Opened 6 years ago

Last modified 6 years ago

#2728 assigned defect

Clipper: math domain error

Reported by: mbk@… 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-4.15.0-72-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.91 (2019-12-23)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde start

> set selectionWidth 4

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 10.1 - if installed, please make sure this is
on your library path before starting ChimeraX.  

Done loading forcefield  

> open /home/bashir/Documents/MRage_1674/Dean_Test_MR_P6122_1.1.pdb

Chain information for Dean_Test_MR_P6122_1.1.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for Dean_Test_MR_P6122_1.1.pdb  
---  
Chain | Description  
1.1/A | No description available  
  
Discarding unrecognised/unsupported data array
/NULL_xname194033/NULL_dname/FOM W  

No free flags detected in this dataset! Automatically generated a new random
set with 171 free from 3541 observed reflections. You should save your data to
a new MTZ file and use this for any future rebuilding/refinement.  

Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
Failed on HKL = ( 0, 0, 60)  
N_bins: 60 Imean: -1437.5044896467866 I: -8858.0 sigI: 9269.0 eobs_sq:
1.027011285158551 sig_eobs_sq: -1.0746633102432388  
Traceback (most recent call last):  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 1271, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 1299, in add_xtal_data  
auto_choose_reflection_data=False)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/map_mgr.py", line 279, in add_xmapset_from_mtz  
auto_choose_reflection_data)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/map_mgr.py", line 301, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/xmapset.py", line 189, in __init__  
fill_with_fcalc, exclude_missing_reflections)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 110, in
french_wilson_analytical  
e_xpct = _expected_E_FW_cen(eobs_sq, sig_eobs_sq)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
ValueError: math domain error  
  
ValueError: math domain error  
  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
  
See log for complete Python traceback.  
  
Discarding unrecognised/unsupported data array
/NULL_xname194033/NULL_dname/FOM W  

No free flags detected in this dataset! Automatically generated a new random
set with 193 free from 3541 observed reflections. You should save your data to
a new MTZ file and use this for any future rebuilding/refinement.  

Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
Failed on HKL = ( 0, 0, 60)  
N_bins: 60 Imean: -1437.5044896467866 I: -8858.0 sigI: 9269.0 eobs_sq:
1.027011285158551 sig_eobs_sq: -1.0746633102432388  
Traceback (most recent call last):  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 1271, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 1299, in add_xtal_data  
auto_choose_reflection_data=False)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/map_mgr.py", line 279, in add_xmapset_from_mtz  
auto_choose_reflection_data)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/map_mgr.py", line 301, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/xmapset.py", line 189, in __init__  
fill_with_fcalc, exclude_missing_reflections)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 110, in
french_wilson_analytical  
e_xpct = _expected_E_FW_cen(eobs_sq, sig_eobs_sq)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
ValueError: math domain error  
  
ValueError: math domain error  
  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
  
See log for complete Python traceback.  
  
Discarding unrecognised/unsupported data array
/NULL_xname194033/NULL_dname/FOM W  

No free flags detected in this dataset! Automatically generated a new random
set with 182 free from 3541 observed reflections. You should save your data to
a new MTZ file and use this for any future rebuilding/refinement.  

Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
Failed on HKL = ( 0, 0, 60)  
N_bins: 60 Imean: -1437.5044896467866 I: -8858.0 sigI: 9269.0 eobs_sq:
1.027011285158551 sig_eobs_sq: -1.0746633102432388  
Traceback (most recent call last):  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 1271, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 1299, in add_xtal_data  
auto_choose_reflection_data=False)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/map_mgr.py", line 279, in add_xmapset_from_mtz  
auto_choose_reflection_data)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/map_mgr.py", line 301, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/xmapset.py", line 189, in __init__  
fill_with_fcalc, exclude_missing_reflections)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 110, in
french_wilson_analytical  
e_xpct = _expected_E_FW_cen(eobs_sq, sig_eobs_sq)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
ValueError: math domain error  
  
ValueError: math domain error  
  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
  
See log for complete Python traceback.  
  
Discarding unrecognised/unsupported data array
/NULL_xname194033/NULL_dname/FOM W  

No free flags detected in this dataset! Automatically generated a new random
set with 189 free from 3541 observed reflections. You should save your data to
a new MTZ file and use this for any future rebuilding/refinement.  

Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
Failed on HKL = ( 0, 0, 60)  
N_bins: 60 Imean: -1437.5044896467866 I: -8858.0 sigI: 9269.0 eobs_sq:
1.027011285158551 sig_eobs_sq: -1.0746633102432388  
Traceback (most recent call last):  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 1271, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 1299, in add_xtal_data  
auto_choose_reflection_data=False)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/map_mgr.py", line 279, in add_xmapset_from_mtz  
auto_choose_reflection_data)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/map_mgr.py", line 301, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/xmapset.py", line 189, in __init__  
fill_with_fcalc, exclude_missing_reflections)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/maps/xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 110, in
french_wilson_analytical  
e_xpct = _expected_E_FW_cen(eobs_sq, sig_eobs_sq)  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
ValueError: math domain error  
  
ValueError: math domain error  
  
File "/home/bashir/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3 (Core Profile) Mesa 19.0.8
OpenGL renderer: AMD JUNIPER (DRM 2.50.0 / 4.15.0-72-generic, LLVM 8.0.0)
OpenGL vendor: X.Org

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

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

in reply to:  2 ; comment:2 by Tristan Croll, 6 years ago 

This error suggests that your data has at least one residue shell where the mean intensity is less than zero. I’ll figure out what to do in this situation, but in the meantime it would be best if you convert to F/sigF internally.

Oh, and I’m afraid you won’t be able to do much with ISOLDE other than look at your model without an OpenCL-capable GPU and driver.
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