Opened 4 years ago

Closed 4 years ago

#5469 closed task (fixed)

Request for help in debugging

Reported by: Tristan Croll Owned by: Greg Couch
Priority: normal Milestone:
Component: Build System Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.3rc202110222254 (2021-10-22 22:54:52 UTC)
Description
Not a ChimeraX bug, but an appeal for suggestions. Offender is a PyBind11-wrapped function taking (amongst other arguments) a vector of doubles, provided to it by Python as a list of floats. Has been working fine on all three platforms, but now breaks in Windows. Usually returns `ValueError: vector too long`, sometimes `MemoryError: bad allocation`, and *extremely* rarely seems to get past it. Very worrying. I added some logging in the wrapped function that never gets hit, so the exception is thrown in the bindings.

Possibilities:

- this is a new (to me) PC, and it came to me with Visual Studio Community 2019 installed so I've been using that to compile Clipper and ISOLDE. I've uninstalled that and am currently installing 2015, in case there's some subtle ABI problem. It's clear there are at least some differences to the underlying libraries - I used to have to add some Microsoft-specific code to define std::basic_string<char>::npos, but with 2019 that now raises a compile-time error.
- a bug in PyBind11 - I just recently bumped the version I'm using up to 2.7.1. Seems unlikely, since casting of Python lists to vectors will be used all over the place.
- something a bit funky about this particular machine. Not impossible, if I'm being honest - it generally seems a little flaky and prone to multi-second hang-ups, so I'm not ruling out some memory fault.

Any ideas?

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3rc202110222254 (2021-10-22)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1un9 structureFactors true

Summary of feedback from opening 1un9 fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1291 free from 25746 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Fetching compressed mmCIF 1un9 from
http://files.rcsb.org/download/1un9.cif  
Fetching CCD ANP from http://ligand-expo.rcsb.org/reports/A/ANP/ANP.cif  
Fetching compressed 1un9 structure factors from
http://files.rcsb.org/download/1un9-sf.cif  
Resolution: 3.1000607613626228  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 26,28,26, pixel
1.01,0.976,0.986, shown at level 0.153, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 26,28,26, pixel 1.01,0.976,0.986,
shown at level -0.0887,0.0887, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_32 as #1.1.1.4, grid size 26,28,26, pixel
1.01,0.976,0.986, shown at level 0.337, step 1, values float32  
1un9 title:  
Crystal structure of the dihydroxyacetone kinase from C. freundii in complex
with AMP-PNP and Mg2+ [more info...]  
  
Chain information for 1un9  
---  
Chain | Description | UniProt  
1.2/A 1.2/B | dihydroxyacetone kinase | DAK_CITFR  
  
Non-standard residues in 1un9 #1.2  
---  
2HA — dihydroxyacetone  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
  

> close #1

Deleting Crystallographic maps (1un9-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_32  

> open 3u9q structureFactors true

Summary of feedback from opening 3u9q fetched from pdb  
---  
notes | Fetching compressed mmCIF 3u9q from
http://files.rcsb.org/download/3u9q.cif  
Fetching CCD DKA from http://ligand-expo.rcsb.org/reports/D/DKA/DKA.cif  
Fetching compressed 3u9q structure factors from
http://files.rcsb.org/download/3u9q-sf.cif  
Resolution: 1.522  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 68,50,50, pixel
0.486,0.503,0.506, shown at level 1.03, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 68,50,50, pixel
0.486,0.503,0.506, shown at level -0.233,0.233, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_22 as #1.1.1.4, grid size 68,50,50, pixel
0.486,0.503,0.506, shown at level 0.614, step 1, values float32  
3u9q title:  
Ligand binding domain of PPARgamma complexed with Decanoic Acid and PGC-1a
peptide [more info...]  
  
