Opened 5 years ago

Closed 3 years ago

#3966 closed defect (fixed)

Clipper: Failure to read BUSTER MTZ file

Reported by: erwin.pannecoucke@… 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-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
I tried to load the mtz file corresponding to my structure. The mtz file is the output from BUSTER, so should be in a classical format.

Log:
Startup Messages  
---  
warnings | QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already
registered  
QWebEngineUrlScheme::registerScheme: Scheme "help" already registered  
QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered  
QWebEngineUrlScheme::registerScheme: Scheme "help" already registered  
QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered  
8 messages similar to the above omitted  
Replacing file-saver for 'DCD coordinates' from MD-crds bundle with that from
MDcrds bundle  
Replacing opener for 'Gromacs full-precision coordinates' from MD-crds bundle
with that from MDcrds bundle  
Replacing opener for 'Gromacs compressed coordinates' from MD-crds bundle with
that from MDcrds bundle  
Replacing opener for 'DCD coordinates' from MD-crds bundle with that from
MDcrds bundle  
notes | Replacing data format 'Gromacs full-precision coordinates' as defined
by ChimeraX-MD-crds bundle with definition from ChimeraX-MDcrds bundle  
Replacing data format 'Gromacs compressed coordinates' as defined by ChimeraX-
MD-crds bundle with definition from ChimeraX-MDcrds bundle  
Replacing data format 'DCD coordinates' as defined by ChimeraX-MD-crds bundle
with definition from ChimeraX-MDcrds bundle  
  
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /mnt/DATA1/Erwin/20170904_Petra3_P14/phenix/Refine_37/20_buster/refine37-buster20.pdb
> format pdb

Summary of feedback from opening
/mnt/DATA1/Erwin/20170904_Petra3_P14/phenix/Refine_37/20_buster/refine37-buster20.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK --------------------- added by autoBUSTER
-------------------------------  
  
Ignored bad PDB record found on line 2  
REMARK run at = Thu Oct 4 11:57:23 CEST 2018  
  
Ignored bad PDB record found on line 11  
REMARK Files used:  
  
Ignored bad PDB record found on line 12  
REMARK PDB = ./pdbchk.pdb  
  
Ignored bad PDB record found on line 13  
REMARK MTZ = /mnt/data1/ErwinP/20170904_Petra3_P14/T343I-hFL/phen  
  
16 messages similar to the above omitted  
  
Chain information for refine37-buster20.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  
  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for refine37-buster20.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  
  
Done loading forcefield  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/FOM W  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLA A  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLB A  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLC A  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLD A  
Traceback (most recent call last):  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 1283, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 1311, in add_xtal_data  
auto_choose_reflection_data=False)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/map_mgr.py", line 284, in add_xmapset_from_mtz  
auto_choose_reflection_data)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/map_mgr.py", line 293, in add_xmapset_from_file  
auto_choose_reflection_data=auto_choose_reflection_data)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/clipper_mtz.py", line 53, in __init__  
self._init_from_hkl_file(hklfile, free_flag_label,
auto_choose_reflection_data)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/clipper_mtz.py", line 61, in _init_from_hkl_file  
auto_choose_reflection_data=auto_choose_reflection_data)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/clipper_mtz.py", line 422, in load_hkl_data  
load_map_coeffs = load_map_coeffs)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/clipper_mtz.py", line 491, in load_mtz_data  
hklinfo, crystal_dict = mtz_read.load_mtz_data(session, filename,
load_map_coeffs=load_map_coeffs)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/io/mtz_read.py", line 103, in load_mtz_data  
ncryst, ndat, nname, ndtype = _parse_column_path(column_paths[i+1])  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/io/mtz_read.py", line 103, in load_mtz_data  
ncryst, ndat, nname, ndtype = _parse_column_path(column_paths[i+1])  
  
See log for complete Python traceback.  
  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/FOM W  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLA A  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLB A  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLC A  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLD A  
Traceback (most recent call last):  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 1283, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 1311, in add_xtal_data  
auto_choose_reflection_data=False)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/map_mgr.py", line 284, in add_xmapset_from_mtz  
auto_choose_reflection_data)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/map_mgr.py", line 293, in add_xmapset_from_file  
auto_choose_reflection_data=auto_choose_reflection_data)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/clipper_mtz.py", line 53, in __init__  
self._init_from_hkl_file(hklfile, free_flag_label,
auto_choose_reflection_data)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/clipper_mtz.py", line 61, in _init_from_hkl_file  
auto_choose_reflection_data=auto_choose_reflection_data)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/clipper_mtz.py", line 422, in load_hkl_data  
load_map_coeffs = load_map_coeffs)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/clipper_mtz.py", line 491, in load_mtz_data  
hklinfo, crystal_dict = mtz_read.load_mtz_data(session, filename,
load_map_coeffs=load_map_coeffs)  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/io/mtz_read.py", line 103, in load_mtz_data  
ncryst, ndat, nname, ndtype = _parse_column_path(column_paths[i+1])  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "/home/erwinp/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/io/mtz_read.py", line 103, in load_mtz_data  
ncryst, ndat, nname, ndtype = _parse_column_path(column_paths[i+1])  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 450.36.06
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-7049GP-TRT
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 64 Intel(R) Xeon(R) Gold 5218 CPU @ 2.30GHz
Cache Size: 22528 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           251G         16G        150G        1.6G         84G        232G
	Swap:          4.0G         59M        3.9G

