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Opened 5 years ago
Closed 3 years ago
#3752 closed defect (fixed)
ISOLDE validation: not enough values to unpack
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/kartikmanne/Documents/SARS/COVID19_antibodies_cryoem/2P-30MFK- > Kartik/RealSpaceRefine_5/RR6-complex-rsr5_real_space_refined.pdb Chain information for RR6-complex-rsr5_real_space_refined.pdb #1 --- Chain | Description A B C | No description available H | No description available L | No description available S X | No description available T Y | No description available > set bgColor white > addh Summary of feedback from adding hydrogens to RR6-complex- rsr5_real_space_refined.pdb #1 --- notes | No usable SEQRES records for RR6-complex-rsr5_real_space_refined.pdb (#1) chain A; guessing termini instead No usable SEQRES records for RR6-complex-rsr5_real_space_refined.pdb (#1) chain B; guessing termini instead No usable SEQRES records for RR6-complex-rsr5_real_space_refined.pdb (#1) chain C; guessing termini instead No usable SEQRES records for RR6-complex-rsr5_real_space_refined.pdb (#1) chain H; guessing termini instead No usable SEQRES records for RR6-complex-rsr5_real_space_refined.pdb (#1) chain L; guessing termini instead 4 messages similar to the above omitted Chain-initial residues that are actual N termini: /A ALA 27, /B ALA 27, /C ALA 27, /H NAG 2, /L NAG 2, /S LEU 23, /T GLU 20, /X LEU 23, /Y GLU 20 Chain-initial residues that are not actual N termini: /A ASP 80, /A ASN 165, /A PHE 186, /A ALA 263, /A GLY 447, /A LYS 462, /A TYR 489, /A VAL 503, /A ASN 641, /A SER 689, /A LYS 854, /B ASP 80, /B ASN 165, /B PHE 186, /B ALA 263, /B GLY 447, /B LYS 462, /B TYR 489, /B VAL 503, /B ASN 641, /B SER 689, /B LYS 854, /C ASP 80, /C ASN 165, /C PHE 186, /C ALA 263, /C GLY 447, /C LYS 462, /C TYR 489, /C VAL 503, /C ASN 641, /C SER 689, /C LYS 854, /H GLU 20, /L LEU 23 Chain-final residues that are actual C termini: /H GLU 246, /L GLY 221, /S GLY 221, /T GLU 246, /X GLY 221, /Y GLU 246 Chain-final residues that are not actual C termini: /A SER 1147, /A HIS 69, /A VAL 143, /A SER 172, /A HIS 245, /A LYS 444, /A ARG 454, /A ILE 468, /A ASN 501, /A VAL 620, /A THR 676, /A THR 827, /B SER 1147, /B HIS 69, /B VAL 143, /B SER 172, /B HIS 245, /B LYS 444, /B ARG 454, /B ILE 468, /B ASN 501, /B VAL 620, /B THR 676, /B THR 827, /C SER 1147, /C HIS 69, /C VAL 143, /C SER 172, /C HIS 245, /C LYS 444, /C ARG 454, /C ILE 468, /C ASN 501, /C VAL 620, /C THR 676, /C THR 827, /H NAG 2, /L NAG 2 3028 hydrogen bonds Adding 'H' to /A ASP 80 Adding 'H' to /A ASN 165 Adding 'H' to /A PHE 186 Adding 'H' to /A ALA 263 Adding 'H' to /A GLY 447 30 messages similar to the above omitted /A SER 1147 is not terminus, removing H atom from 'C' /A HIS 69 is not terminus, removing H atom from 'C' /A VAL 143 is not terminus, removing H atom from 'C' /A SER 172 is not terminus, removing H atom from 'C' /A HIS 245 is not terminus, removing H atom from 'C' 31 messages similar to the above omitted 32474 hydrogens added > open /home/kartikmanne/Documents/SARS/COVID19_antibodies_cryoem/2P-30MFK- > Kartik/cryosparc_P4_J20_008_volume_map_sharp_local.mrc Opened cryosparc_P4_J20_008_volume_map_sharp_local.mrc, grid size 320,320,320, pixel 1.06, shown at level 0.196, step 2, values float32 > clipper associate #2 toModel #1 Chain information for RR6-complex-rsr5_real_space_refined.pdb --- Chain | Description 1.2/A 1.2/B 1.2/C | No description available 1.2/H | No description available 1.2/L | No description available 1.2/S 1.2/X | No description available 1.2/T 1.2/Y | No description available > isolde start > set selectionWidth 4 Done loading forcefield > clipper spotlight radius 32.00 > clipper spotlight radius 32.00 > select #1 65825 atoms, 66664 bonds, 68 pseudobonds, 13 models selected Deleted the following atoms from residue NAG I1: H11, H12 Deleted the following atoms from residue NAG B1321: H11, H12 Deleted the following atoms from residue NAG B1302: H12, H11 Deleted the following atoms from residue NAG B1301: H11, H12 > select #1 65822 atoms, 66661 bonds, 68 pseudobonds, 19 models selected Deleted the following atoms from residue NAG I1: HO4 Traceback (most recent call last): File "/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data ValueError: not enough values to unpack (expected 3, got 2) ValueError: not enough values to unpack (expected 3, got 2) File "/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data See log for complete Python traceback. Traceback (most recent call last): File "/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data ValueError: not enough values to unpack (expected 3, got 2) ValueError: not enough values to unpack (expected 3, got 2) File "/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data See log for complete Python traceback. > select #1 65821 atoms, 66660 bonds, 68 pseudobonds, 19 models selected Traceback (most recent call last): File "/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data ValueError: not enough values to unpack (expected 3, got 2) ValueError: not enough values to unpack (expected 3, got 2) File "/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 430.40 OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: TYAN Model: B7105F48TV8HR-2T-G OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 64 Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz Cache Size: 22528 KB Memory: total used free shared buff/cache available Mem: 187G 10G 170G 348M 6.9G 176G Swap: 9G 0B 9G Graphics: 04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41) Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] Kernel driver in use: ast PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE validation: not enough values to unpack |
comment:2 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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