Chain information for 3u9q  
---  
Chain | Description | UniProt  
1.2/A | Peroxisome proliferator-activated receptor γ | PPARG_HUMAN  
1.2/B | PGC-1a peptide | PRGC1_HUMAN  
  
Non-standard residues in 3u9q #1.2  
---  
DKA — decanoic acid  
  

> close #1

Deleting Crystallographic maps (3u9q-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_22  

> open 1zgy structureFactors true

Summary of feedback from opening 1zgy fetched from pdb  
---  
notes | Fetching compressed mmCIF 1zgy from
http://files.rcsb.org/download/1zgy.cif  
Fetching CCD BRL from http://ligand-expo.rcsb.org/reports/B/BRL/BRL.cif  
Fetching compressed 1zgy structure factors from
http://files.rcsb.org/download/1zgy-sf.cif  
Resolution: 1.8034515382614822  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,46,42, pixel
0.57,0.568,0.594, shown at level 0.499, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,46,42, pixel 0.57,0.568,0.594,
shown at level -0.149,0.149, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_18 as #1.1.1.4, grid size 50,46,42, pixel
0.57,0.568,0.594, shown at level 0.376, step 1, values float32  
1zgy title:  
Structural and Biochemical Basis for Selective Repression of the Orphan
Nuclear Receptor LRH-1 by SHP [more info...]  
  
Chain information for 1zgy  
---  
Chain | Description | UniProt  
1.2/A | Peroxisome proliferator activated receptor γ | PPAT_HUMAN  
1.2/B | Nuclear receptor subfamily 0, group B, member 2 | P97947_RAT  
  
Non-standard residues in 1zgy #1.2  
---  
BRL — 2,4-thiazolidiinedione,
5-[[4-[2-(methyl-2-pyridinylamino)ethoxy]phenyl]methyl]-(9CL) (BRL49653;
rosiglitazone)  
  

> close #1

Deleting Crystallographic maps (1zgy-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_18  

> open 4prg structureFactors true

Summary of feedback from opening 4prg fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1540 free from 30801 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Fetching compressed mmCIF 4prg from
http://files.rcsb.org/download/4prg.cif  
Fetching CCD 072 from http://ligand-expo.rcsb.org/reports/0/072/072.cif  
Fetching compressed 4prg structure factors from
http://files.rcsb.org/download/4prg-sf.cif  
Resolution: 2.5906391632025545  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 151, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 75, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 349, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
ValueError: vector too long  
  
ValueError: vector too long  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
  
See log for complete Python traceback.  
  

> open 4prg structureFactors true

Summary of feedback from opening 4prg fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1550 free from 30801 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 2.5906391632025545  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 151, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 75, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 349, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
ValueError: vector too long  
  
ValueError: vector too long  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
  
See log for complete Python traceback.  
  

> open 4prg structureFactors true

Summary of feedback from opening 4prg fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1549 free from 30801 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 2.5906391632025545  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 151, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 75, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 349, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
ValueError: vector too long  
  
ValueError: vector too long  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
  
See log for complete Python traceback.  
  

> open 4prg structureFactors true

Summary of feedback from opening 4prg fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1509 free from 30801 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 2.5906391632025545  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 151, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 75, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 349, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
ValueError: vector too long  
  
ValueError: vector too long  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
  
See log for complete Python traceback.  
  

> open 4prg structureFactors true

Summary of feedback from opening 4prg fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1547 free from 30801 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 2.5906391632025545  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 151, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 75, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 349, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
ValueError: vector too long  
  
ValueError: vector too long  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
  
See log for complete Python traceback.  
  

> open 4prg structureFactors true

Summary of feedback from opening 4prg fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1560 free from 30801 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 2.5906391632025545  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 151, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 75, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 349, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
ValueError: vector too long  
  
ValueError: vector too long  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
  
See log for complete Python traceback.  
  

> open 4prg structureFactors true

Summary of feedback from opening 4prg fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1560 free from 30801 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 2.5906391632025545  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 151, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 75, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 349, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
ValueError: vector too long  
  
ValueError: vector too long  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
  
See log for complete Python traceback.  
  

