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Opened 5 years ago
Closed 3 years ago
#3569 closed defect (fixed)
Problem reading MTZ data: list index out of range
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | 0.93 |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.93 (2020-04-03) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open2 C:/Users/Manoj/Desktop/Ti_new_TF/titanium_refine_7-coot-0.pdb Summary of feedback from opening <_io.textiowrapper name="C:/Users/Manoj/Desktop/Ti_new_TF/titanium_refine_7-coot-0.pdb" mode="rt" encoding="utf-8"> --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2018-04-28 Time 11:55:38 Pacific Daylight Time (Mexico) -0700 (15249 Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : C:\Users\Manoj\Desktop\C13_Ti\buster.03\refine.mtz 32 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (339 ) Chain information for titanium_refine_7-coot-0.pdb #1 --- Chain | Description A | No description available B | No description available > open2 C:/Users/Manoj/Desktop/Ti_new_TF/refine_SLAC_buster_27_april.mtz Unrecognized file suffix '.mtz' > open2 > C:/Users/Manoj/Desktop/Ti_new_TF/FFT_36/refine_SLAC_buster_27_april_3.ccp4 Opened refine_SLAC_buster_27_april_3.ccp4, grid size 120,144,270, pixel 0.709,0.698,0.741, shown at level 2.32, step 1, values float32 > volume #2 level 1.394 > open2 > C:/Users/Manoj/Desktop/Ti_new_TF/FFT_36/refine_SLAC_buster_27_april_2mFo- > DFc.ccp4 Opened refine_SLAC_buster_27_april_2mFo-DFc.ccp4, grid size 120,144,270, pixel 0.709,0.698,0.741, shown at level 3.24, step 1, values float32 > volume #2 level 1.154 > volume #3 level 2.317 > volume #3 level 0.7448 > toolshed show "Fit in Map" > hide #!3 models > show #!3 models > select #3 2 models selected > ~select #3 Nothing selected > select #1 10330 atoms, 10601 bonds, 3 pseudobonds, 2 models selected > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > ~select #1 Nothing selected > hide #!3 models > select #1 10330 atoms, 10601 bonds, 3 pseudobonds, 2 models selected > show #!3 models > open2 > C:/Users/Manoj/Desktop/Ti_new_TF/FFT_36/refine_SLAC_buster_27_april_mFo- > DFc.ccp4 Opened refine_SLAC_buster_27_april_mFo-DFc.ccp4, grid size 120,144,270, pixel 0.709,0.698,0.741, shown at level 2.32, step 1, values float32 > volume #4 level -0.8246 > volume #4 level 1.005 > open2 C:/Users/Manoj/Desktop/Ti_new_TF/refine_SLAC_buster_27_april.mtz Unrecognized file suffix '.mtz' > toolshed show ISOLDE > set selectionWidth 4 Chain information for titanium_refine_7-coot-0.pdb --- Chain | Description 1.2/A | No description available 1.2/B | 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 "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py", line 1271, in _choose_reflections_file self.add_xtal_data(filename) File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py", line 1299, in add_xtal_data auto_choose_reflection_data=False) File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\maps\map_mgr.py", line 279, in add_xmapset_from_mtz auto_choose_reflection_data) File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\maps\map_mgr.py", line 288, in add_xmapset_from_file auto_choose_reflection_data=auto_choose_reflection_data) File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\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 "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\clipper_mtz.py", line 61, in _init_from_hkl_file auto_choose_reflection_data=auto_choose_reflection_data) File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\clipper_mtz.py", line 422, in load_hkl_data load_map_coeffs = load_map_coeffs) File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\clipper_mtz.py", line 490, in load_mtz_data hklinfo, crystal_dict = mtz_read.load_mtz_data(session, filename, load_map_coeffs=load_map_coeffs) File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\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 "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\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 - Build 20.19.15.4531 OpenGL renderer: Intel(R) HD Graphics 5500 OpenGL vendor: Intel Manufacturer: Dell Inc. Model: Inspiron 7348 OS: Microsoft Windows 10 Home (Build 18362) Memory: 8,501,149,696 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i7-5500U CPU @ 2.40GHz"
Change History (3)
comment:1 by , 5 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem reading MTZ data: list index out of range |
| Version: | → 0.93 |
comment:2 by , 5 years ago
comment:3 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Clearing out old tickets - this was fixed quite some time ago.
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Improving on MTZ reading isn't something I'm going to be able to get to immediately, but it is on my to-do list. The issue here is that the reader currently expects the columns to be laid out in a matched sequence : F must be followed by the matching sigF or phi, I must be followed by sigI, etc.. If you use a HKL editor such as the one bundled into Phenix to rearrange things accordingly, you should be able to move forward.