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Opened 5 years ago
Closed 5 years ago
#3622 closed defect (duplicate)
ISOLDE: cannot import name 'save' from 'chimerax.core.commands'
| 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/HexaProStructures/3-down/1-2G12/Hexapro-2G12-coot-0.updated.pdb Chain information for Hexapro-2G12-coot-0.updated.pdb #1 --- Chain | Description A B C | No description available H M | No description available K | No description available L | No description available > set bgColor white > addh Summary of feedback from adding hydrogens to Hexapro-2G12-coot-0.updated.pdb #1 --- warnings | Not adding hydrogens to /A SER 59 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A ASN 80 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 101 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLN 114 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A PHE 134 CB because it is missing heavy-atom bond partners 136 messages similar to the above omitted notes | No usable SEQRES records for Hexapro-2G12-coot-0.updated.pdb (#1) chain A; guessing termini instead No usable SEQRES records for Hexapro-2G12-coot-0.updated.pdb (#1) chain B; guessing termini instead No usable SEQRES records for Hexapro-2G12-coot-0.updated.pdb (#1) chain C; guessing termini instead No usable SEQRES records for Hexapro-2G12-coot-0.updated.pdb (#1) chain H; guessing termini instead No usable SEQRES records for Hexapro-2G12-coot-0.updated.pdb (#1) chain K; guessing termini instead 2 messages similar to the above omitted Chain-initial residues that are actual N termini: /A ALA 26, /B ALA 26, /C ALA 26, /H GLU 1, /K ASP 1, /L VAL 2, /M GLU 1 Chain-initial residues that are not actual N termini: /A ASN 80, /A SER 154, /A LYS 186, /A PRO 216, /A ALA 262, /A TYR 448, /A ASN 459, /A ASN 486, /A VAL 502, /A THR 637, /A VAL 686, /A GLN 852, /B ASN 80, /B SER 154, /B LYS 186, /B PRO 216, /B ALA 262, /B TYR 448, /B ASN 459, /B ASN 486, /B VAL 502, /B THR 637, /B VAL 686, /B GLN 852, /C ASN 80, /C SER 154, /C LYS 186, /C PRO 216, /C ALA 262, /C TYR 448, /C ASN 459, /C ASN 486, /C VAL 502, /C THR 637, /C VAL 686, /C GLN 852, /H GLY 136, /M GLY 136 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A ASP 1145, /A HIS 65, /A LEU 140, /A LEU 175, /A PRO 208, /A LEU 241, /A SER 442, /A ARG 453, /A TYR 472, /A THR 499, /A VAL 619, /A ALA 671, /A LEU 827, /B ASP 1145, /B HIS 65, /B LEU 140, /B LEU 175, /B PRO 208, /B LEU 241, /B SER 442, /B ARG 453, /B TYR 472, /B THR 499, /B VAL 619, /B ALA 671, /B LEU 827, /C ASP 1145, /C HIS 65, /C LEU 140, /C LEU 175, /C PRO 208, /C LEU 241, /C SER 442, /C ARG 453, /C TYR 472, /C THR 499, /C VAL 619, /C ALA 671, /C LEU 827, /H LYS 228, /H SER 127, /K GLU 213, /L GLY 212, /M LYS 228, /M SER 127 2538 hydrogen bonds Adding 'H' to /A ASN 80 Adding 'H' to /A SER 154 Adding 'H' to /A LYS 186 Adding 'H' to /A ALA 262 Adding 'H' to /A TYR 448 28 messages similar to the above omitted /A ASP 1145 is not terminus, removing H atom from 'C' /A HIS 65 is not terminus, removing H atom from 'C' /A LEU 140 is not terminus, removing H atom from 'C' /A LEU 175 is not terminus, removing H atom from 'C' /A PRO 208 is not terminus, removing H atom from 'C' 40 messages similar to the above omitted 116 hydrogens added > open > /home/kartikmanne/Documents/SARS/HexaProStructures/3-down/1-2G12/cryosparc_P1_J37_007_volume_map_sharp_local.mrc Opened cryosparc_P1_J37_007_volume_map_sharp_local.mrc, grid size 320,320,320, pixel 1.06, shown at level 0.157, step 2, values float32 > volume #2 step 1 > clipper associate #2 toModel #1 Chain information for Hexapro-2G12-coot-0.updated.pdb --- Chain | Description 1.2/A 1.2/B 1.2/C | No description available 1.2/H 1.2/M | No description available 1.2/K | No description available 1.2/L | No description available > isolde start > set selectionWidth 4 Done loading forcefield > clipper spotlight radius 32.00 > clipper spotlight radius 32.00 > select #1 58096 atoms, 58827 bonds, 76 pseudobonds, 13 models selected Loading residue template for BEZ from internal database Loading residue template for GOL from internal database > volume #1.1.1.1 level 0.8947 > delete H > delete H > addh Summary of feedback from adding hydrogens to Hexapro-2G12-coot-0.updated.pdb #1.2 --- warnings | Not adding hydrogens to /A SER 59 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A ASN 80 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 101 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLN 114 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A PHE 134 CB because it is missing heavy-atom bond partners 136 messages similar to the above omitted notes | No usable SEQRES records for Hexapro-2G12-coot-0.updated.