> open 4prg structureFactors true

Summary of feedback from opening 4prg fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1558 free from 30801 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 2.5906391632025545  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 151, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 75, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 349, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
ValueError: vector too long  
  
ValueError: vector too long  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
  
See log for complete Python traceback.  
  

> open 4prg structureFactors true

Summary of feedback from opening 4prg fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1549 free from 30801 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 2.5906391632025545  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 151, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 75, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 349, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
ValueError: vector too long  
  
ValueError: vector too long  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
  
See log for complete Python traceback.  
  

> open 4prg structureFactors true

Summary of feedback from opening 4prg fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1550 free from 30801 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 2.5906391632025545  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 151, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 75, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 349, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
ValueError: vector too long  
  
ValueError: vector too long  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
  
See log for complete Python traceback.  
  

> open 4prg structureFactors true

Summary of feedback from opening 4prg fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1533 free from 30801 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 2.5906391632025545  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 151, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 75, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 349, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
ValueError: vector too long  
  
ValueError: vector too long  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
  
See log for complete Python traceback.  
  

> open 4prg structureFactors true

Summary of feedback from opening 4prg fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1522 free from 30801 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 2.5906391632025545  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 151, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 75, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 349, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
ValueError: vector too long  
  
ValueError: vector too long  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
  
See log for complete Python traceback.  
  

> open 4prg structureFactors true

Summary of feedback from opening 4prg fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 1518 free from 30801 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 2.5906391632025545  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 151, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 75, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 349, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
MemoryError: bad allocation  
  
MemoryError: bad allocation  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\reflection_tools\french_wilson.py", line 80, in
french_wilson_analytical  
rfn = ResolutionFn(hkls, basisfn, target, params)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 471.11
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1.1
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3rc202110222254
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3.dev32
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.2
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.4
    ChimeraX-ModelPanel: 1.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.5
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.6
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.5.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.8.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.21
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.0
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (8)

comment:1 by pett, 4 years ago

Cc: chimera-programmers added
Component: Unassigned → Build System
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Request for help in debugging
Type: defect → task

comment:2 by Greg Couch, 4 years ago

While it could be the machine, it's unlikely.

As you know the big difference between Windows and the other platform is that sizeof long is 4 on Windows and 8 elsewhere. So bug might be due to PyBind11 switching from using int/long to size_t, nor the interface description not using size_t where it should. You could look at the generated files by the two versions of PyBind11 and look for differences.

comment:3 by Tom Goddard, 4 years ago

Seems worth figuring out what "vector too long" means. I guess PyBind11 generated code is producing that and looking at the generated code and possibly adding debugging output to it to see exactly what it is not happy with (which function argument and what it is checking for) would go a long way to debugging this.

in reply to:  4 ; comment:4 by Tristan Croll, 4 years ago 

Problem is that PyBind11 doesn't generate any code that gets written out - everything's done by template meta-programming in the compiler. I've done a little digging around and adding some logging into its headers, but haven't found the right spot yet.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 25 October 2021 22:14
Cc: chimera-programmers@cgl.ucsf.edu <chimera-programmers@cgl.ucsf.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5469: Request for help in debugging

#5469: Request for help in debugging
------------------------------------+------------------------
          Reporter:  Tristan Croll  |      Owner:  Greg Couch
              Type:  task           |     Status:  assigned
          Priority:  normal         |  Milestone:
         Component:  Build System   |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+------------------------

Comment (by Tom Goddard):

 Seems worth figuring out what "vector too long" means.  I guess PyBind11
 generated code is producing that and looking at the generated code and
 possibly adding debugging output to it to see exactly what it is not happy
 with (which function argument and what it is checking for) would go a long
 way to debugging this.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5469#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:5 by Tristan Croll, 4 years ago

Looks like Greg's on the money. It *was* actually making it into the constructor for the actual C++ object, but my first logging line was after the error point. Fixed that, and it seems there's an incorrect cast happening on the length of the list (should be 60, C++ thinks the resulting vector has length 17293822980146895658). Will try to reduce it to a simple test case and report it to the PyBind11 devs... meanwhile, I my be able to work around it by first converting the list to a Numpy array.

comment:6 by Tristan Croll, 4 years ago

Ugh. There's something nasty and non-trivial going on here, and it scares me. I can work around the problem with some ugly hackery at this particular site (coercing the offending argument to a Numpy array (py:array_t) in the C++ signature, then using a lambda to construct the needed vector and pass it on), but of course that doesn't guard against it raising its ugly head elsewhere. Worse, when I create a simple test case of a C++ class taking a std::vector<double> in its constructor, wrap that, and instantiate it from a list in Python, it works just fine.

