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Opened 4 years ago
Closed 4 years ago
#4648 closed defect (duplicate)
Error in toolshed error message
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-20.3.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> toolshed show
Downloading bundle ChimeraX_ISOLDE-1.1.0-cp37-cp37m-macosx_10_13_x86_64.whl
Traceback (most recent call last):
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/help_viewer/tool.py", line 389, in download_finished
session=self.session)
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 903, in install_bundle
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)
AttributeError: 'str' object has no attribute 'name'
AttributeError: 'str' object has no attribute 'name'
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)
See log for complete Python traceback.
> ui tool show ISOLDE
> set selectionWidth 4
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.
Done loading forcefield
> open /Users/navid/WORK/hIP3R2-Apo-coot-0.pdb
Chain information for hIP3R2-Apo-coot-0.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
Chain information for hIP3R2-Apo-coot-0.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/C | No description available
1.2/D | No description available
1.2/E | No description available
1.2/F | No description available
1.2/G | No description available
1.2/H | No description available
1.2/I | No description available
1.2/J | No description available
1.2/K | No description available
1.2/L | No description available
1.2/M | No description available
1.2/N | No description available
1.2/O | No description available
1.2/P | No description available
1.2/Q | No description available
1.2/R | No description available
1.2/S | No description available
1.2/T | No description available
1.2/U | No description available
1.2/V | No description available
1.2/W | No description available
1.2/X | No description available
1.2/Y | No description available
1.2/Z | No description available
1.2/a | No description available
1.2/b | No description available
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> open /Users/navid/Downloads/cryosparc_P6_J1194_010_volume_map_sharp.mrc
Opened cryosparc_P6_J1194_010_volume_map_sharp.mrc, grid size 384,384,384,
pixel 1.06, shown at level 0.176, step 2, values float32
> clipper associate #2 toModel #1
> clipper associate #1 toModel #1
> hide #!1 models
> show #!1 models
> clipper associate #1 toModel #1.1
Invalid "toModel" argument: Must specify 1 structure, got 0 for "#1.1"
> clipper associate #1.1 toModel #1
> clipper associate #1.2 toModel #1.1
Invalid "toModel" argument: Must specify 1 structure, got 0 for "#1.1"
> clipper associate #1.1 toModel #1.2
> view
> addh
Summary of feedback from adding hydrogens to hIP3R2-Apo-coot-0.pdb #1.2
---
notes | No usable SEQRES records for hIP3R2-Apo-coot-0.pdb (#1.2) chain A;
guessing termini instead
No usable SEQRES records for hIP3R2-Apo-coot-0.pdb (#1.2) chain B; guessing
termini instead
No usable SEQRES records for hIP3R2-Apo-coot-0.pdb (#1.2) chain C; guessing
termini instead
No usable SEQRES records for hIP3R2-Apo-coot-0.pdb (#1.2) chain D; guessing
termini instead
No usable SEQRES records for hIP3R2-Apo-coot-0.pdb (#1.2) chain E; guessing
termini instead
23 messages similar to the above omitted
Chain-initial residues that are actual N termini: /B SER 6, /F PRO 435, /G ASP
1736, /K LEU 2264, /N PRO 791, /O PRO 659, /Q ASP 1598, /W GLY 2286, /X LEU
2264, /Z ASP 2136, /a PRO 2028
Chain-initial residues that are not actual N termini: /A LEU 1264, /B THR 84,
/C ARG 230, /C ILE 350, /D LYS 1655, /E LYS 859, /E ASP 963, /E ASP 1026, /E
ASN 1045, /F SER 534, /G ASN 1786, /G MET 1911, /H ASN 2215, /H GLU 2378, /H
GLY 2474, /I ASN 601, /I TYR 730, /J PHE 2220, /J LEU 2304, /L LEU 770, /M LYS
830, /O GLU 692, /P ALA 738, /R LEU 1682, /S VAL 1627, /T SER 1618, /U LYS
1766, /V SER 1741, /Y THR 2560, /a ASP 2091, /b LEU 1100, /b SER 1176
