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#5499 closed defect (fixed)

MD template error

Reported by:	jopark@…	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-3.10.0-1160.42.2.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
I tried to use ISOLDE on my pdb, but I get the following error: Failed to add atoms ['H43'] to atom N4 because this will lead to having 4 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (MC_DCP). If this template is built into ISOLDE, please report this using Help/Report a bug. 

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

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.2.2-cp38-cp38-manylinux_2_17_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.16.0 ChimeraX-ISOLDE-1.2.2  
Installed ChimeraX-Clipper (0.16.0)  
Installed ChimeraX-ISOLDE (1.2.2)  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 23227, resource id:
34683170, major code: 40 (TranslateCoords), minor code: 0  

> open /data1/jopark/deepEMhancer/P27_J962_E_E_hR.mrc format mrc

No such file/path: /data1/jopark/deepEMhancer/P27_J962_E_E_hR.mrc  

> 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Forcefield cache not found or out of date.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 /data1/jopark/phenix/polgamma_R-
> ter/RealSpaceRefine_83/CM_Ternary_R_rsr83_27-1063-coot-0.pdb

Chain information for CM_Ternary_R_rsr83_27-1063-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
D | No description available  
P | No description available  
T | No description available  
  
Chain information for CM_Ternary_R_rsr83_27-1063-coot-0.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/D | No description available  
1.2/P | No description available  
1.2/T | 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  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 22452, resource id:
34688573, major code: 40 (TranslateCoords), minor code: 0  

> show cartoons

> open /data1/jopark/deepemhancer/dEMh_CM_Ternary_R-27-1063_nS-halfA.mrc

Opened dEMh_CM_Ternary_R-27-1063_nS-halfA.mrc as #2, grid size 288,288,288,
pixel 0.85, shown at level 0.00715, step 2, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 23902, resource id:
34690074, major code: 40 (TranslateCoords), minor code: 0  

> volume #2 step 1

> clipper associate #2 toModel #1

Opened dEMh_CM_Ternary_R-27-1063_nS-halfA.mrc as #1.1.1.1, grid size
288,288,288, pixel 0.85, shown at step 1, values float32  

> set bgColor white

> addh

Summary of feedback from adding hydrogens to
CM_Ternary_R_rsr83_27-1063-coot-0.pdb #1.2  
---  
warnings | Not adding hydrogens to /A ARG 627 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LYS 990 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /T DG 2 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /P DA 3 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /B ARG 364 CB because it is missing heavy-atom bond
partners  
1 messages similar to the above omitted  
Skipped 7 atom(s) with bad connectivities; see log for details  
notes | No usable SEQRES records for CM_Ternary_R_rsr83_27-1063-coot-0.pdb
(#1.2) chain A; guessing termini instead  
No usable SEQRES records for CM_Ternary_R_rsr83_27-1063-coot-0.pdb (#1.2)
chain B; guessing termini instead  
No usable SEQRES records for CM_Ternary_R_rsr83_27-1063-coot-0.pdb (#1.2)
chain D; guessing termini instead  
No usable SEQRES records for CM_Ternary_R_rsr83_27-1063-coot-0.pdb (#1.2)
chain P; guessing termini instead  
No usable SEQRES records for CM_Ternary_R_rsr83_27-1063-coot-0.pdb (#1.2)
chain T; guessing termini instead  
Chain-initial residues that are actual N termini: /A LEU 69, /B ALA 64, /D GLU
67, /P DA 3, /T DG 2  
Chain-initial residues that are not actual N termini: /A ASP 260, /A ILE 342,
/A LEU 530, /A VAL 645, /A PRO 730, /A TRP 1049, /D ALA 228, /D HIS 368  
Chain-final residues that are actual C termini: /B VAL 485, /P DC 24, /T DT 26  
Chain-final residues that are not actual C termini: /A SER 1235, /A THR 251,
/A LYS 316, /A LYS 499, /A LEU 631, /A GLN 663, /A LEU 997, /D ALA 487, /D ALA
219, /D GLN 355  
Skipping possible acceptor with bad geometry: /D VAL 485 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /D VAL 485 OXT  
  