Graphics:
	05:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	Subsystem: Super Micro Computer Inc Device [15d9:096d]	
	Kernel driver in use: ast
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
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Change History (8)

comment:1 by Tristan Croll, 5 years ago

Platform: → all
Project: → ChimeraX

Hmm... thanks for reporting this! Would it be possible to get a copy of the MTZ file (confidentially, for testing purposes only of course) at tic20@…?

The problem with MTZ files is that while the overall container is a standard format, the contents are somewhat free-form and everyone seems to have a different idea of how they should be laid out.

comment:2 by Tristan Croll, 5 years ago

In the meantime, to get yourself up and running the easiest thing to do would be to write an MTZ file containing just your F, sigF and free flags.

comment:3 by Tristan Croll, 5 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Status: new → assigned
Summary: ChimeraX bug report submission → Clipper: Failure to read BUSTER MTZ file

in reply to:  4 ; comment:4 by erwin.pannecoucke@…, 5 years ago 

Dear, 

I'm not sure if this is the way to respond to this issue, but the problem has been resolved. This ticket can be closed.


Kind regards,
Erwin


---
Erwin Pannecoucke 
Unit for Structural Biology
Dept. of Biochemistry and Microbiology, Ghent University
VIB Center for Inflammation Research
Tel: +32-(0)9-331-3664

-----Oorspronkelijk bericht-----
Van: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Verzonden: vrijdag 20 november 2020 16:45
Aan: undisclosed-recipients:
CC: erwin.pannecoucke@irc.vib-ugent.be
Onderwerp: Re: [ChimeraX] #3966: ChimeraX bug report submission

#3966: ChimeraX bug report submission
------------------------------------------+--------------------
          Reporter:  erwin.pannecoucke@…  |      Owner:  (none)
              Type:  defect               |     Status:  new
          Priority:  normal               |  Milestone:
         Component:  Unassigned           |    Version:
        Resolution:                       |   Keywords:
        Blocked By:                       |   Blocking:
Notify when closed:                       |   Platform:  all
           Project:  ChimeraX             |
------------------------------------------+--------------------
Changes (by Tristan Croll):

 * project:   => ChimeraX
 * platform:   => all


Comment:

 Hmm... thanks for reporting this! Would it be possible to get a copy of  the MTZ file (confidentially, for testing purposes only of course) at  tic20@cam.ac.uk?

 The problem with MTZ files is that while the overall container is a  standard format, the contents are somewhat free-form and everyone seems to  have a different idea of how they should be laid out.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3966#comment:1>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  4 comment:5 by erwin.pannecoucke@…, 5 years ago 

Dear, 

I'm not sure if this is the way to respond to this issue, but the problem has been resolved. This ticket can be closed.


Kind regards,
Erwin


---
Erwin Pannecoucke 
Unit for Structural Biology
Dept. of Biochemistry and Microbiology, Ghent University
VIB Center for Inflammation Research
Tel: +32-(0)9-331-3664



-----Oorspronkelijk bericht-----
Van: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Verzonden: vrijdag 20 november 2020 16:48
Aan: undisclosed-recipients:
CC: erwin.pannecoucke@irc.vib-ugent.be; tic20@cam.ac.uk
Onderwerp: Re: [ChimeraX] #3966: Clipper: Failure to read BUSTER MTZ file (was: ChimeraX bug report submission)

#3966: Clipper: Failure to read BUSTER MTZ file
------------------------------------------+---------------------------
          Reporter:  erwin.pannecoucke@…  |      Owner:  Tristan Croll
              Type:  defect               |     Status:  assigned
          Priority:  normal               |  Milestone:
         Component:  Third Party          |    Version:
        Resolution:                       |   Keywords:
        Blocked By:                       |   Blocking:
Notify when closed:                       |   Platform:  all
           Project:  ChimeraX             |
------------------------------------------+---------------------------
Changes (by Tristan Croll):

 * owner:  (none) => Tristan Croll
 * status:  new => assigned
 * component:  Unassigned => Third Party


--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3966#comment:3>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  6 ; comment:6 by erwin.pannecoucke@…, 5 years ago 

Dear, 

I'm not sure if this is the way to respond to this issue, but the problem has been resolved. This ticket can be closed.


