Clipper: Floating point exception

[andong.li@…]

The following bug report has been submitted:
Platform:        Linux-5.13.0-28-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Floating point exception

Current thread 0x00007fe9ea83d740 (most recent call first):
  File "/home/whitelab2/.local/share/ChimeraX/1.3/site-packages/chimerax/clipper/symmetry.py", line 502 in __init__
  File "/home/whitelab2/.local/share/ChimeraX/1.3/site-packages/chimerax/clipper/symmetry.py", line 610 in add_model
  File "/home/whitelab2/.local/share/ChimeraX/1.3/site-packages/chimerax/clipper/symmetry.py", line 579 in __init__
  File "/home/whitelab2/.local/share/ChimeraX/1.3/site-packages/chimerax/clipper/symmetry.py", line 170 in _get_symmetry_handler
  File "/home/whitelab2/.local/share/ChimeraX/1.3/site-packages/chimerax/clipper/symmetry.py", line 159 in get_symmetry_handler
  File "/home/whitelab2/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/isolde.py", line 2528 in _change_selected_model
  File "/home/whitelab2/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/isolde.py", line 1050 in _update_model_list
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134 in invoke
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 217 in _activate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 186 in activate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 354 in activate_trigger
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/models.py", line 677 in add
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 223 in provider_open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 118 in cmd_open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 846 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main


Log:
> set selectionWidth 4

UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 470.103.01
OpenGL renderer: NVIDIA RTX A6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-7049GP-TRT
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 64 Intel(R) Xeon(R) Gold 6226R CPU @ 2.90GHz
Cache Size: 22528 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          376Gi        13Gi        43Gi       397Mi       320Gi       360Gi
	Swap:         2.0Gi       1.4Gi       592Mi

Graphics:
	05:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	DeviceName: ASPEED Video AST2500	
	Subsystem: Super Micro Computer Inc ASPEED Graphics Family [15d9:096d]
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
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[Tristan Croll]

Hmm... that's an interesting one. Would it be possible for you to share the model with me (to tic20@…; I'll keep it confidential) so I can try to diagnose the problem?

[andong.li@…]

Hello Dr. Croll,

Thanks for following up. I was going through a bunch of iterations of
modeling through ISOLDE among other programs and figured out that I was not
working with the correct file.

If you still want the botched file let me know but it isn't hindering me
anymore at the moment.

Thanks for all your work on ISOLDE,
  --
Andong Li
M.S. Student, White Lab
Dept. Molecular and Cell Biology
University of Connecticut




On Tue, Feb 22, 2022 at 12:31 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tristan Croll]

Hi Andong,

Even if the root cause is a deficiency in the input file, if it crashes ChimeraX entirely then that's a bug I should fix. I'd be very grateful if you could share it.

Thanks,
Tristan
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 22 February 2022 19:29
To: andong.li@uconn.edu <andong.li@uconn.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #6219: Clipper: Floating point exception

#6219: Clipper: Floating point exception
----------------------------------+---------------------------
          Reporter:  andong.li@…  |      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     |
----------------------------------+---------------------------

Comment (by andong.li@…):

 {{{
 Hello Dr. Croll,

 Thanks for following up. I was going through a bunch of iterations of
 modeling through ISOLDE among other programs and figured out that I was
 not
 working with the correct file.

 If you still want the botched file let me know but it isn't hindering me
 anymore at the moment.

 Thanks for all your work on ISOLDE,
   --
 Andong Li
 M.S. Student, White Lab
 Dept. Molecular and Cell Biology
 University of Connecticut




 On Tue, Feb 22, 2022 at 12:31 PM ChimeraX <ChimeraX-bugs-
 admin@cgl.ucsf.edu>
 wrote:


 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6219#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[andong.li@…]

I've attached the file below. Please ignore the messy name.

Tony

On Tue, Feb 22, 2022 at 2:32 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

Bot_mirror_isolde1.cif-coot-0p.pdb​

[andong.li@…]

Added by email2trac

[Tristan Croll]

Thanks very much for that. Seems the problem is being caused by the 3 misplaced hydrogens (that are some thousand angstroms out of position) - delete them and it goes away. Looks like something in Clipper's core code never expected a unit cell that big:

from chimerax.clipper.symmetry import symmetry_from_model_metadata
m = session.models.list()[0]
cell, spacegroup, grid, res, _ = symmetry_from_model_metadata(m)
cell.dim
Out[7]: array([3222.129, 2452.932, 4132.851])
grid.dim
Out[21]: array([3240, 2500,    0])

(where grid is supposed to be an evenly-spaced grid of points over the unit cell). I guess that 0 in the last dimension is causing a divide-by-zero somewhere... will try to figure out why it's happening.

[Tristan Croll]

Fixed. When deciding on the grid spacing for each cell dimension, Clipper does a search to minimise a target function to find the number of grid points that should give the best FFT performance. Unfortunately Kevin seeded the starting value of the target function with a value of 1e12 (I guess he assumed that was big enough for any conceivable crystal), which is below the minimum value achievable on the longest axis of the box enclosing your structure. To make matters worse the nbest value was seeded as zero rather than the more sensible minimum number giving the target grid spacing... since that was never updated the function returns zero for very large cell dimensions. Replaced the starting target function value with std::numeric_limits<double>::infinity(), and the problem model now loads fine.