Workaround:

    py::class_<ResolutionFn>(m, "ResolutionFn")
        /*
        For some as-yet-unknown reason, in Windows the commented-out init method leads to incorrect 
        conversion of the vector, with its size being reported as very large numbers.
        */
        // .def(py::init<const HKL_info&, const BasisFn_base&, const TargetFn_base&,
        //         const std::vector<ftype>&, const ftype, const bool>(),
        //     py::arg("hkl_info"), py::arg("basis_fn"), py::arg("target_fn"),
        //     py::arg("params"), py::arg("damp") = 0.0, py::arg("debug") = false)
        .def(py::init([](const HKL_info& hkl_info, const BasisFn_base& basis_fn, const TargetFn_base& target_fn,
            py::array_t<ftype> params, ftype damp, bool debug) {
                std::vector<ftype> params_;
                for (size_t i=0; i<basis_fn.num_params(); ++i)
                    params_.push_back(params.at(i));
                return std::unique_ptr<ResolutionFn>(new ResolutionFn(hkl_info, basis_fn, target_fn, params_, damp, debug));
            }),
            py::arg("hkl_info"), py::arg("basis_fn"), py::arg("target_fn"),
            py::arg("params"), py::arg("damp") = 0.0, py::arg("debug") = false)

Working test case:

#include <vector>
#include <iostream>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>

class VecTest
{
public:
    VecTest(const std::vector<double>& test)
    {
        std::cout << "Length of test vector is " << test.size();
        size_=test.size();
    }
private:
    double size_;
};

namespace py=pybind11;

PYBIND11_MODULE(test_vector, m) {
    py::class_<VecTest>(m, "VecTest")
        .def(py::init<const std::vector<double>&>(), py::arg("test_vector"));

I know this isn't your problem. Just... venting, I guess. I *really* hate chasing this sort of bug. Will do a little more probing to see if it's just the *length* of the vector that's wrong, or if the values are borked too.

comment:7 by Tristan Croll, 4 years ago

Double ugh. Same code works fine in the official Windows Clipper build for ChimeraX 1.2 (that wasn't necessarily guaranteed - this code only gets hit if the user loads a structure factor file containing *only* intensities rather than amplitudes, which is fairly rare). Tried rolling back PyBind11 to the same version used for that - no luck. So either the problem is specific to Python 3.9, or it's (unlikely, I know) something about this specific machine. Will try building on my old Windows PC anyway.

comment:8 by Tristan Croll, 4 years ago

Resolution: → fixed
Status: assigned → closed

Looks like the problem is in passing the std::vector by const reference - it looks like the temporary vector produced by the implicit conversion from a Python list or Numpy array is already out of scope by the time it gets to the constructor, and the garbage collection is winning the race. Replacing the binding above with one that takes the vector by value rather than reference works fine:

        .def(py::init([](const HKL_info& hkl_info, const BasisFn_base& basis_fn, const TargetFn_base& target_fn,
            std::vector<ftype> params, ftype damp, bool debug) {
                return std::unique_ptr<ResolutionFn>(new ResolutionFn(hkl_info, basis_fn, target_fn,
                    params, damp, debug));
            }),
            py::arg("hkl_info"), py::arg("basis_fn"), py::arg("target_fn"),
            py::arg("params"), py::arg("damp") = 0.0, py::arg("debug") = false)

Not sure if this is a known issue with PyBind11 (I haven't found it clearly stated in their documentation), but will bring it up on their bug tracker.

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