Skipping possible acceptor with bad geometry: /D VAL 485 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /D VAL 485 OXT  
  
Skipping possible acceptor with bad geometry: /D VAL 485 O  
Wrong number of grandchild atoms for phi/psi acceptor /D VAL 485 O  
  
Skipping possible acceptor with bad geometry: /D VAL 485 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /D VAL 485 OXT  
  
Skipping possible acceptor with bad geometry: /D VAL 485 O  
Wrong number of grandchild atoms for phi/psi acceptor /D VAL 485 O  
  
2 messages similar to the above omitted  
1389 hydrogen bonds  
Adding 'H' to /A ASP 260  
Adding 'H' to /A ILE 342  
Adding 'H' to /A LEU 530  
Adding 'H' to /A VAL 645  
Adding 'H' to /A TRP 1049  
2 messages similar to the above omitted  
/A SER 1235 is not terminus, removing H atom from 'C'  
/D ALA 487 is not terminus, removing H atom from 'C'  
14797 hydrogens added  
  

> hide HC

> isolde restrain ligands #1

> select #1

30186 atoms, 30670 bonds, 8 pseudobonds, 1846 residues, 15 models selected  
Loading residue template for DCP from internal database  
ISOLDE: stopped sim  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 60196, resource id:
34695503, major code: 40 (TranslateCoords), minor code: 0  

Deleted the following atoms from residue DCP N4003: H5'', H2', H2'', H41, H42,
H5'  
Failed to add atoms ['H43'] to atom N4 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_DCP). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Failed to add atoms ['H43'] to atom N4 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_DCP). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Failed to add atoms ['H43'] to atom N4 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_DCP). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Traceback (most recent call last):  
File "/home/jopark/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
File "/home/jopark/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
  
See log for complete Python traceback.  
  
Failed to add atoms ['H43'] to atom N4 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_DCP). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Traceback (most recent call last):  
File "/home/jopark/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
File "/home/jopark/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/jopark/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
File "/home/jopark/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
  
See log for complete Python traceback.  
  

> select /N

40 atoms, 41 bonds, 1 residue, 1 model selected  

> delete elements.H

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete elements.H sel

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete sel

> delete sel

Failed to add atoms ['H43'] to atom N4 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_DCP). If this template is
built into ISOLDE, please report this using Help/Report a bug  

> delete sel

Fetching CCD ATP from http://ligand-expo.rcsb.org/reports/A/ATP/ATP.cif  
Fetching CCD GTP from http://ligand-expo.rcsb.org/reports/G/GTP/GTP.cif  
Failed to add atoms ['H43'] to atom N4 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_DCP). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Traceback (most recent call last):  
File "/home/jopark/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
File "/home/jopark/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
  
See log for complete Python traceback.  
  
Failed to add atoms ['H43'] to atom N4 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_DCP). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Failed to add atoms ['H43'] to atom N4 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_DCP). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Failed to add atoms ['H43'] to atom N4 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_DCP). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Failed to add atoms ['H43'] to atom N4 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_DCP). If this template is
built into ISOLDE, please report this using Help/Report a bug  




OpenGL version: 3.3.0 NVIDIA 465.19.01
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: empty
Model: B7105F48TV4HR-2T-N
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
Cache Size: 11264 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           187G         20G        3.7G        447M        163G        165G
	Swap:           63G        600M         63G

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
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
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    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
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    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
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    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
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    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
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    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
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    ChimeraX-ModelSeries: 1.0
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    ChimeraX-Morph: 1.0
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    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    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: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
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    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (3)

comment:1 by pett, 4 years ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → MD template error

comment:2 by Tristan Croll, 4 years ago

Thanks for the bug report. Most of ISOLDE's ligands are the result of an automatic parameterisation project by Nigel Moriarty and Dave Case - while the majority are fine, a few have errors in chemistry. This is one - N4 has been misassigned as a primary amine when it's actually an aromatic NH2. Will see about correcting it tomorrow, and send you a copy of the resulting parameter file to help get you moving in the meantime.

comment:3 by Tristan Croll, 4 years ago

Resolution:	→ fixed
Status:	assigned → closed

Updated template in ISOLDE's DB, and sent a copy to the user.

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