Kind regards,
Erwin


---
Erwin Pannecoucke 
Unit for Structural Biology
Dept. of Biochemistry and Microbiology, Ghent University
VIB Center for Inflammation Research
Tel: +32-(0)9-331-3664

-----Oorspronkelijk bericht-----
Van: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Verzonden: vrijdag 20 november 2020 14:25
Aan: erwin.pannecoucke@irc.vib-ugent.be
Onderwerp: [ChimeraX] #3966: ChimeraX bug report submission

#3966: ChimeraX bug report submission
---------------------------------+-----------------------------
 Reporter:  erwin.pannecoucke@…  |                Type:  defect
   Status:  new                  |            Priority:  normal
Component:  Unassigned           |          Blocked By:
 Blocking:                       |  Notify when closed:
---------------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-
 centos-7.8.2003-Core
 ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)  Description  I tried to load the mtz file corresponding to my structure. The mtz file  is the output from BUSTER, so should be in a classical format.

 Log:
 Startup Messages
 ---
 warnings | QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already  registered
 QWebEngineUrlScheme::registerScheme: Scheme "help" already registered
 QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered
 QWebEngineUrlScheme::registerScheme: Scheme "help" already registered
 QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered
 8 messages similar to the above omitted  Replacing file-saver for 'DCD coordinates' from MD-crds bundle with that  from  MDcrds bundle  Replacing opener for 'Gromacs full-precision coordinates' from MD-crds  bundle  with that from MDcrds bundle  Replacing opener for 'Gromacs compressed coordinates' from MD-crds bundle  with  that from MDcrds bundle  Replacing opener for 'DCD coordinates' from MD-crds bundle with that from  MDcrds bundle  notes | Replacing data format 'Gromacs full-precision coordinates' as  defined  by ChimeraX-MD-crds bundle with definition from ChimeraX-MDcrds bundle  Replacing data format 'Gromacs compressed coordinates' as defined by
 ChimeraX-
 MD-crds bundle with definition from ChimeraX-MDcrds bundle  Replacing data format 'DCD coordinates' as defined by ChimeraX-MD-crds  bundle  with definition from ChimeraX-MDcrds bundle

 UCSF ChimeraX version: 1.1 (2020-09-09)  © 2016-2020 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > open
 >
 /mnt/DATA1/Erwin/20170904_Petra3_P14/phenix/Refine_37/20_buster/refine37-buster20.pdb
 > format pdb

 Summary of feedback from opening
 /mnt/DATA1/Erwin/20170904_Petra3_P14/phenix/Refine_37/20_buster/refine37-buster20.pdb
 ---
 warnings | Ignored bad PDB record found on line 1  REMARK --------------------- added by autoBUSTER
 -------------------------------

 Ignored bad PDB record found on line 2
 REMARK run at = Thu Oct 4 11:57:23 CEST 2018

 Ignored bad PDB record found on line 11  REMARK Files used:

 Ignored bad PDB record found on line 12  REMARK PDB = ./pdbchk.pdb

 Ignored bad PDB record found on line 13  REMARK MTZ = /mnt/data1/ErwinP/20170904_Petra3_P14/T343I-hFL/phen

 16 messages similar to the above omitted

 Chain information for refine37-buster20.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


 > ui tool show ISOLDE

 > set selectionWidth 4

 Chain information for refine37-buster20.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

 Done loading forcefield
 Discarding unrecognised/unsupported data array /HKL_base/HKL_base/FOM W  Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLA A  Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLB A  Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLC A  Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLD A  Traceback (most recent call last):
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/isolde/isolde.py", line 1283, in  _choose_reflections_file
 self.add_xtal_data(filename)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/isolde/isolde.py", line 1311, in add_xtal_data
 auto_choose_reflection_data=False)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/maps/map_mgr.py", line 284, in  add_xmapset_from_mtz
 auto_choose_reflection_data)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/maps/map_mgr.py", line 293, in  add_xmapset_from_file
 auto_choose_reflection_data=auto_choose_reflection_data)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/clipper_mtz.py", line 53, in __init__  self._init_from_hkl_file(hklfile, free_flag_label,
 auto_choose_reflection_data)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/clipper_mtz.py", line 61, in _init_from_hkl_file
 auto_choose_reflection_data=auto_choose_reflection_data)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/clipper_mtz.py", line 422, in load_hkl_data  load_map_coeffs = load_map_coeffs)  File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/clipper_mtz.py", line 491, in load_mtz_data  hklinfo, crystal_dict = mtz_read.load_mtz_data(session, filename,
 load_map_coeffs=load_map_coeffs)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/io/mtz_read.py", line 103, in load_mtz_data  ncryst, ndat, nname, ndtype = _parse_column_path(column_paths[i+1])
 IndexError: list index out of range

 IndexError: list index out of range

 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/io/mtz_read.py", line 103, in load_mtz_data  ncryst, ndat, nname, ndtype = _parse_column_path(column_paths[i+1])

 See log for complete Python traceback.