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for Hexapro-2G12-coot-0.updated.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for Hexapro-2G12-coot-0.updated.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for Hexapro-2G12-coot-0.updated.pdb (#1.2) chain H; guessing termini instead No usable SEQRES records for Hexapro-2G12-coot-0.updated.pdb (#1.2) chain K; guessing termini instead 2 messages similar to the above omitted Chain-initial residues that are actual N termini: /A ALA 26, /B ALA 26, /C ALA 26, /H GLU 1, /K ASP 1, /L VAL 2, /M GLU 1 Chain-initial residues that are not actual N termini: /A ASN 80, /A SER 154, /A LYS 186, /A PRO 216, /A ALA 262, /A TYR 448, /A ASN 459, /A ASN 486, /A VAL 502, /A THR 637, /A VAL 686, /A GLN 852, /B ASN 80, /B SER 154, /B LYS 186, /B PRO 216, /B ALA 262, /B TYR 448, /B ASN 459, /B ASN 486, /B VAL 502, /B THR 637, /B VAL 686, /B GLN 852, /C ASN 80, /C SER 154, /C LYS 186, /C PRO 216, /C ALA 262, /C TYR 448, /C ASN 459, /C ASN 486, /C VAL 502, /C THR 637, /C VAL 686, /C GLN 852, /H GLY 136, /M GLY 136 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A ASP 1145, /A HIS 65, /A LEU 140, /A LEU 175, /A PRO 208, /A LEU 241, /A SER 442, /A ARG 453, /A TYR 472, /A THR 499, /A VAL 619, /A ALA 671, /A LEU 827, /B ASP 1145, /B HIS 65, /B LEU 140, /B LEU 175, /B PRO 208, /B LEU 241, /B SER 442, /B ARG 453, /B TYR 472, /B THR 499, /B VAL 619, /B ALA 671, /B LEU 827, /C ASP 1145, /C HIS 65, /C LEU 140, /C LEU 175, /C PRO 208, /C LEU 241, /C SER 442, /C ARG 453, /C TYR 472, /C THR 499, /C VAL 619, /C ALA 671, /C LEU 827, /H LYS 228, /H SER 127, /K GLU 213, /L GLY 212, /M LYS 228, /M SER 127 2827 hydrogen bonds Adding 'H' to /A ASN 80 Adding 'H' to /A SER 154 Adding 'H' to /A LYS 186 Adding 'H' to /A ALA 262 Adding 'H' to /A TYR 448 30 messages similar to the above omitted /A ASP 1145 is not terminus, removing H atom from 'C' /A HIS 65 is not terminus, removing H atom from 'C' /A LEU 140 is not terminus, removing H atom from 'C' /A LEU 175 is not terminus, removing H atom from 'C' /A PRO 208 is not terminus, removing H atom from 'C' 40 messages similar to the above omitted 28526 hydrogens added > select #1 58090 atoms, 58821 bonds, 76 pseudobonds, 19 models selected > select #1 58096 atoms, 58827 bonds, 76 pseudobonds, 19 models selected > volume #1.1.1.1 level 0.3506 > volume #1.1.1.1 level 0.2418 > volume #1.1.1.1 level 0.1824 > volume #1.1.1.1 level 0.4396 > select #1 58096 atoms, 58827 bonds, 76 pseudobonds, 19 models selected > volume #1.1.1.1 level 0.8452 Traceback (most recent call last): File "/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py", line 1165, in _save_cif_file self.save_cif_file(self._selected_model, filename) File "/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py", line 1177, in save_cif_file from chimerax.core.commands import save ImportError: cannot import name 'save' from 'chimerax.core.commands' (/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/__init__.py) ImportError: cannot import name 'save' from 'chimerax.core.commands' (/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/__init__.py) File "/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py", line 1177, in save_cif_file from chimerax.core.commands import save 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 171G 163M 5.4G 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: cannot import name 'save' from 'chimerax.core.commands' |
comment:2 by , 5 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Yes, sorry about that. That button is long since obsolete, and I should have removed it at least a year ago - it does nothing that the standard ChimeraX save options can't, and as you've discovered I failed to update its code to reflect ChimeraX API changes. It will be gone in the next incremental release.