ISOLDE: restrain torsions: Each residue selection must be from a single chain

[pett]

The following bug report has been submitted:
Platform: Linux-3.10.0-1160.6.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX

open /data1/cryoem/cryoem_krios/002-02/Phenix_refine61 format dicom

open
/data1/cryoem/cryoem_krios/002-02/Phenix_refine61/spike2up1downRBD_compositemap_SOLDE_NAG-
coot_real_space_refined_061.pdb

Chain information for spike2up1downRBD_compositemap_SOLDE_NAG-
coot_real_space_refined_061.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
F I | No description available
G J | No description available

show cartoons

style stick

Changed 32765 atom styles

open
/data1/cryoem/cryoem_krios/002-02/Phenix_refine52/spike_mab_002_02_composite_box.ccp4

Opened spike_mab_002_02_composite_box.ccp4 as #2, grid size 145,145,231, pixel
1.07, shown at level 17.8, step 1, values float32

volume #2 level 8.797

clipper associate #2 toModel #1

Opened spike_mab_002_02_composite_box.ccp4 as #1.1.1.1, grid size 145,145,231,
pixel 1.07, shown at level 13.2, step 1, values float32
Chain information for spike2up1downRBD_compositemap_SOLDE_NAG-
coot_real_space_refined_061.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/C | No description available
1.2/F 1.2/I | No description available
1.2/G 1.2/J | No description available

addh

Summary of feedback from adding hydrogens to
spike2up1downRBD_compositemap_SOLDE_NAG-coot_real_space_refined_061.pdb #1.2
---
notes | No usable SEQRES records for spike2up1downRBD_compositemap_SOLDE_NAG-
coot_real_space_refined_061.pdb (#1.2) chain A; guessing termini instead
No usable SEQRES records for spike2up1downRBD_compositemap_SOLDE_NAG-
coot_real_space_refined_061.pdb (#1.2) chain B; guessing termini instead
No usable SEQRES records for spike2up1downRBD_compositemap_SOLDE_NAG-
coot_real_space_refined_061.pdb (#1.2) chain C; guessing termini instead
No usable SEQRES records for spike2up1downRBD_compositemap_SOLDE_NAG-
coot_real_space_refined_061.pdb (#1.2) chain F; guessing termini instead
No usable SEQRES records for spike2up1downRBD_compositemap_SOLDE_NAG-
coot_real_space_refined_061.pdb (#1.2) chain G; guessing termini instead
2 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A GLN 14, /B GLN 14, /C GLN
14, /F GLU 1, /G GLU 1, /I GLU 1, /J GLU 1
Chain-initial residues that are not actual N termini: /A THR 76, /A ASN 544,
/A TRP 633, /A GLN 690, /A ALA 852, /B THR 76, /B TYR 451, /B ASN 487, /B VAL
503, /B THR 630, /B GLN 690, /B ALA 852, /C THR 76, /C PRO 631, /C GLN 690, /C
CYS 743, /C ALA 852
Chain-final residues that are actual C termini: /F CYS 214, /G LYS 222, /I CYS
214, /J LYS 222
Chain-final residues that are not actual C termini: /A LYS 1149, /A VAL 70, /A
ASN 542, /A ALA 623, /A GLN 675, /A LEU 828, /B LYS 1149, /B VAL 70, /B LEU
441, /B ALA 475, /B PHE 497, /B ALA 623, /B GLN 675, /B LEU 828, /C LYS 1149,
/C VAL 70, /C ILE 624, /C GLN 675, /C TYR 741, /C LEU 828
2937 hydrogen bonds
Adding 'H' to /A THR 76
Adding 'H' to /A ASN 544
Adding 'H' to /A TRP 633
Adding 'H' to /A GLN 690
Adding 'H' to /A ALA 852
11 messages similar to the above omitted
/A LYS 1149 is not terminus, removing H atom from 'C'
/B LYS 1149 is not terminus, removing H atom from 'C'
/C LYS 1149 is not terminus, removing H atom from 'C'
32068 hydrogens added

hide HC

select #1

64833 atoms, 65631 bonds, 17 pseudobonds, 4163 residues, 8 models selected

open /data1/cryoem/cryoem_krios/RBD_model1.pdb

Summary of feedback from opening /data1/cryoem/cryoem_krios/RBD_model1.pdb
---
note | Combining 2 symmetry atoms into HOH /Z:779 O

