > >
comment:12 by , 18 months ago
Previous fix was wrong; actual bug was I was using residue name instead of atom name for indexing into backbone atom-name list.
fix: https://github.com/RBVI/ChimeraX/commit/47c81a86c2740840b598d80c1e2a3c66179756fa
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