 Discarding unrecognised/unsupported data array /HKL_base/HKL_base/FOM W  Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLA A  Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLB A  Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLC A  Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLD A  Traceback (most recent call last):
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/isolde/isolde.py", line 1283, in  _choose_reflections_file
 self.add_xtal_data(filename)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/isolde/isolde.py", line 1311, in add_xtal_data
 auto_choose_reflection_data=False)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/maps/map_mgr.py", line 284, in  add_xmapset_from_mtz
 auto_choose_reflection_data)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/maps/map_mgr.py", line 293, in  add_xmapset_from_file
 auto_choose_reflection_data=auto_choose_reflection_data)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/clipper_mtz.py", line 53, in __init__  self._init_from_hkl_file(hklfile, free_flag_label,
 auto_choose_reflection_data)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/clipper_mtz.py", line 61, in _init_from_hkl_file
 auto_choose_reflection_data=auto_choose_reflection_data)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/clipper_mtz.py", line 422, in load_hkl_data  load_map_coeffs = load_map_coeffs)  File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/clipper_mtz.py", line 491, in load_mtz_data  hklinfo, crystal_dict = mtz_read.load_mtz_data(session, filename,
 load_map_coeffs=load_map_coeffs)
 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/io/mtz_read.py", line 103, in load_mtz_data  ncryst, ndat, nname, ndtype = _parse_column_path(column_paths[i+1])
 IndexError: list index out of range

 IndexError: list index out of range

 File "/home/erwinp/.local/share/ChimeraX/1.1/site-
 packages/chimerax/clipper/io/mtz_read.py", line 103, in load_mtz_data  ncryst, ndat, nname, ndtype = _parse_column_path(column_paths[i+1])

 See log for complete Python traceback.





 OpenGL version: 3.3.0 NVIDIA 450.36.06
 OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2  OpenGL vendor: NVIDIA Corporation
 Manufacturer: Supermicro
 Model: SYS-7049GP-TRT
 OS: CentOS Linux 7 Core
 Architecture: 64bit ELF
 CPU: 64 Intel(R) Xeon(R) Gold 5218 CPU @ 2.30GHz  Cache Size: 22528 KB
 Memory:
                       total        used        free      shared
 buff/cache   available
         Mem:           251G         16G        150G        1.6G
 84G        232G
         Swap:          4.0G         59M        3.9G

 Graphics:
         05:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc.
 ASPEED Graphics Family [1a03:2000] (rev 41)
         Subsystem: Super Micro Computer Inc Device [15d9:096d]
         Kernel driver in use: ast
 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
     Babel: 2.8.0
     backcall: 0.2.0
     blockdiag: 2.0.1
     certifi: 2020.6.20
     chardet: 3.0.4
     ChimeraX-AddH: 2.1.1
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.1
     ChimeraX-Arrays: 1.0
     ChimeraX-Atom-Search: 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-Bug-Reporter: 1.0
     ChimeraX-BugReporter: 1.0
     ChimeraX-BuildStructure: 2.0
     ChimeraX-Bumps: 1.0
     ChimeraX-BundleBuilder: 1.0
     ChimeraX-ButtonPanel: 1.0
     ChimeraX-Cage-Builder: 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-Connect-Structure: 1.0
     ChimeraX-ConnectStructure: 2.0
     ChimeraX-Contacts: 1.0
     ChimeraX-Core: 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-Dist-Monitor: 1.0
     ChimeraX-Dist-UI: 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-LinuxSupport: 1.0
     ChimeraX-List-Info: 0.1
     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-MD-crds: 1.0
     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-Preset-Mgr: 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-Rotamer-Lib-Mgr: 1.0
     ChimeraX-RotamerLibMgr: 2.0
     ChimeraX-RotamerLibsDunbrack: 2.0
     ChimeraX-RotamerLibsDynameomics: 2.0
     ChimeraX-RotamerLibsRichardson: 2.0
     ChimeraX-SaveCommand: 1.2
     ChimeraX-Scheme-Mgr: 1.0
     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-Std-Commands: 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-Texture: 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
     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: 0.16
     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

 }}}

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3966>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:7 by Tristan Croll, 5 years ago

Status: assigned → feedback

That's great! If you're so inclined, it would be great to get a copy of a BUSTER MTZ file that triggers the traceback so I can fix things to ensure it opens correctly.

comment:8 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: feedback → closed

Seems I never closed this. Doing so now.

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