Chain information for RBD_model1.pdb #2
---
Chain | Description
Z | No description available

select #2

1629 atoms, 1599 bonds, 274 residues, 1 model selected

hide #2 models

show #2 models

hide #2 models

show #2 models

hide #2 models

show #2 models

hide #2 models

show #2 models

show target m

ui tool show Matchmaker

matchmaker #2 to #1.2/A pairing bs

Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O

---

H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2

Matchmaker spike2up1downRBD_compositemap_SOLDE_NAG-
coot_real_space_refined_061.pdb, chain A (#1.2) with RBD_model1.pdb, chain Z
(#2), sequence alignment score = 939.5
RMSD between 169 pruned atom pairs is 1.139 angstroms; (across all 194 pairs:
1.473)

isolde restrain torsions #1/A:334-527/B

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.

334-527/c334-527 tempelate #2/Z

Unknown command: 334-527/c334-527 tempelate #2/Z

isolde restrain torsions #1/A:334-527/B

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.

334-527/C:334-527 tempelate #2/Z

Unknown command: 334-527/C:334-527 tempelate #2/Z

isolde restrain torsions #1/A:334-527/B:334-527/C:334-527 tempelate #2/Z

Expected a keyword

isolde restrain torsions #1/A:334-527/B:334-527/C:334-527 templateResidues
#2/Z

Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute
cmd.run(cmd_text)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, kw_args)
File "/home/cryoem/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/restraints/cmd.py", line 171, in restrain_torsions
restrain_torsions_to_template(session, tres, pres,
File "/home/cryoem/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/restraints/restraint_utils.py", line 159, in
restrain_torsions_to_template
trs, rrs = sequence_align_all_residues(
File "/home/cryoem/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/restraints/restraint_utils.py", line 317, in
sequence_align_all_residues
raise TypeError('Each residue selection must be from a single chain!')
TypeError: Each residue selection must be from a single chain!

TypeError: Each residue selection must be from a single chain!

File "/home/cryoem/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/restraints/restraint_utils.py", line 317, in
sequence_align_all_residues
raise TypeError('Each residue selection must be from a single chain!')

See log for complete Python traceback.

OpenGL version: 3.3.0 NVIDIA 450.80.02
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-7048GR-TR
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 24 Intel(R) Xeon(R) CPU E5-2620 v3 @ 2.40GHz
Cache Size: 15360 KB
Memory:

total used free shared buff/cache available

Mem: 125G 7.2G 5.3G 79M 113G 117G
Swap: 15G 462M 15G

Graphics:

02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 GTX 1080 Ti [10de:1b06] (rev a1)
Subsystem: ZOTAC International (MCO) Ltd. Device [19da:1470]
Kernel driver in use: nvidia

Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:

alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.16.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
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ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.2.2
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ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
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ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
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ChimeraX-MatchMaker: 1.2.1
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ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
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ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
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ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
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ChimeraX-Phenix: 0.3
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
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ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
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ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
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ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
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python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
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scipy: 1.5.2
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wcwidth: 0.2.5
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wheel: 0.36.0
wheel-filename: 1.2.0

[pett]

Actually anonymously reported, but had to paste in from my mail since run_email2trac failed

[Tristan Croll]

The error is pretty much what it says it is: the user should be applying the restraints one chain at a time. But of course this should never have been a TypeError - in ISOLDE 1.3 it's now a UserError.