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A ASP 1433, /B TYR 229,
/B ALA 78, /C VAL 434, /C PRO 320, /D MET 1681, /E LEU 1099, /E ASP 894, /E
ASN 1004, /E ALA 1039, /F HIS 600, /F LYS 527, /G ASN 2027, /G MET 1738, /G
VAL 1825, /H LYS 2559, /H LEU 2219, /H LYS 2429, /I PHE 737, /I SER 658, /J
ARG 2377, /J GLY 2251, /K GLY 2303, /L ASP 790, /M ASN 858, /N ARG 829, /O TYR
729, /O GLN 674, /P SER 769, /Q PHE 1617, /R LYS 1705, /S SER 1654, /T SER
1626, /U GLY 1785, /V THR 1765, /W GLY 2303, /X VAL 2285, /Y VAL 2635, /Z ARG
2214, /a GLY 2129, /a GLN 2083, /b PHE 1263, /b VAL 1130
1343 hydrogen bonds
Adding 'H' to /B THR 84
Adding 'H' to /C ILE 350
Adding 'H' to /E ASP 963
Adding 'H' to /E ASP 1026
Adding 'H' to /E ASN 1045
5 messages similar to the above omitted
/A ASP 1433 is not terminus, removing H atom from 'C'
/B TYR 229 is not terminus, removing H atom from 'C'
/C VAL 434 is not terminus, removing H atom from 'C'
/D MET 1681 is not terminus, removing H atom from 'C'
/E LEU 1099 is not terminus, removing H atom from 'C'
23 messages similar to the above omitted
13293 hydrogens added
> hide HC
> select #1.2
34743 atoms, 35011 bonds, 30 pseudobonds, 2124 residues, 6 models selected
> select clear
Fetching CCD SER_LL from http://ligand-
expo.rcsb.org/reports/S/SER_LL/SER_LL.cif
Fetching CCD LYS_LL from http://ligand-
expo.rcsb.org/reports/L/LYS_LL/LYS_LL.cif
> swapaa lys #1.2:258.C
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys #1.2:258.c
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys #1:258.c
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys #1.2:258.C
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys #1.2:C.258
Missing or invalid "residues" argument: invalid residues specifier
> swapaa #1.2:258.C lys
Missing or invalid "residues" argument: only initial part "#1.2:258" of atom
specifier valid
> swapaa #1.2:258 lys
Using Dunbrack library
/C LYS 258: phi 58.5, psi 73.0 trans
Applying LYS rotamer (chi angles: -68.8 67.1 -96.4 106.8) to /C LYS 258
> ui dockable false ISOLDE
> select #1.2
34732 atoms, 35000 bonds, 30 pseudobonds, 2124 residues, 12 models selected
> select #1.2
34732 atoms, 35000 bonds, 30 pseudobonds, 2124 residues, 12 models selected
> close #1.2
Deleting atomic symmetry model...
Deleting atomic symmetry model...
> open /Users/navid/WORK/hIP3R2-Apo-coot-3.pdb
Chain information for hIP3R2-Apo-coot-3.pdb #2
---
Chain | Description
A | No description available
Deleting atomic symmetry model...
Chain information for hIP3R2-Apo-coot-3.pdb
---
Chain | Description
2.2/A | No description available
> addh
Summary of feedback from adding hydrogens to hIP3R2-Apo-coot-3.pdb #2.2
---
notes | No usable SEQRES records for hIP3R2-Apo-coot-3.pdb (#2.2) chain A;
guessing termini instead
Chain-initial residues that are actual N termini: /A SER 6
Chain-initial residues that are not actual N termini: /A THR 84, /A ILE 350,
/A SER 534, /A GLU 692, /A ASP 963, /A ASP 1026, /A ASN 1045, /A SER 1176, /A
ASP 1598, /A ASP 1736, /A SER 1741, /A MET 1911, /A ASP 2091, /A ASP 2136, /A
LEU 2264, /A GLY 2474
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A VAL 2635, /A ALA 78, /A
PRO 320, /A LYS 527, /A GLN 674, /A ASP 894, /A ASN 1004, /A ALA 1039, /A VAL
1130, /A ASP 1433, /A LYS 1705, /A MET 1738, /A VAL 1825, /A GLN 2083, /A GLY
2129, /A GLY 2251, /A LYS 2429
1270 hydrogen bonds
Adding 'H' to /A THR 84
Adding 'H' to /A ILE 350
Adding 'H' to /A SER 534
Adding 'H' to /A GLU 692
Adding 'H' to /A ASP 963
9 messages similar to the above omitted
/A VAL 2635 is not terminus, removing H atom from 'C'
12990 hydrogens added
> hide HC
> hide HC
> close #2.2
Deleting atomic symmetry model...
Deleting atomic symmetry model...
Deleting atomic symmetry model...
Deleting atomic symmetry model...
> open /Users/navid/WORK/hIP3R2-Apo-coot-4.pdb
Chain information for hIP3R2-Apo-coot-4.pdb #3
---
Chain | Description
A | No description available
Deleting atomic symmetry model...
Deleting atomic symmetry model...
