Opened 4 years ago

Closed 4 years ago

#4649 closed defect (duplicate)

ISOLDE: 'PositionRestraintMgr' object has no attribute '_c_pointer'

Reported by: chimerax-bug-report@… 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:        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.  
  

> select up

33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 2 models selected  

> select up

33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 2 models selected  

> select up

33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 3 models selected  

> select up

33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 3 models selected  

> select up

33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 3 models selected  

> select up

33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 3 models selected  

> select up

33988 atoms, 34304 bonds, 32 pseudobonds, 2084 residues, 3 models selected  

> clipper associate #1 toModel #3.1

Invalid "toModel" argument: Must specify 1 structure, got 0 for "#3.1"  

> clipper associate #3.1 toModel #1

Deleting atomic symmetry model...  
Chain information for hIP3R2-Apo-coot-4.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> clipper associate #1 toModel #3.1

Invalid "toModel" argument: Must specify 1 structure, got 0 for "#3.1"  

> clipper associate #1.2 toModel #3.1

Invalid "toModel" argument: Must specify 1 structure, got 0 for "#3.1"  

> clipper associate #1.2 toModel #3.1.1.1

Invalid "toModel" argument: Must specify 1 structure, got 0 for "#3.1.1.1"  

> clipper associate #3.1.1.1 toModel #1

> close #1

Deleting atomic symmetry model...  

> close

Deleting atomic symmetry model...  

> close #

Expected a models specifier or a keyword  

> close #

Expected a models specifier or a keyword  

> close #

Expected a models specifier or a keyword  

> open /Users/navid/WORK/hIP3R2-Apo-coot-4.pdb

Chain information for hIP3R2-Apo-coot-4.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for hIP3R2-Apo-coot-4.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> 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  

> clipper associate #2 toModel #1

> select #1.2

21020 atoms, 21336 bonds, 32 pseudobonds, 2084 residues, 6 models selected  

> addh

Summary of feedback from adding hydrogens to hIP3R2-Apo-coot-4.pdb #1.2  
---  
notes | No usable SEQRES records for hIP3R2-Apo-coot-4.pdb (#1.2) 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  
  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> select clear

> select clear

> select clear

> volume #1.1.1.1 level 0.2098

> volume #1.1.1.1 level 0.3223

> volume #1.1.1.1 level 0.192

> volume #1.1.1.1 level 0.3283

> volume #1.1.1.1 level 0.3698

No rotamer preview selected! Ignoring command.  

> volume #1.1.1.1 level 0.2927

> volume #1.1.1.1 level 0.5653

> clipper spotlight radius 7.00

> clipper spotlight radius 15.00

> clipper spotlight radius 15.00

> clipper spotlight radius 14.00

> clipper spotlight radius 11.00

> clipper spotlight radius 11.00

> select clear

> select clear

> select clear

> clipper spotlight radius 6.00

> clipper spotlight radius 7.00

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> volume #1.1.1.1 level 0.3636

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  

> select clear

> volume #1.1.1.1 level 0.2261

> select clear

> select clear

> volume #1.1.1.1 level 0.5561

> volume #1.1.1.1 level 0.4186

> volume #1.1.1.1 level 0.3453

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/delayed_reaction.py", line 79, in callback  
if self.tf is None or self.tf():  
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 245, in
thread_finished  
return f(self._c_pointer)  
AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer'  
  
Error processing trigger "new frame":  
AttributeError: 'OpenMM_Thread_Handler' 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/openmm/openmm_interface.py", line 245, in
thread_finished  
return f(self._c_pointer)  
  
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 4:19

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 Eric Pettersen, 4 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: 'PositionRestraintMgr' object has no attribute '_c_pointer'

comment:2 by Tristan Croll, 4 years ago

Resolution: → duplicate
Status: assigned → closed

User closed the model with a simulation running. I *will* eventually make ISOLDE handle this gracefully, but it's not high priority.

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