ChimeraX bug report submission

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The following bug report has been submitted:
Platform:        Linux-4.15.0-48-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.9 (2019-06-06)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/u/azsha/AS/CVI03/Buster/corrected_test7_moreloop120_added400_built_deleted_n3N100_210819/refine-
coot-1.pdb

Summary of feedback from opening
/u/azsha/AS/CVI03/Buster/corrected_test7_moreloop120_added400_built_deleted_n3N100_210819/refine-
coot-1.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 = Wed Aug 21 12:15:40 CEST 2019  
  
Ignored bad PDB record found on line 16  
REMARK Files used:  
  
Ignored bad PDB record found on line 17  
REMARK PDB = /u/azsha/AS/CVI03/Buster/corrected_test7_moreloop120  
  
Ignored bad PDB record found on line 18  
REMARK MTZ = /u/azsha/AS/CVI03/090819/xscale_CVI03Sy7_merged_p21_  
  
81 messages similar to the above omitted  
  
Chain information for refine-coot-1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Downloading bundle ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl  
Downloading bundle ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl  
Error parsing
/u/azsha/Downloads/ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl: No such
file: /u/azsha/Downloads/ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl  
Bundle saved as
/u/azsha/Downloads/ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.9.7 ChimeraX-ISOLDE-1.0b3  
Installed ChimeraX-Clipper (0.9.7)  
Installed ChimeraX-ISOLDE (1.0b3)  

'clip' is a prefix of an existing command 'clipper'  

> toolshed show ISOLDE

> set selectionWidth 4

Chain information for refine-coot-1.pdb  
---  
Chain | Description  
1.3/A | No description available  
1.3/B | No description available  
1.3/C | 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 "/u/azsha/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 1256, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/u/azsha/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 1283, in add_xtal_data  
xmapset = map_mgr.add_xmapset_from_mtz(filename, self.params.map_shannon_rate)  
File "/u/azsha/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/map_mgr.py", line 271, in add_xmapset_from_mtz  
return self.add_xmapset_from_file(mtzfile, oversampling_rate)  
File "/u/azsha/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/map_mgr.py", line 276, in add_xmapset_from_file  
shannon_rate = oversampling_rate)  
File "/u/azsha/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/clipper_mtz.py", line 48, in __init__  
hklinfo, free, exp, calc = load_hkl_data(session, hklfile,
free_flag_label=free_flag_label)  
File "/u/azsha/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/clipper_mtz.py", line 325, in load_hkl_data  
load_map_coeffs = load_map_coeffs)  
File "/u/azsha/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/clipper_mtz.py", line 393, in load_mtz_data  
hklinfo, crystal_dict = mtz_read.load_mtz_data(session, filename,
load_map_coeffs=load_map_coeffs)  
File "/u/azsha/.local/share/ChimeraX/0.9/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 "/u/azsha/.local/share/ChimeraX/0.9/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 418.40.04
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

There are two problems going on here. First, this is another instance of ToolShed bug #2219 (copying in Conrad on that) where the incorrect version of Clipper is being installed when fetched as a dependency of ISOLDE. The last version of Clipper compatible with ChimeraX 0.9 is 0.9.4. I'd recommend updating ChimeraX to the latest daily build and installing ISOLDE from the ToolShed into that. That'll give you the latest dev builds of ISOLDE and Clipper.

The bug actually leading to the traceback is one I'll fix ASAP. The underlying problem, however, is that ISOLDE expects a fairly strict order of columns in your MTZ file. Specifically, every F column needs to be followed immediately by either Phi or sigF (and similar for I/sigI, F+/sigF+/F-/sigI- etc.). While I eventually expect to provide a user interface allowing you to specify exactly which columns go together, that won't be happening for a while. For now you'll need to use a MTZ editor to rearrange your input file.

[Tristan Croll]

Clearing out old tickets (this was fixed long ago, but I forgot to close it at the time).