Chain information for hIP3R2-Apo-coot-4.pdb
---
Chain | Description
3.2/A | No description available
> addh
Summary of feedback from adding hydrogens to hIP3R2-Apo-coot-4.pdb #3.2
---
notes | No usable SEQRES records for hIP3R2-Apo-coot-4.pdb (#3.2) chain A;
guessing termini instead
Chain-initial residues that are actual N termini: /A SER 6
Chain-initial residues that are not actual N termini: /A THR 84, /A ILE 350,
/A SER 534, /A GLU 692, /A ASP 963, /A ASP 1026, /A ASN 1045, /A SER 1176, /A
ASP 1598, /A ASP 1736, /A SER 1741, /A MET 1911, /A ASP 2091, /A ASP 2136, /A
LEU 2264, /A GLY 2474
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A VAL 2635, /A ALA 78, /A
PRO 320, /A LYS 527, /A GLN 674, /A ASP 894, /A ASN 1004, /A ALA 1039, /A VAL
1130, /A ASP 1433, /A LYS 1705, /A MET 1738, /A VAL 1825, /A GLN 2083, /A GLY
2129, /A GLY 2251, /A LYS 2429
1268 hydrogen bonds
Adding 'H' to /A THR 84
Adding 'H' to /A ILE 350
Adding 'H' to /A SER 534
Adding 'H' to /A GLU 692
Adding 'H' to /A ASP 963
9 messages similar to the above omitted
/A VAL 2635 is not terminus, removing H atom from 'C'
12968 hydrogens added
> hide HC
> hide HC
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 6 models selected
> set bgColor black
reverting to start
> close #2#1#1.1
Deleting atomic symmetry model...
Deleting atomic symmetry model...
> open /Users/navid/Downloads/cryosparc_P6_J1110_011_volume_map_sharp.mrc
Opened cryosparc_P6_J1110_011_volume_map_sharp.mrc, grid size 384,384,384,
pixel 1.06, shown at level 0.207, step 2, values float32
> volume #1 step 1
> volume #1 level 0.5255
> hide sel atoms
> show sel atoms
> volume #1 style mesh
> volume #1 level 0.4929
> volume #1 color #9ecaff
> volume #1 color #9fcaff
> volume #1 color #9ec9ff
> volume #1 color #9cc6ff
> volume #1 color #9bc5ff
> volume #1 color #98c2ff
> volume #1 color #95bfff
> volume #1 color #93bcff
> volume #1 color #91baff
> volume #1 color #8fb8ff
> volume #1 color #8cb4ff
> volume #1 color #8ab0ff
> volume #1 color #86abff
> volume #1 color #83a5ff
> volume #1 color #80a1ff
> volume #1 color #7d9bff
> volume #1 color #7a95ff
> volume #1 color #7385ff
> volume #1 color #7283ff
> volume #1 color #707fff
> volume #1 color #707eff
> volume #1 color #6f7dff
> volume #1 color #6e7dff
> volume #1 color #6d7cff
> volume #1 color #6a7bff
> volume #1 color #667bff
> volume #1 color #607bff
> volume #1 color #577dff
> volume #1 color #4e7fff
> volume #1 color #4381ff
> volume #1 color #3583ff
> volume #1 color #2c84ff
> volume #1 color #2485ff
> volume #1 color #1e86ff
> volume #1 color #1888ff
> volume #1 color #148aff
> volume #1 color #118bff
> volume #1 color #0f8cff
> volume #1 color #0d8cff
> volume #1 color #0d8dff
> volume #1 color #0b8eff
> volume #1 color #0490ff
> volume #1 color #0092ff
> volume #1 color #0095ff
> volume #1 color #0099ff
> volume #1 color #009eff
> volume #1 color #00a3ff
> volume #1 color #00a7ff
> volume #1 color #00b4ff
> volume #1 color #00beff
> volume #1 color #00c1ff
> volume #1 color #00c3ff
> volume #1 color #00c5ff
> volume #1 color #00c8ff
> volume #1 color #00c9ff
> volume #1 color #00cbff
> volume #1 color #00cfff
> volume #1 color #00d4ff
> volume #1 color #00d8ff
> volume #1 color #00deff
> volume #1 color #00e2ff
> volume #1 color #00e5ff
> volume #1 color #00eaff
> volume #1 color #00f1ff
> volume #1 color #00f5ff
> volume #1 color #00f8ff
> volume #1 color cyan
> volume #1 color #00fffe
> volume #1 color #00fffc
> volume #1 color #00fffb
> volume #1 color #00fff8
> volume #1 color #00fff5
> volume #1 color #00fff4
> volume #1 color #00fff1
> volume #1 color #00ffee
> volume #1 color #00ffe8
> volume #1 color #00ffe1
> volume #1 color #00ffcb
> volume #1 color #00ffc2
> volume #1 color #00ffbe
> volume #1 color #00ffbc
> volume #1 color #00ffbb
> volume #1 color #00ffbc
> volume #1 color #00ffbd
> volume #1 color #00ffbe
> volume #1 color #00ffc0
> volume #1 color #00ffc2
> volume #1 color #00ffc4
> volume #1 color #00ffc6
> volume #1 color #00ffc8
> volume #1 color #00ffca
> volume #1 color #00ffcc
> volume #1 color #00ffcd
> volume #1 color #00ffd1
> volume #1 color #00ffd3
> volume #1 color #00ffd6
> volume #1 color #00ffd9
> volume #1 color #00ffdc
> volume #1 color #00ffde
> volume #1 color #00ffe0
> volume #1 color #00ffe4
> volume #1 color #00ffe6
> volume #1 color #00ffea
> volume #1 color #00ffed
> volume #1 color #00ffef
> volume #1 color #00fff1
> volume #1 color #00fff2
> volume #1 color #00fff4
> volume #1 color #00fff5
> volume #1 color #00fff6
> volume #1 color #00fff7
> volume #1 color #00fff8
> volume #1 color #00fff9
> volume #1 color #00fffa
> volume #1 color #00fffb
> volume #1 color #00fffc
> volume #1 color #00fffd
> volume #1 color #00fffe
> volume #1 color cyan
> volume #1 color #00feff
> volume #1 color #00fdff
> volume #1 color #00fcff
> volume #1 color #00fbff
> volume #1 color #00f9ff
> volume #1 color #00f7ff
> volume #1 color #00f6ff
> volume #1 color #00f4ff
> volume #1 color #00f3ff
> set bgColor white
> set bgColor black
> show sel atoms
> show sel atoms
> show sel atoms
> show sel atoms
> show sel atoms
> clipper associate #1 toModel #3.2
> select #3.1.1
4 models selected
> ~select #3.1.1
Nothing selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> ~select #3.2
Nothing selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> ~select #3.2
Nothing selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> ~select #3.2
Nothing selected
> select #3
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 19 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select clear
> volume #3.1.1.1 level 0.3519
> volume #3.1.1.1 level 0.2458
Unable to flip peptide bond after 50 rounds. Giving up.
> volume #3.1.1.1 style surface
> volume #3.1.1.1 color #00fffffe
> volume #3.1.1.1 color #00ffffd0
> volume #3.1.1.1 color #00ffffbd
> volume #3.1.1.1 color #00ffffbc
> volume #3.1.1.1 color #00ffffba
> volume #3.1.1.1 color #00ffffb8
> volume #3.1.1.1 color #00ffffb0
> volume #3.1.1.1 color #00ffffac
> volume #3.1.1.1 color #00ffffa9
> volume #3.1.1.1 color #00ffffa7
> volume #3.1.1.1 color #00ffff9f
> volume #3.1.1.1 color #00ffff9b
> volume #3.1.1.1 color #00ffff93
> volume #3.1.1.1 color #00ffff90
> volume #3.1.1.1 color #00ffff89
> volume #3.1.1.1 color #00ffff88
> volume #3.1.1.1 color #00ffff81
> volume #3.1.1.1 color #00ffff80
> volume #3.1.1.1 color #00ffff68
> volume #3.1.1.1 color #00ffff67
> volume #3.1.1.1 color #00ffff53
> volume #3.1.1.1 color #00ffff52
> volume #3.1.1.1 color #00ffff51
> volume #3.1.1.1 level 0.3927
> volume #3.1.1.1 level 0.244
> volume #3.1.1.1 level 0.6602
> select #3.1.1.1.2
1 model selected
> ~select #3.1.1.1.2
Nothing selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> ~select #3.2
Nothing selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> ~select #3.2
Nothing selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> hide #!3.2 models
> show #!3.2 models
> show sel atoms
> hide sel atoms
> show sel atoms
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> ~select #3.2
Nothing selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> ~select #3.2
Nothing selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> ~select #3.2
Nothing selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> ~select #3.2
Nothing selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> ~select #3.2
Nothing selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> ~select #3.2
Nothing selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> hide #3.2.2 models
> show #3.2.2 models
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> hide #!3.2 models
> show #!3.2 models
> clipper spotlight radius 13.00
> clipper spotlight radius 14.00
> clipper spotlight radius 15.00
> clipper spotlight radius 16.00
> clipper spotlight radius 17.00
> clipper spotlight radius 18.00
> clipper spotlight radius 19.00
> clipper spotlight radius 20.00
> clipper spotlight radius 21.00
> clipper spotlight radius 22.00
> clipper spotlight radius 23.00
> clipper spotlight radius 24.00
> clipper spotlight radius 25.00
> clipper spotlight radius 26.00
> clipper spotlight radius 27.00
> clipper spotlight radius 28.00
> clipper spotlight radius 29.00
> clipper spotlight radius 30.00
> clipper spotlight radius 31.00
> select #3
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 19 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select clear
> select clear
> select clear
> show atoms
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> clipper spotlight radius 20.00
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> select #3.2
33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 12 models selected
> ~select #3.2
Nothing selected
> hide #!3.2 models
> show #!3.2 models
> open /Users/navid/WORK/hIP3R2-Apo-coot-4.pdb
Chain information for hIP3R2-Apo-coot-4.pdb #1
---
Chain | Description
A | No description available
> close #3.2
Deleting atomic symmetry model...
Deleting atomic symmetry model...
> select #3
6 models selected
> ~select #3
Nothing selected
> select #1
21020 atoms, 21336 bonds, 32 pseudobonds, 2084 residues, 2 models selected
> addh
Summary of feedback from adding hydrogens to hIP3R2-Apo-coot-4.pdb #1
---
notes | No usable SEQRES records for hIP3R2-Apo-coot-4.pdb (#1) chain A;
guessing termini instead
Chain-initial residues that are actual N termini: /A SER 6
Chain-initial residues that are not actual N termini: /A THR 84, /A ILE 350,
/A SER 534, /A GLU 692, /A ASP 963, /A ASP 1026, /A ASN 1045, /A SER 1176, /A
ASP 1598, /A ASP 1736, /A SER 1741, /A MET 1911, /A ASP 2091, /A ASP 2136, /A
LEU 2264, /A GLY 2474
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A VAL 2635, /A ALA 78, /A
PRO 320, /A LYS 527, /A GLN 674, /A ASP 894, /A ASN 1004, /A ALA 1039, /A VAL
1130, /A ASP 1433, /A LYS 1705, /A MET 1738, /A VAL 1825, /A GLN 2083, /A GLY
2129, /A GLY 2251, /A LYS 2429
1268 hydrogen bonds
Adding 'H' to /A THR 84
Adding 'H' to /A ILE 350
Adding 'H' to /A SER 534
Adding 'H' to /A GLU 692
Adding 'H' to /A ASP 963
9 messages similar to the above omitted
/A VAL 2635 is not terminus, removing H atom from 'C'
12968 hydrogens added
> style sel stick
Changed 21020 atom styles
> style sel ball
Changed 21020 atom styles
> show sel atoms
> hide sel cartoons
Traceback (most recent call last):
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1017, in
_sim_end_cb
self._pr_sim_end_cb()
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1074, in
_pr_sim_end_cb
restraints =
self.position_restraint_mgr.get_restraints(self.sim_construct.all_atoms)
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/molobject.py", line 2329, in get_restraints
return self._get_restraints(atoms)
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/molobject.py", line 2282, in _get_restraints
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/molobject.py", line 2282, in _get_restraints
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/validation/ramaplot.py", line 197, in _sim_end_cb
self._mode_change_cb()
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/validation/ramaplot.py", line 233, in _mode_change_cb
self.selection_mode = mode
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/validation/ramaplot.py", line 288, in selection_mode
self.set_target_residues(self.current_model.residues)
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'residues' property raised
AttributeError
Error processing trigger "simulation terminated":
AttributeError: Execution of 'Structure' object's 'residues' property raised
AttributeError
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
OpenGL version: 4.1 ATI-4.2.15
OpenGL renderer: AMD Radeon Pro Vega 56 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac Pro
Model Identifier: iMacPro1,1
Processor Name: 8-Core Intel Xeon W
Processor Speed: 3.2 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 1 MB
L3 Cache: 11 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)
Software:
System Software Overview:
System Version: macOS 11.2.3 (20D91)
Kernel Version: Darwin 20.3.0
Time since boot: 3 days 3:27
Graphics/Displays:
Radeon Pro Vega 56:
Chipset Model: Radeon Pro Vega 56
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x6867
Revision ID: 0x0000
ROM Revision: 113-D0500D-114
VBIOS Version: 113-D05001A1XL-018
Option ROM Version: 113-D05001A1XL-018
EFI Driver Version: 01.01.114
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: 5120 x 2880 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.0
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-Clipper: 0.15.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
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: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-ISOLDE: 1.1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Tool Shed |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Error in toolshed error message |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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